https://launchpad.net/ubuntu/+source/macromoleculebuilder/4.0.0+dfsg-2/+build/24934404 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-ppc64el-003 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:14 UTC 2023 ppc64le Buildd toolchain package versions: launchpad-buildd_229~619~ubuntu20.04.1 python3-lpbuildd_229~619~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.8 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 4 Feb 01:53:14 ntpdate[1964]: adjust time server 10.211.37.1 offset -0.026208 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=ppc64el PACKAGEBUILD-24934404 --image-type chroot /home/buildd/filecache-default/7984b9498478de1d58b749dc057a3cf5e3226d68 Creating target for build PACKAGEBUILD-24934404 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=ppc64el PACKAGEBUILD-24934404 Starting target for build PACKAGEBUILD-24934404 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=ppc64el PACKAGEBUILD-24934404 'deb http://ftpmaster.internal/ubuntu lunar main universe' 'deb http://ftpmaster.internal/ubuntu lunar-security main universe' 'deb http://ftpmaster.internal/ubuntu lunar-updates main universe' 'deb http://ftpmaster.internal/ubuntu lunar-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-24934404 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=ppc64el PACKAGEBUILD-24934404 Updating target for build PACKAGEBUILD-24934404 Get:1 http://ftpmaster.internal/ubuntu lunar InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main ppc64el Packages [1335 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [508 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/universe ppc64el Packages [14.6 MB] Get:8 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5896 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el Packages [59.8 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main Translation-en [29.3 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/universe ppc64el Packages [297 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [138 kB] Fetched 23.5 MB in 5s (5169 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: adduser advancecomp apt bash binutils binutils-common binutils-powerpc64le-linux-gnu coreutils cpp-12 debconf diffutils dpkg dpkg-dev fakeroot g++-12 gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv grep libacl1 libapt-pkg6.0 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcc1-0 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libdb5.3 libdpkg-perl libfakeroot libgcc-12-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libitm1 liblsan0 liblzma5 libmpfr6 libncurses6 libncursesw6 libp11-kit0 libpcre2-8-0 libperl5.36 libquadmath0 libreadline8 libselinux1 libsemanage-common libsemanage2 libsqlite3-0 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libtsan2 libubsan1 libudev1 libzstd1 linux-libc-dev lsb-base ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.36 pkgbinarymangler readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tzdata xz-utils zlib1g 91 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 100 MB of archives. After this operation, 4309 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu lunar/main ppc64el bash ppc64el 5.2.15-2ubuntu1 [956 kB] Get:2 http://ftpmaster.internal/ubuntu lunar/main ppc64el coreutils ppc64el 9.1-1ubuntu2 [1508 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main ppc64el diffutils ppc64el 1:3.8-3 [196 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libc-bin ppc64el 2.37-0ubuntu1 [736 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main ppc64el libcrypt-dev ppc64el 1:4.4.33-2 [143 kB] Get:6 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libc6-dev ppc64el 2.37-0ubuntu1 [2057 kB] Get:7 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libc-dev-bin ppc64el 2.37-0ubuntu1 [20.9 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main ppc64el libcrypt1 ppc64el 1:4.4.33-2 [106 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el linux-libc-dev ppc64el 6.1.0-14.14 [1461 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main ppc64el libcc1-0 ppc64el 12.2.0-14ubuntu1 [48.9 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main ppc64el libctf0 ppc64el 2.40-2ubuntu1 [110 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main ppc64el libctf-nobfd0 ppc64el 2.40-2ubuntu1 [109 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.40-2ubuntu1 [2446 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main ppc64el libbinutils ppc64el 2.40-2ubuntu1 [728 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main ppc64el binutils-common ppc64el 2.40-2ubuntu1 [226 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main ppc64el binutils ppc64el 2.40-2ubuntu1 [3082 B] Get:17 http://ftpmaster.internal/ubuntu lunar/main ppc64el gcc-12-base ppc64el 12.2.0-14ubuntu1 [19.3 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgcc-s1 ppc64el 12.2.0-14ubuntu1 [34.0 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgomp1 ppc64el 12.2.0-14ubuntu1 [139 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main ppc64el libitm1 ppc64el 12.2.0-14ubuntu1 [32.6 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main ppc64el libatomic1 ppc64el 12.2.0-14ubuntu1 [10.6 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main ppc64el libasan8 ppc64el 12.2.0-14ubuntu1 [2450 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main ppc64el liblsan0 ppc64el 12.2.0-14ubuntu1 [1082 kB] Get:24 http://ftpmaster.internal/ubuntu lunar/main ppc64el libtsan2 ppc64el 12.2.0-14ubuntu1 [2568 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main ppc64el libubsan1 ppc64el 12.2.0-14ubuntu1 [992 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main ppc64el libquadmath0 ppc64el 12.2.0-14ubuntu1 [155 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main ppc64el g++-12 ppc64el 12.2.0-14ubuntu1 [11.4 MB] Get:28 http://ftpmaster.internal/ubuntu lunar/main ppc64el libstdc++-12-dev ppc64el 12.2.0-14ubuntu1 [2289 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgcc-12-dev ppc64el 12.2.0-14ubuntu1 [1512 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main ppc64el gcc-12 ppc64el 12.2.0-14ubuntu1 [19.8 MB] Get:31 http://ftpmaster.internal/ubuntu lunar/main ppc64el cpp-12 ppc64el 12.2.0-14ubuntu1 [10.0 MB] Get:32 http://ftpmaster.internal/ubuntu lunar/main ppc64el libstdc++6 ppc64el 12.2.0-14ubuntu1 [787 kB] Get:33 http://ftpmaster.internal/ubuntu lunar/main ppc64el zlib1g ppc64el 1:1.2.13.dfsg-1ubuntu4 [70.1 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main ppc64el libmpfr6 ppc64el 4.2.0-1 [343 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/main ppc64el libzstd1 ppc64el 1.5.2+dfsg2-3 [354 kB] Get:36 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libc6 ppc64el 2.37-0ubuntu1 [3178 kB] Get:37 http://ftpmaster.internal/ubuntu lunar/main ppc64el liblzma5 ppc64el 5.4.1-0.0 [154 kB] Get:38 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgcrypt20 ppc64el 1.10.1-3ubuntu1 [718 kB] Get:39 http://ftpmaster.internal/ubuntu lunar/main ppc64el libacl1 ppc64el 2.3.1-3 [20.4 kB] Get:40 http://ftpmaster.internal/ubuntu lunar/main ppc64el libaudit-common all 1:3.0.7-1.1 [5108 B] Get:41 http://ftpmaster.internal/ubuntu lunar/main ppc64el libaudit1 ppc64el 1:3.0.7-1.1 [50.8 kB] Get:42 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libcap2 ppc64el 1:2.66-3ubuntu1 [33.2 kB] Get:43 http://ftpmaster.internal/ubuntu lunar/main ppc64el libpcre2-8-0 ppc64el 10.42-1 [256 kB] Get:44 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libselinux1 ppc64el 3.4-1build3 [96.4 kB] Get:45 http://ftpmaster.internal/ubuntu lunar/main ppc64el libperl5.36 ppc64el 5.36.0-7 [4848 kB] Get:46 http://ftpmaster.internal/ubuntu lunar/main ppc64el perl ppc64el 5.36.0-7 [235 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main ppc64el perl-base ppc64el 5.36.0-7 [1855 kB] Get:48 http://ftpmaster.internal/ubuntu lunar/main ppc64el perl-modules-5.36 all 5.36.0-7 [2984 kB] Get:49 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdb5.3 ppc64el 5.3.28+dfsg2-1 [847 kB] Get:50 http://ftpmaster.internal/ubuntu lunar/main ppc64el debconf all 1.5.82 [125 kB] Get:51 http://ftpmaster.internal/ubuntu lunar/main ppc64el libssl3 ppc64el 3.0.7-1ubuntu1 [2133 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/main ppc64el systemd-sysv ppc64el 252.4-1ubuntu1 [11.4 kB] Get:53 http://ftpmaster.internal/ubuntu lunar/main ppc64el systemd ppc64el 252.4-1ubuntu1 [3199 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsystemd-shared ppc64el 252.4-1ubuntu1 [1964 kB] Get:55 http://ftpmaster.internal/ubuntu lunar/main ppc64el libp11-kit0 ppc64el 0.24.1-2ubuntu1 [258 kB] Get:56 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsystemd0 ppc64el 252.4-1ubuntu1 [406 kB] Get:57 http://ftpmaster.internal/ubuntu lunar/main ppc64el libudev1 ppc64el 252.4-1ubuntu1 [111 kB] Get:58 http://ftpmaster.internal/ubuntu lunar/main ppc64el libapt-pkg6.0 ppc64el 2.5.5 [1016 kB] Get:59 http://ftpmaster.internal/ubuntu lunar/main ppc64el dpkg ppc64el 1.21.19ubuntu3 [1416 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/main ppc64el grep ppc64el 3.8-5 [170 kB] Get:61 http://ftpmaster.internal/ubuntu lunar/main ppc64el ncurses-bin ppc64el 6.4-2 [196 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main ppc64el sed ppc64el 4.9-1 [208 kB] Get:63 http://ftpmaster.internal/ubuntu lunar/main ppc64el ncurses-base all 6.4-2 [21.3 kB] Get:64 http://ftpmaster.internal/ubuntu lunar/main ppc64el sysvinit-utils ppc64el 3.05-7ubuntu2 [28.5 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main ppc64el lsb-base all 11.5 [4296 B] Get:66 http://ftpmaster.internal/ubuntu lunar/main ppc64el adduser all 3.129ubuntu1 [59.0 kB] Get:67 http://ftpmaster.internal/ubuntu lunar/main ppc64el gpgv ppc64el 2.2.40-1ubuntu2 [171 kB] Get:68 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgnutls30 ppc64el 3.7.8-4ubuntu1 [1038 kB] Get:69 http://ftpmaster.internal/ubuntu lunar/main ppc64el apt ppc64el 2.5.5 [1417 kB] Get:70 http://ftpmaster.internal/ubuntu lunar/main ppc64el libattr1 ppc64el 1:2.5.1-4 [13.2 kB] Get:71 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libsemanage-common all 3.4-1build3 [9808 B] Get:72 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libsemanage2 ppc64el 3.4-1build3 [113 kB] Get:73 http://ftpmaster.internal/ubuntu lunar/main ppc64el libncurses6 ppc64el 6.4-2 [144 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/main ppc64el libncursesw6 ppc64el 6.4-2 [179 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main ppc64el libtinfo6 ppc64el 6.4-2 [124 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main ppc64el sensible-utils all 0.0.17+nmu1 [19.3 kB] Get:77 http://ftpmaster.internal/ubuntu lunar/main ppc64el readline-common all 8.2-1.3 [55.7 kB] Get:78 http://ftpmaster.internal/ubuntu lunar/main ppc64el libreadline8 ppc64el 8.2-1.3 [175 kB] Get:79 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsqlite3-0 ppc64el 3.40.1-1 [749 kB] Get:80 http://ftpmaster.internal/ubuntu lunar/main ppc64el openssl ppc64el 3.0.7-1ubuntu1 [1195 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/main ppc64el tzdata all 2022g-2ubuntu1 [397 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/main ppc64el xz-utils ppc64el 5.4.1-0.0 [246 kB] Get:83 http://ftpmaster.internal/ubuntu lunar/main ppc64el advancecomp ppc64el 2.5-1 [235 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main ppc64el dpkg-dev all 1.21.19ubuntu3 [1067 kB] Get:85 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdpkg-perl all 1.21.19ubuntu3 [247 kB] Get:86 http://ftpmaster.internal/ubuntu lunar/main ppc64el libfakeroot ppc64el 1.30.1-1.1ubuntu1 [32.8 kB] Get:87 http://ftpmaster.internal/ubuntu lunar/main ppc64el fakeroot ppc64el 1.30.1-1.1ubuntu1 [62.1 kB] Get:88 http://ftpmaster.internal/ubuntu lunar/main ppc64el gpg ppc64el 2.2.40-1ubuntu2 [646 kB] Get:89 http://ftpmaster.internal/ubuntu lunar/main ppc64el gpgconf ppc64el 2.2.40-1ubuntu2 [103 kB] Get:90 http://ftpmaster.internal/ubuntu lunar/main ppc64el gpg-agent ppc64el 2.2.40-1ubuntu2 [253 kB] Get:91 http://ftpmaster.internal/ubuntu lunar/main ppc64el pkgbinarymangler all 151 [16.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 100 MB in 4s (24.4 MB/s) (Reading database ... 13031 files and directories currently installed.) 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Setting up libstdc++-12-dev:ppc64el (12.2.0-14ubuntu1) ... Setting up binutils (2.40-2ubuntu1) ... Setting up dpkg-dev (1.21.19ubuntu3) ... Setting up gcc-12 (12.2.0-14ubuntu1) ... Setting up g++-12 (12.2.0-14ubuntu1) ... Processing triggers for debianutils (5.7-0.4) ... Processing triggers for libc-bin (2.37-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-24934404 ppc64el lunar-proposed -c chroot:build-PACKAGEBUILD-24934404 --arch=ppc64el --dist=lunar-proposed --nolog macromoleculebuilder_4.0.0+dfsg-2.dsc Initiating build PACKAGEBUILD-24934404 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:14 UTC 2023 ppc64le sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-ppc64el-003.buildd +==============================================================================+ | macromoleculebuilder 4.0.0+dfsg-2 (ppc64el) Sat, 04 Feb 2023 01:53:43 +0000 | +==============================================================================+ Package: macromoleculebuilder Version: 4.0.0+dfsg-2 Source Version: 4.0.0+dfsg-2 Distribution: lunar-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-24934404/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-6HHPTV/resolver-FVjEgm' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- macromoleculebuilder_4.0.0+dfsg-2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-6HHPTV/macromoleculebuilder-4.0.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-6HHPTV' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: asciidoc-base, cmake, debhelper-compat (= 13), docbook-xml, gemmi-dev (>= 0.5.3), libopenmm-dev, libseqan2-dev, libsimbody-dev, libsimtkmolmodel-dev (>= 3.1.0), libsimtkmolmodel-plugins, libstb-dev, tao-pegtl-dev, zlib1g-dev, build-essential, fakeroot Filtered Build-Depends: asciidoc-base, cmake, debhelper-compat (= 13), docbook-xml, gemmi-dev (>= 0.5.3), libopenmm-dev, libseqan2-dev, libsimbody-dev, libsimtkmolmodel-dev (>= 3.1.0), libsimtkmolmodel-plugins, libstb-dev, tao-pegtl-dev, zlib1g-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [467 B] Get:5 copy:/<>/apt_archive ./ Packages [553 B] Fetched 1977 B in 0s (131 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: asciidoc-base asciidoc-common autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data debhelper debugedit dh-autoreconf dh-strip-nondeterminism docbook-xml docbook-xsl dwz file freeglut3-dev gemmi-dev gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libblas-dev libblas3 libbrotli1 libbsd0 libcurl4 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm-nouveau2 libdrm-radeon1 libdrm2 libdw1 libedit2 libegl-dev libegl-mesa0 libegl1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgbm1 libgfortran5 libgl-dev libgl1 libgl1-mesa-dev libgl1-mesa-dri libglapi-mesa libgles-dev libgles1 libgles2 libglu1-mesa libglu1-mesa-dev libglut-dev libglut3.12 libglvnd-core-dev libglvnd-dev libglvnd0 libglx-dev libglx-mesa0 libglx0 libice-dev libice6 libicu71 libjsoncpp25 liblapack-dev liblapack3 libldap2 libllvm15 libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libopengl-dev libopengl0 libopenmm-dev libopenmm7.7 libpipeline1 libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libseqan2-dev libsimbody-dev libsimbody3.7 libsimtkmolmodel-dev libsimtkmolmodel-plugins libsimtkmolmodel3.1 libsm-dev libsm6 libssh-4 libstb-dev libstb0 libsub-override-perl libtool libuchardet0 libuv1 libwayland-client0 libwayland-server0 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes-dev libxfixes3 libxi-dev libxi6 libxml2 libxml2-utils libxmu-dev libxmu-headers libxmu6 libxshmfence1 libxslt1.1 libxt-dev libxt6 libxxf86vm1 m4 man-db media-types po-debconf python3 python3-minimal python3.11 python3.11-minimal sgml-base sgml-data tao-pegtl-dev x11-common x11proto-dev xml-core xorg-sgml-doctools xsltproc xtrans-dev zlib1g-dev Suggested packages: asciidoc-doc docbook-utils source-highlight autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format elpa-cmake-mode ninja-build dh-make docbook docbook-dsssl docbook-defguide dbtoepub docbook-xsl-doc-html | docbook-xsl-doc-pdf | docbook-xsl-doc-text | docbook-xsl-doc docbook-xsl-saxon fop libsaxon-java libxalan2-java libxslthl-java xalan gettext-doc libasprintf-dev libgettextpo-dev groff lrzip liblapack-doc libice-doc lm-sensors libsm-doc libtool-doc gfortran | fortran95-compiler gcj-jdk libx11-doc libxcb-doc libxext-doc libxt-doc m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.11-venv python3.11-doc binfmt-support sgml-base-doc perlsgml w3-recs opensp Recommended packages: xmlto curl | wget | lynx libarchive-cpio-perl libgl1-amber-dri libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: asciidoc-base asciidoc-common autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data debhelper debugedit dh-autoreconf dh-strip-nondeterminism docbook-xml docbook-xsl dwz file freeglut3-dev gemmi-dev gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libblas-dev libblas3 libbrotli1 libbsd0 libcurl4 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm-nouveau2 libdrm-radeon1 libdrm2 libdw1 libedit2 libegl-dev libegl-mesa0 libegl1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgbm1 libgfortran5 libgl-dev libgl1 libgl1-mesa-dev libgl1-mesa-dri libglapi-mesa libgles-dev libgles1 libgles2 libglu1-mesa libglu1-mesa-dev libglut-dev libglut3.12 libglvnd-core-dev libglvnd-dev libglvnd0 libglx-dev libglx-mesa0 libglx0 libice-dev libice6 libicu71 libjsoncpp25 liblapack-dev liblapack3 libldap2 libllvm15 libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libopengl-dev libopengl0 libopenmm-dev libopenmm7.7 libpipeline1 libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libseqan2-dev libsimbody-dev libsimbody3.7 libsimtkmolmodel-dev libsimtkmolmodel-plugins libsimtkmolmodel3.1 libsm-dev libsm6 libssh-4 libstb-dev libstb0 libsub-override-perl libtool libuchardet0 libuv1 libwayland-client0 libwayland-server0 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes-dev libxfixes3 libxi-dev libxi6 libxml2 libxml2-utils libxmu-dev libxmu-headers libxmu6 libxshmfence1 libxslt1.1 libxt-dev libxt6 libxxf86vm1 m4 man-db media-types po-debconf python3 python3-minimal python3.11 python3.11-minimal sbuild-build-depends-main-dummy sgml-base sgml-data tao-pegtl-dev x11-common x11proto-dev xml-core xorg-sgml-doctools xsltproc xtrans-dev zlib1g-dev 0 upgraded, 161 newly installed, 0 to remove and 0 not upgraded. Need to get 102 MB of archives. After this operation, 447 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [778 B] Get:2 http://ftpmaster.internal/ubuntu lunar/main ppc64el libpython3.11-minimal ppc64el 3.11.1-2 [831 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main ppc64el libexpat1 ppc64el 2.5.0-1 [95.3 kB] Get:4 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3.11-minimal ppc64el 3.11.1-2 [2367 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3-minimal ppc64el 3.11.1-0ubuntu1 [24.2 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main ppc64el media-types all 8.0.0 [24.9 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/main ppc64el libmpdec3 ppc64el 2.5.1-2build2 [116 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main ppc64el libpython3.11-stdlib ppc64el 3.11.1-2 [1833 kB] Get:9 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3.11 ppc64el 3.11.1-2 [561 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main ppc64el libpython3-stdlib ppc64el 3.11.1-0ubuntu1 [6870 B] Get:11 http://ftpmaster.internal/ubuntu lunar/main ppc64el python3 ppc64el 3.11.1-0ubuntu1 [22.5 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main ppc64el sgml-base all 1.31 [11.4 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main ppc64el libbsd0 ppc64el 0.11.7-2 [60.1 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main ppc64el libelf1 ppc64el 0.188-2.1 [63.2 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main ppc64el libicu71 ppc64el 71.1-3ubuntu1 [10.9 MB] Get:16 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxml2 ppc64el 2.9.14+dfsg-1.1 [820 kB] Get:17 http://ftpmaster.internal/ubuntu lunar/main ppc64el bsdextrautils ppc64el 2.38.1-4ubuntu1 [76.4 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main ppc64el libmagic-mgc ppc64el 1:5.44-3 [293 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main ppc64el libmagic1 ppc64el 1:5.44-3 [104 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main ppc64el file ppc64el 1:5.44-3 [22.4 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main ppc64el gettext-base ppc64el 0.21-11 [40.7 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main ppc64el libuchardet0 ppc64el 0.0.7-1build2 [80.4 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main ppc64el groff-base ppc64el 1.22.4-9 [1004 kB] Get:24 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdrm-common all 2.4.114-1 [5940 B] Get:25 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdrm2 ppc64el 2.4.114-1 [47.2 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main ppc64el libedit2 ppc64el 3.1-20221030-2 [122 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main ppc64el libnghttp2-14 ppc64el 1.51.0-1 [87.1 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main ppc64el libpipeline1 ppc64el 1.5.7-1 [25.8 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main ppc64el libpsl5 ppc64el 0.21.0-1.2build2 [60.3 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main ppc64el libuv1 ppc64el 1.44.2-1 [106 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxau6 ppc64el 1:1.0.9-1build5 [8028 B] Get:32 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxdmcp6 ppc64el 1:1.1.3-0ubuntu5 [12.3 kB] Get:33 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb1 ppc64el 1.15-1 [55.5 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main ppc64el libx11-data all 2:1.8.3-3 [118 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/main ppc64el libx11-6 ppc64el 2:1.8.3-3 [737 kB] Get:36 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxext6 ppc64el 2:1.3.4-1build1 [40.0 kB] Get:37 http://ftpmaster.internal/ubuntu lunar/main ppc64el man-db ppc64el 2.11.2-1 [1256 kB] Get:38 http://ftpmaster.internal/ubuntu lunar/universe ppc64el asciidoc-common all 10.2.0-1 [104 kB] Get:39 http://ftpmaster.internal/ubuntu lunar/main ppc64el xml-core all 0.18+nmu1 [21.6 kB] Get:40 http://ftpmaster.internal/ubuntu lunar/universe ppc64el docbook-xsl all 1.79.2+dfsg-2 [1074 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxml2-utils ppc64el 2.9.14+dfsg-1.1 [41.7 kB] Get:42 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxslt1.1 ppc64el 1.1.35-1 [185 kB] Get:43 http://ftpmaster.internal/ubuntu lunar/main ppc64el xsltproc ppc64el 1.1.35-1 [16.0 kB] Get:44 http://ftpmaster.internal/ubuntu lunar/universe ppc64el asciidoc-base all 10.2.0-1 [83.7 kB] Get:45 http://ftpmaster.internal/ubuntu lunar/main ppc64el m4 ppc64el 1.4.19-2 [275 kB] Get:46 http://ftpmaster.internal/ubuntu lunar/main ppc64el autoconf all 2.71-3 [339 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main ppc64el autotools-dev all 20220109.1 [44.9 kB] Get:48 http://ftpmaster.internal/ubuntu lunar/main ppc64el automake all 1:1.16.5-1.3 [558 kB] Get:49 http://ftpmaster.internal/ubuntu lunar/main ppc64el autopoint all 0.21-11 [420 kB] Get:50 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libarchive13 ppc64el 3.6.2-1ubuntu1 [525 kB] Get:51 http://ftpmaster.internal/ubuntu lunar/main ppc64el libbrotli1 ppc64el 1.0.9-2build7 [369 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsasl2-modules-db ppc64el 2.1.28+dfsg-10 [22.7 kB] Get:53 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsasl2-2 ppc64el 2.1.28+dfsg-10 [69.2 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main ppc64el libldap2 ppc64el 2.6.3+dfsg-1~exp1ubuntu1 [217 kB] Get:55 http://ftpmaster.internal/ubuntu lunar/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d.1-2build4 [65.5 kB] Get:56 http://ftpmaster.internal/ubuntu lunar/main ppc64el libssh-4 ppc64el 0.10.4-2 [235 kB] Get:57 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libcurl4 ppc64el 7.87.0-2ubuntu1 [358 kB] Get:58 http://ftpmaster.internal/ubuntu lunar/main ppc64el libjsoncpp25 ppc64el 1.9.5-4 [89.4 kB] Get:59 http://ftpmaster.internal/ubuntu lunar/main ppc64el librhash0 ppc64el 1.4.3-3 [144 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/main ppc64el cmake-data all 3.25.1-1 [2049 kB] Get:61 http://ftpmaster.internal/ubuntu lunar/main ppc64el cmake ppc64el 3.25.1-1 [9432 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdebhelper-perl all 13.11.4ubuntu3 [66.1 kB] Get:63 http://ftpmaster.internal/ubuntu lunar/main ppc64el libtool all 2.4.7-5 [166 kB] Get:64 http://ftpmaster.internal/ubuntu lunar/main ppc64el dh-autoreconf all 20 [16.1 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] Get:66 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsub-override-perl all 0.09-4 [8706 B] Get:67 http://ftpmaster.internal/ubuntu lunar/main ppc64el libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:68 http://ftpmaster.internal/ubuntu lunar/main ppc64el dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:69 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdw1 ppc64el 0.188-2.1 [284 kB] Get:70 http://ftpmaster.internal/ubuntu lunar/main ppc64el debugedit ppc64el 1:5.0-5 [51.1 kB] Get:71 http://ftpmaster.internal/ubuntu lunar/main ppc64el dwz ppc64el 0.15-1 [139 kB] Get:72 http://ftpmaster.internal/ubuntu lunar/main ppc64el gettext ppc64el 0.21-11 [970 kB] Get:73 http://ftpmaster.internal/ubuntu lunar/main ppc64el intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main ppc64el debhelper all 13.11.4ubuntu3 [925 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main ppc64el sgml-data all 2.0.11+nmu1 [171 kB] Get:77 http://ftpmaster.internal/ubuntu lunar/main ppc64el docbook-xml all 4.5-12 [74.6 kB] Get:78 http://ftpmaster.internal/ubuntu lunar/main ppc64el libglvnd0 ppc64el 1.6.0-1 [82.8 kB] Get:79 http://ftpmaster.internal/ubuntu lunar/main ppc64el libglapi-mesa ppc64el 22.2.5-0ubuntu1 [34.6 kB] Get:80 http://ftpmaster.internal/ubuntu lunar/main ppc64el libx11-xcb1 ppc64el 2:1.8.3-3 [7836 B] Get:81 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb-dri2-0 ppc64el 1.15-1 [7444 B] Get:82 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb-dri3-0 ppc64el 1.15-1 [7392 B] Get:83 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb-glx0 ppc64el 1.15-1 [26.2 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb-present0 ppc64el 1.15-1 [5814 B] Get:85 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb-shm0 ppc64el 1.15-1 [5896 B] Get:86 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb-sync1 ppc64el 1.15-1 [9720 B] Get:87 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb-xfixes0 ppc64el 1.15-1 [10.6 kB] Get:88 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxfixes3 ppc64el 1:6.0.0-2 [11.6 kB] Get:89 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxshmfence1 ppc64el 1.3-1build4 [5566 B] Get:90 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxxf86vm1 ppc64el 1:1.1.4-1build3 [11.8 kB] Get:91 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdrm-amdgpu1 ppc64el 2.4.114-1 [23.8 kB] Get:92 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdrm-nouveau2 ppc64el 2.4.114-1 [20.5 kB] Get:93 http://ftpmaster.internal/ubuntu lunar/main ppc64el libdrm-radeon1 ppc64el 2.4.114-1 [25.8 kB] Get:94 http://ftpmaster.internal/ubuntu lunar-proposed/main ppc64el libllvm15 ppc64el 1:15.0.7-1 [26.3 MB] Get:95 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsensors-config all 1:3.6.0-7ubuntu1 [5274 B] Get:96 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsensors5 ppc64el 1:3.6.0-7ubuntu1 [32.3 kB] Get:97 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgl1-mesa-dri ppc64el 22.2.5-0ubuntu1 [6093 kB] Get:98 http://ftpmaster.internal/ubuntu lunar/main ppc64el libglx-mesa0 ppc64el 22.2.5-0ubuntu1 [175 kB] Get:99 http://ftpmaster.internal/ubuntu lunar/main ppc64el libglx0 ppc64el 1.6.0-1 [42.2 kB] Get:100 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgl1 ppc64el 1.6.0-1 [109 kB] Get:101 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxi6 ppc64el 2:1.8-1build1 [38.1 kB] Get:102 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libglut3.12 ppc64el 3.4.0-1 [129 kB] Get:103 http://ftpmaster.internal/ubuntu lunar/main ppc64el xorg-sgml-doctools all 1:1.11-1.1 [10.9 kB] Get:104 http://ftpmaster.internal/ubuntu lunar/main ppc64el x11proto-dev all 2022.1-1 [605 kB] Get:105 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxau-dev ppc64el 1:1.0.9-1build5 [10.3 kB] Get:106 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxdmcp-dev ppc64el 1:1.1.3-0ubuntu5 [28.1 kB] Get:107 http://ftpmaster.internal/ubuntu lunar/main ppc64el xtrans-dev all 1.4.0-1 [68.9 kB] Get:108 http://ftpmaster.internal/ubuntu lunar/main ppc64el libpthread-stubs0-dev ppc64el 0.4-1build2 [5510 B] Get:109 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxcb1-dev ppc64el 1.15-1 [96.0 kB] Get:110 http://ftpmaster.internal/ubuntu lunar/main ppc64el libx11-dev ppc64el 2:1.8.3-3 [830 kB] Get:111 http://ftpmaster.internal/ubuntu lunar/main ppc64el libglx-dev ppc64el 1.6.0-1 [14.1 kB] Get:112 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgl-dev ppc64el 1.6.0-1 [102 kB] Get:113 http://ftpmaster.internal/ubuntu lunar/main ppc64el libglvnd-core-dev ppc64el 1.6.0-1 [12.7 kB] Get:114 http://ftpmaster.internal/ubuntu lunar/main ppc64el libwayland-server0 ppc64el 1.21.0-1 [39.7 kB] Get:115 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgbm1 ppc64el 22.2.5-0ubuntu1 [37.5 kB] Get:116 http://ftpmaster.internal/ubuntu lunar/main ppc64el libwayland-client0 ppc64el 1.21.0-1 [29.3 kB] Get:117 http://ftpmaster.internal/ubuntu lunar/main ppc64el libegl-mesa0 ppc64el 22.2.5-0ubuntu1 [125 kB] Get:118 http://ftpmaster.internal/ubuntu lunar/main ppc64el libegl1 ppc64el 1.6.0-1 [33.1 kB] Get:119 http://ftpmaster.internal/ubuntu lunar/main ppc64el libegl-dev ppc64el 1.6.0-1 [18.1 kB] Get:120 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgles1 ppc64el 1.6.0-1 [12.1 kB] Get:121 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgles2 ppc64el 1.6.0-1 [18.2 kB] Get:122 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgles-dev ppc64el 1.6.0-1 [50.4 kB] Get:123 http://ftpmaster.internal/ubuntu lunar/main ppc64el libopengl0 ppc64el 1.6.0-1 [36.7 kB] Get:124 http://ftpmaster.internal/ubuntu lunar/main ppc64el libopengl-dev ppc64el 1.6.0-1 [3402 B] Get:125 http://ftpmaster.internal/ubuntu lunar/main ppc64el libglvnd-dev ppc64el 1.6.0-1 [3164 B] Get:126 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgl1-mesa-dev ppc64el 22.2.5-0ubuntu1 [6504 B] Get:127 http://ftpmaster.internal/ubuntu lunar/main ppc64el libglu1-mesa ppc64el 9.0.2-1.1 [262 kB] Get:128 http://ftpmaster.internal/ubuntu lunar/main ppc64el libglu1-mesa-dev ppc64el 9.0.2-1.1 [368 kB] Get:129 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxext-dev ppc64el 2:1.3.4-1build1 [96.3 kB] Get:130 http://ftpmaster.internal/ubuntu lunar/main ppc64el x11-common all 1:7.7+23ubuntu2 [23.4 kB] Get:131 http://ftpmaster.internal/ubuntu lunar/main ppc64el libice6 ppc64el 2:1.0.10-1build2 [49.3 kB] Get:132 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsm6 ppc64el 2:1.2.3-1build2 [18.5 kB] Get:133 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxt6 ppc64el 1:1.2.1-1 [202 kB] Get:134 http://ftpmaster.internal/ubuntu lunar/main ppc64el libice-dev ppc64el 2:1.0.10-1build2 [60.0 kB] Get:135 http://ftpmaster.internal/ubuntu lunar/main ppc64el libsm-dev ppc64el 2:1.2.3-1build2 [20.7 kB] Get:136 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxt-dev ppc64el 1:1.2.1-1 [442 kB] Get:137 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libglut-dev ppc64el 3.4.0-1 [172 kB] Get:138 http://ftpmaster.internal/ubuntu lunar/universe ppc64el freeglut3-dev ppc64el 3.4.0-1 [2018 B] Get:139 http://ftpmaster.internal/ubuntu lunar/universe ppc64el gemmi-dev ppc64el 0.5.6+ds-2ubuntu2 [422 kB] Get:140 http://ftpmaster.internal/ubuntu lunar/main ppc64el libblas3 ppc64el 3.11.0-2 [209 kB] Get:141 http://ftpmaster.internal/ubuntu lunar/main ppc64el libblas-dev ppc64el 3.11.0-2 [293 kB] Get:142 http://ftpmaster.internal/ubuntu lunar/main ppc64el libgfortran5 ppc64el 12.2.0-14ubuntu1 [546 kB] Get:143 http://ftpmaster.internal/ubuntu lunar/main ppc64el liblapack3 ppc64el 3.11.0-2 [2599 kB] Get:144 http://ftpmaster.internal/ubuntu lunar/main ppc64el liblapack-dev ppc64el 3.11.0-2 [5504 kB] Get:145 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libopenmm7.7 ppc64el 7.7.0+dfsg-9build1 [836 kB] Get:146 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libopenmm-dev ppc64el 7.7.0+dfsg-9build1 [342 kB] Get:147 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libseqan2-dev all 2.4.0+dfsg-15ubuntu1 [1207 kB] Get:148 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libsimbody3.7 ppc64el 3.7+dfsg-3 [3364 kB] Get:149 http://ftpmaster.internal/ubuntu lunar-proposed/universe ppc64el libsimtkmolmodel3.1 ppc64el 3.1.0-2build1 [754 kB] Get:150 http://ftpmaster.internal/ubuntu lunar-proposed/universe ppc64el libsimtkmolmodel-dev ppc64el 3.1.0-2build1 [1864 kB] Get:151 http://ftpmaster.internal/ubuntu lunar-proposed/universe ppc64el libsimtkmolmodel-plugins ppc64el 3.1.0-2build1 [17.6 kB] Get:152 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libstb0 ppc64el 0.0~git20220908.8b5f1f3+ds-1 [331 kB] Get:153 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libstb-dev ppc64el 0.0~git20220908.8b5f1f3+ds-1 [729 kB] Get:154 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxfixes-dev ppc64el 1:6.0.0-2 [13.3 kB] Get:155 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxi-dev ppc64el 2:1.8-1build1 [197 kB] Get:156 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxmu6 ppc64el 2:1.1.3-3 [57.2 kB] Get:157 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxmu-headers all 2:1.1.3-3 [54.1 kB] Get:158 http://ftpmaster.internal/ubuntu lunar/main ppc64el libxmu-dev ppc64el 2:1.1.3-3 [69.3 kB] Get:159 http://ftpmaster.internal/ubuntu lunar/universe ppc64el tao-pegtl-dev all 3.2.7-1 [59.6 kB] Get:160 http://ftpmaster.internal/ubuntu lunar/main ppc64el zlib1g-dev ppc64el 1:1.2.13.dfsg-1ubuntu4 [901 kB] Get:161 http://ftpmaster.internal/ubuntu lunar/universe ppc64el libsimbody-dev ppc64el 3.7+dfsg-3 [2818 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 102 MB in 6s (16.9 MB/s) Selecting previously unselected package libpython3.11-minimal:ppc64el. (Reading database ... 15079 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.1-2_ppc64el.deb ... Unpacking libpython3.11-minimal:ppc64el (3.11.1-2) ... Selecting previously unselected package libexpat1:ppc64el. Preparing to unpack .../libexpat1_2.5.0-1_ppc64el.deb ... Unpacking libexpat1:ppc64el (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.1-2_ppc64el.deb ... Unpacking python3.11-minimal (3.11.1-2) ... Setting up libpython3.11-minimal:ppc64el (3.11.1-2) ... Setting up libexpat1:ppc64el (2.5.0-1) ... Setting up python3.11-minimal (3.11.1-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 15393 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.1-0ubuntu1_ppc64el.deb ... Unpacking python3-minimal (3.11.1-0ubuntu1) ... Selecting previously unselected package media-types. 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Selecting previously unselected package libwayland-client0:ppc64el. Preparing to unpack .../105-libwayland-client0_1.21.0-1_ppc64el.deb ... Unpacking libwayland-client0:ppc64el (1.21.0-1) ... Selecting previously unselected package libegl-mesa0:ppc64el. Preparing to unpack .../106-libegl-mesa0_22.2.5-0ubuntu1_ppc64el.deb ... Unpacking libegl-mesa0:ppc64el (22.2.5-0ubuntu1) ... Selecting previously unselected package libegl1:ppc64el. Preparing to unpack .../107-libegl1_1.6.0-1_ppc64el.deb ... Unpacking libegl1:ppc64el (1.6.0-1) ... Selecting previously unselected package libegl-dev:ppc64el. Preparing to unpack .../108-libegl-dev_1.6.0-1_ppc64el.deb ... Unpacking libegl-dev:ppc64el (1.6.0-1) ... Selecting previously unselected package libgles1:ppc64el. Preparing to unpack .../109-libgles1_1.6.0-1_ppc64el.deb ... Unpacking libgles1:ppc64el (1.6.0-1) ... Selecting previously unselected package libgles2:ppc64el. Preparing to unpack .../110-libgles2_1.6.0-1_ppc64el.deb ... 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Unpacking libsm6:ppc64el (2:1.2.3-1build2) ... Selecting previously unselected package libxt6:ppc64el. Preparing to unpack .../122-libxt6_1%3a1.2.1-1_ppc64el.deb ... Unpacking libxt6:ppc64el (1:1.2.1-1) ... Selecting previously unselected package libice-dev:ppc64el. Preparing to unpack .../123-libice-dev_2%3a1.0.10-1build2_ppc64el.deb ... Unpacking libice-dev:ppc64el (2:1.0.10-1build2) ... Selecting previously unselected package libsm-dev:ppc64el. Preparing to unpack .../124-libsm-dev_2%3a1.2.3-1build2_ppc64el.deb ... Unpacking libsm-dev:ppc64el (2:1.2.3-1build2) ... Selecting previously unselected package libxt-dev:ppc64el. Preparing to unpack .../125-libxt-dev_1%3a1.2.1-1_ppc64el.deb ... Unpacking libxt-dev:ppc64el (1:1.2.1-1) ... Selecting previously unselected package libglut-dev:ppc64el. Preparing to unpack .../126-libglut-dev_3.4.0-1_ppc64el.deb ... Unpacking libglut-dev:ppc64el (3.4.0-1) ... Selecting previously unselected package freeglut3-dev:ppc64el. 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Unpacking tao-pegtl-dev (3.2.7-1) ... Selecting previously unselected package zlib1g-dev:ppc64el. Preparing to unpack .../149-zlib1g-dev_1%3a1.2.13.dfsg-1ubuntu4_ppc64el.deb ... Unpacking zlib1g-dev:ppc64el (1:1.2.13.dfsg-1ubuntu4) ... Selecting previously unselected package libsimbody-dev:ppc64el. Preparing to unpack .../150-libsimbody-dev_3.7+dfsg-3_ppc64el.deb ... Unpacking libsimbody-dev:ppc64el (3.7+dfsg-3) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../151-sbuild-build-depends-main-dummy_0.invalid.0_ppc64el.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up media-types (8.0.0) ... Setting up libpipeline1:ppc64el (1.5.7-1) ... Setting up libicu71:ppc64el (71.1-3ubuntu1) ... Setting up libwayland-server0:ppc64el (1.21.0-1) ... Setting up libxau6:ppc64el (1:1.0.9-1build5) ... Setting up libpsl5:ppc64el (0.21.0-1.2build2) ... Setting up bsdextrautils (2.38.1-4ubuntu1) ... Setting up libglvnd-core-dev:ppc64el (1.6.0-1) ... Setting up libopenmm7.7 (7.7.0+dfsg-9build1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglvnd0:ppc64el (1.6.0-1) ... Setting up libdebhelper-perl (13.11.4ubuntu3) ... Setting up libbrotli1:ppc64el (1.0.9-2build7) ... Setting up gemmi-dev (0.5.6+ds-2ubuntu2) ... Setting up x11-common (1:7.7+23ubuntu2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libsensors-config (1:3.6.0-7ubuntu1) ... Setting up libnghttp2-14:ppc64el (1.51.0-1) ... Setting up libmagic1:ppc64el (1:5.44-3) ... Setting up gettext-base (0.21-11) ... Setting up m4 (1.4.19-2) ... Setting up file (1:5.44-3) ... Setting up libpthread-stubs0-dev:ppc64el (0.4-1build2) ... Setting up libopenmm-dev (7.7.0+dfsg-9build1) ... Setting up libopengl0:ppc64el (1.6.0-1) ... Setting up libseqan2-dev (2.4.0+dfsg-15ubuntu1) ... Setting up libsasl2-modules-db:ppc64el (2.1.28+dfsg-10) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:ppc64el (3.11.0-2) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode Setting up libuv1:ppc64el (1.44.2-1) ... Setting up libgles2:ppc64el (1.6.0-1) ... Setting up libx11-data (2:1.8.3-3) ... Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libgles1:ppc64el (1.6.0-1) ... Setting up libstb0:ppc64el (0.0~git20220908.8b5f1f3+ds-1) ... Setting up autopoint (0.21-11) ... Setting up libjsoncpp25:ppc64el (1.9.5-4) ... Setting up libsensors5:ppc64el (1:3.6.0-7ubuntu1) ... Setting up libglapi-mesa:ppc64el (22.2.5-0ubuntu1) ... Setting up libsasl2-2:ppc64el (2.1.28+dfsg-10) ... Setting up libssh-4:ppc64el (0.10.4-2) ... Setting up libgfortran5:ppc64el (12.2.0-14ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:ppc64el (1:1.2.13.dfsg-1ubuntu4) ... Setting up libstb-dev:ppc64el (0.0~git20220908.8b5f1f3+ds-1) ... Setting up libxshmfence1:ppc64el (1.3-1build4) ... Setting up librhash0:ppc64el (1.4.3-3) ... Setting up libuchardet0:ppc64el (0.0.7-1build2) ... Setting up libmpdec3:ppc64el (2.5.1-2build2) ... Setting up libsub-override-perl (0.09-4) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.25.1-1) ... Setting up libglu1-mesa:ppc64el (9.0.2-1.1) ... Setting up libopengl-dev:ppc64el (1.6.0-1) ... Setting up libbsd0:ppc64el (0.11.7-2) ... Setting up libdrm-common (2.4.114-1) ... Setting up libelf1:ppc64el (0.188-2.1) ... Setting up libxml2:ppc64el (2.9.14+dfsg-1.1) ... Setting up libldap2:ppc64el (2.6.3+dfsg-1~exp1ubuntu1) ... Setting up libblas-dev:ppc64el (3.11.0-2) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so to provide /usr/lib/powerpc64le-linux-gnu/libblas.so (libblas.so-powerpc64le-linux-gnu) in auto mode Setting up tao-pegtl-dev (3.2.7-1) ... Setting up libwayland-client0:ppc64el (1.21.0-1) ... 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 (2022.1-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libice6:ppc64el (2:1.0.10-1build2) ... Setting up libdw1:ppc64el (0.188-2.1) ... Setting up libxdmcp6:ppc64el (1:1.1.3-0ubuntu5) ... Setting up liblapack3:ppc64el (3.11.0-2) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode Setting up libxcb1:ppc64el (1.15-1) ... Setting up gettext (0.21-11) ... Setting up libxcb-xfixes0:ppc64el (1.15-1) ... Setting up libxau-dev:ppc64el (1:1.0.9-1build5) ... Setting up libice-dev:ppc64el (2:1.0.10-1build2) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:ppc64el (3.6.2-1ubuntu1) ... Setting up libxcb-glx0:ppc64el (1.15-1) ... Setting up libpython3.11-stdlib:ppc64el (3.11.1-2) ... Setting up libedit2:ppc64el (3.1-20221030-2) ... Setting up libxcb-shm0:ppc64el (1.15-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libxcb-present0:ppc64el (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up libxdmcp-dev:ppc64el (1:1.1.3-0ubuntu5) ... Setting up libxcb-sync1:ppc64el (1.15-1) ... Setting up liblapack-dev:ppc64el (3.11.0-2) ... update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so (liblapack.so-powerpc64le-linux-gnu) in auto mode Setting up libxcb-dri2-0:ppc64el (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:ppc64el (2.4.114-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-9) ... Setting up xml-core (0.18+nmu1) ... Setting up libllvm15:ppc64el (1:15.0.7-1) ... Setting up libxslt1.1:ppc64el (1.1.35-1) ... Setting up debugedit (1:5.0-5) ... Setting up libcurl4:ppc64el (7.87.0-2ubuntu1) ... Setting up libx11-6:ppc64el (2:1.8.3-3) ... Setting up libxml2-utils (2.9.14+dfsg-1.1) ... Setting up libsm6:ppc64el (2:1.2.3-1build2) ... Setting up libpython3-stdlib:ppc64el (3.11.1-0ubuntu1) ... Setting up libdrm-amdgpu1:ppc64el (2.4.114-1) ... Setting up libxcb-dri3-0:ppc64el (1.15-1) ... Setting up libx11-xcb1:ppc64el (2:1.8.3-3) ... Setting up python3.11 (3.11.1-2) ... Setting up libdrm-nouveau2:ppc64el (2.4.114-1) ... Setting up libxcb1-dev:ppc64el (1.15-1) ... Setting up libgbm1:ppc64el (22.2.5-0ubuntu1) ... Setting up libsm-dev:ppc64el (2:1.2.3-1build2) ... Setting up libdrm-radeon1:ppc64el (2.4.114-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libgl1-mesa-dri:ppc64el (22.2.5-0ubuntu1) ... Setting up xsltproc (1.1.35-1) ... Setting up libx11-dev:ppc64el (2:1.8.3-3) ... Setting up libxext6:ppc64el (2:1.3.4-1build1) ... Setting up python3 (3.11.1-0ubuntu1) ... Setting up man-db (2.11.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libxxf86vm1:ppc64el (1:1.1.4-1build3) ... Setting up asciidoc-common (10.2.0-1) ... Setting up libegl-mesa0:ppc64el (22.2.5-0ubuntu1) ... Setting up libxfixes3:ppc64el (1:6.0.0-2) ... Setting up libxt6:ppc64el (1:1.2.1-1) ... Setting up libxext-dev:ppc64el (2:1.3.4-1build1) ... Setting up libegl1:ppc64el (1.6.0-1) ... Setting up cmake (3.25.1-1) ... Setting up libxmu-headers (2:1.1.3-3) ... Setting up libxmu6:ppc64el (2:1.1.3-3) ... Setting up libglx-mesa0:ppc64el (22.2.5-0ubuntu1) ... Setting up libxi6:ppc64el (2:1.8-1build1) ... Setting up libglx0:ppc64el (1.6.0-1) ... Setting up debhelper (13.11.4ubuntu3) ... Setting up libxfixes-dev:ppc64el (1:6.0.0-2) ... Setting up libgl1:ppc64el (1.6.0-1) ... Setting up libxt-dev:ppc64el (1:1.2.1-1) ... Setting up libglut3.12:ppc64el (3.4.0-1) ... Setting up libsimbody3.7:ppc64el (3.7+dfsg-3) ... Setting up libglx-dev:ppc64el (1.6.0-1) ... Setting up libxi-dev:ppc64el (2:1.8-1build1) ... Setting up libgl-dev:ppc64el (1.6.0-1) ... Setting up libsimtkmolmodel3.1:ppc64el (3.1.0-2build1) ... Setting up libegl-dev:ppc64el (1.6.0-1) ... Setting up libxmu-dev:ppc64el (2:1.1.3-3) ... Setting up libglu1-mesa-dev:ppc64el (9.0.2-1.1) ... Setting up libgles-dev:ppc64el (1.6.0-1) ... Setting up libsimtkmolmodel-plugins (3.1.0-2build1) ... Setting up libsimtkmolmodel-dev:ppc64el (3.1.0-2build1) ... Setting up libglvnd-dev:ppc64el (1.6.0-1) ... Setting up libgl1-mesa-dev:ppc64el (22.2.5-0ubuntu1) ... Setting up libglut-dev:ppc64el (3.4.0-1) ... Setting up freeglut3-dev:ppc64el (3.4.0-1) ... Setting up libsimbody-dev:ppc64el (3.7+dfsg-3) ... Processing triggers for libc-bin (2.37-0ubuntu1) ... Processing triggers for systemd (252.4-1ubuntu1) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-xsl (1.79.2+dfsg-2) ... Setting up sgml-data (2.0.11+nmu1) ... Setting up asciidoc-base (10.2.0-1) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-xml (4.5-12) ... Processing triggers for sgml-base (1.31) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (ppc64el included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-137-generic #154-Ubuntu SMP Thu Jan 5 17:03:14 UTC 2023 ppc64el (ppc64le) Toolchain package versions: binutils_2.40-2ubuntu1 dpkg-dev_1.21.19ubuntu3 g++-12_12.2.0-14ubuntu1 gcc-12_12.2.0-14ubuntu1 libc6-dev_2.37-0ubuntu1 libstdc++-12-dev_12.2.0-14ubuntu1 libstdc++6_12.2.0-14ubuntu1 linux-libc-dev_6.1.0-14.14 Package versions: adduser_3.129ubuntu1 advancecomp_2.5-1 apt_2.5.5 asciidoc-base_10.2.0-1 asciidoc-common_10.2.0-1 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-11 autotools-dev_20220109.1 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signature for ./macromoleculebuilder_4.0.0+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting macromoleculebuilder in /<> dpkg-source: info: unpacking macromoleculebuilder_4.0.0+dfsg.orig.tar.xz dpkg-source: info: unpacking macromoleculebuilder_4.0.0+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying drop-CMAKE_CXX_STANDARD.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-24934404 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-24934404 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-24934404 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package macromoleculebuilder dpkg-buildpackage: info: source version 4.0.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture ppc64el debian/rules clean dh clean dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' 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 -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0" cd obj-powerpc64le-linux-gnu && 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/powerpc64le-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 -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0" .. -- The CXX compiler identification is GNU 12.2.0 -- 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/powerpc64le-linux-gnu/libz.so (found version "1.2.13") -- Found gemmi version 0.5.6 -- Looking for copy_file_range -- Looking for copy_file_range - found -- Looking for sendfile -- Looking for sendfile - found -- Configuring done -- Generating done 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: /<>/obj-powerpc64le-linux-gnu make[1]: Leaving directory '/<>' dh_auto_build -a cd obj-powerpc64le-linux-gnu && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<>/obj-powerpc64le-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-powerpc64le-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-powerpc64le-linux-gnu/CMakeFiles /<>/obj-powerpc64le-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-powerpc64le-linux-gnu' make -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/depend make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/CMakeFiles/MMB.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' make -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/build make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' [ 3%] Building CXX object CMakeFiles/MMB.dir/src/Utils.cpp.o [ 6%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -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 /<>/src/Utils.cpp /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -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 /<>/src/BiopolymerClass.cpp [ 9%] Building CXX object CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o [ 12%] 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/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -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 /<>/src/UnitCellParameters.cpp /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -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 /<>/src/AtomSpringContainer.cpp In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/Simbody.h:38, from /usr/include/molmodel/SimTKmolmodel.h:47, from /<>/include/UnitCellParameters.h:3, from /<>/src/UnitCellParameters.cpp:4: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /<>/include/Utils.h:22, from /<>/include/AtomSpringContainer.h:14, from /<>/src/AtomSpringContainer.cpp:12: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /usr/include/molmodel/molmodel/internal/Compound.h:36, from /<>/include/BiopolymerClass.h:16, from /<>/src/BiopolymerClass.cpp:14: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /<>/include/Utils.h:22, from /<>/src/Utils.cpp:12: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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 /<>/include/Mutation.h:4, from /<>/include/BiopolymerClass.h:20: /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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); }; | ~~^~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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); }; | ~~^~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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); }; | ~~^~~~~~~~~~~~~~~~~ /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/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 /<>/include/Threading.h:2, from /<>/include/AtomSpringContainer.h:15: /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /<>/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();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/BiopolymerClass.cpp: In function ‘bool letterIsPurine(char)’: /<>/src/BiopolymerClass.cpp:51:14: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 51 | return c == 'A' | c == 'G'; | ~~^~~~~~ /<>/src/BiopolymerClass.cpp: In function ‘bool letterIsRNA(char)’: /<>/src/BiopolymerClass.cpp:57:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 57 | c == 'A' | | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:59:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 59 | c == 'G' | | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:60:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 60 | c == 'U' | ~~^~~~~~ /<>/src/BiopolymerClass.cpp: In function ‘bool letterIsDNA(char)’: /<>/src/BiopolymerClass.cpp:67:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 67 | c == 'A' | | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:69:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 69 | c == 'G' | | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:70:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 70 | c == 'T' | ~~^~~~~~ /<>/src/BiopolymerClass.cpp: In function ‘bool letterIsProtein(char)’: /<>/src/BiopolymerClass.cpp:77:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 77 | c == 'C' | | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:79:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 79 | c == 'H' | | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:80:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 80 | c == 'I' | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:86:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 86 | c == 'M' | | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:88:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 88 | c == 'V' | | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:89:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 89 | c == 'A' | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:95:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 95 | c == 'G' | | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:97:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 97 | c == 'P' | | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:98:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 98 | c == 'T' | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:104:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 104 | c == 'R' | | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:106:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 106 | c == 'Y' | | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:107:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 107 | c == 'W' | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:113:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 113 | c == 'D' | | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:115:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 115 | c == 'E' | | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:116:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 116 | c == 'Q' | | ~~^~~~~~ /<>/src/BiopolymerClass.cpp:117:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 117 | c == 'K' | ~~^~~~~~ /<>/src/AtomSpringContainer.cpp: In member function ‘double AtomSpringContainer::calcRmsd(SimTK::State&, BiopolymerClassContainer&)’: /<>/src/AtomSpringContainer.cpp:65:12: warning: unused variable ‘myExtension’ [-Wunused-variable] 65 | double myExtension = 0.0; | ^~~~~~~~~~~ /<>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClass::modifyResidue(BiopolymerModification, SimTK::Compound, SimTK::DuMMForceFieldSubsystem&)’: /<>/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))); | ^~~~~~~~~~~~~~~~~~~~~~ /<>/src/BiopolymerClass.cpp:135:29: warning: unused variable ‘myOrdinality’ [-Wunused-variable] 135 | Ordinality::Residue myOrdinality(SimTK::Ordinality::Any); | ^~~~~~~~~~~~ /<>/src/BiopolymerClass.cpp:147:32: warning: unused variable ‘myBondMobility’ [-Wunused-variable] 147 | BondMobility::Mobility myBondMobility = stringToBondMobility("Rigid"); | ^~~~~~~~~~~~~~ /<>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::deleteAtomSpring(int)’: /<>/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()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateAtomSpring(int, const AtomSpring&, BiopolymerClassContainer&)’: /<>/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()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::checkResidueNumbersAndInsertionCodes()’: /<>/src/BiopolymerClass.cpp:244:15: warning: variable ‘myResidueID’ set but not used [-Wunused-but-set-variable] 244 | ResidueID myResidueID = getFirstResidueID(); | ^~~~~~~~~~~ /<>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::deleteThreading(int)’: /<>/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()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateThreading(int, const ThreadingStruct&, BiopolymerClassContainer&)’: /<>/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()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateThreading(int, SimTK::String, ResidueID, ResidueID, SimTK::String, ResidueID, ResidueID, double, bool, BiopolymerClassContainer&)’: /<>/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()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::deleteGappedThreading(int)’: /<>/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()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateGappedThreading(int, const ThreadingStruct&, BiopolymerClassContainer&)’: /<>/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()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateGappedThreading(int, SimTK::String, SimTK::String, double, bool, BiopolymerClassContainer&)’: /<>/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()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::createSpringsFromGappedThreading(BiopolymerClassContainer&)’: /<>/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)) && | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/AtomSpringContainer.cpp:489:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘seqan::Size > >::Type’ {aka ‘long unsigned int’} [-Wsign-compare] 489 | (bIndex < length(thread.updThreadingPartner(1).sequence))) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 /<>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClass::setPdbResidueNumbersFromResidueIDVector()’: /<>/src/BiopolymerClass.cpp:518:15: warning: variable ‘myFirstResidueID’ set but not used [-Wunused-but-set-variable] 518 | ResidueID myFirstResidueID = getFirstResidueID() ; | ^~~~~~~~~~~~~~~~ /<>/src/BiopolymerClass.cpp:520:9: warning: unused variable ‘numResidues’ [-Wunused-variable] 520 | int numResidues = -1; | ^~~~~~~~~~~ /<>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClass::renumberPdbResidues(ResidueID)’: /<>/src/BiopolymerClass.cpp:551:9: warning: unused variable ‘myNewResidueNumberWithoutInsertionCode’ [-Wunused-variable] 551 | int myNewResidueNumberWithoutInsertionCode = firstResidueID.getResidueNumber() ; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 /<>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::matchCoordinates(const SimTK::PdbStructure&, bool, bool, bool, bool, bool, bool, double, double)’: /<>/src/BiopolymerClass.cpp:669:45: warning: variable ‘biopolymerAtomTargetsIterator’ set but not used [-Wunused-but-set-variable] 669 | Compound::AtomTargetLocations::iterator biopolymerAtomTargetsIterator = biopolymerAtomTargets.begin(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/BiopolymerClass.cpp: In member function ‘bool BiopolymerClass::hasAtom(ResidueID, SimTK::String)’: /<>/src/BiopolymerClass.cpp:1053:9: warning: unused variable ‘myResidueIndex’ [-Wunused-variable] 1053 | int myResidueIndex = getResidueIndex(myResidueID); | ^~~~~~~~~~~~~~ /<>/src/BiopolymerClass.cpp: In member function ‘SimTK::Vec3 BiopolymerClass::calcDefaultAtomLocationInGroundFrame(const ResidueID&, const SimTK::String&) const’: /<>/src/BiopolymerClass.cpp:1316:25: warning: variable ‘myAtomIndex’ set but not used [-Wunused-but-set-variable] 1316 | Compound::AtomIndex myAtomIndex = atomIndex(myResidueID,atomName); | ^~~~~~~~~~~ /<>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClass::addGeneralSterics(SimTK::GeneralContactSubsystem&, SimTK::ContactSetIndex, SimTK::HuntCrossleyForce&, SimTK::SimbodyMatterSubsystem&, double, double, ResidueID, ResidueID, bool, bool)’: /<>/src/BiopolymerClass.cpp:1437:12: warning: unused variable ‘huntCrossleyDissipation’ [-Wunused-variable] 1437 | double huntCrossleyDissipation =.0; | ^~~~~~~~~~~~~~~~~~~~~~~ /<>/src/BiopolymerClass.cpp: In member function ‘ResidueID BiopolymerClass::sum(ResidueID, int) const’: /<>/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())) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClassContainer::waterDropletAboutResidues(std::vector, WaterDropletContainer&)’: /<>/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 | ^~~~~~~~~~ /<>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClassContainer::substituteResidue(SimTK::String, ResidueID, SimTK::String, bool)’: /<>/src/BiopolymerClass.cpp:4130:15: warning: variable ‘myFirstResidueNumber’ set but not used [-Wunused-but-set-variable] 4130 | ResidueID myFirstResidueNumber = myOldBiopolymerClass.getFirstResidueID(); | ^~~~~~~~~~~~~~~~~~~~ /<>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClassContainer::substituteResidue(Mutation, bool, bool, bool)’: /<>/src/BiopolymerClass.cpp:4519:15: warning: variable ‘myFirstResidueNumber’ set but not used [-Wunused-but-set-variable] 4519 | ResidueID myFirstResidueNumber = myOldBiopolymerClass.getFirstResidueID(); | ^~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 In file included from /<>/include/ContactContainer.h:15, from /<>/src/BiopolymerClass.cpp:16: /<>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’: /<>/src/BiopolymerClass.cpp:4682:61: required from here /<>/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++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/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++) { | ~~^~~~~~~~~~~~~~~~~~~~~ [ 15%] Building CXX object CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -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 /<>/src/DisplacementContainer.cpp /<>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = MobilizerStretch]’: /<>/src/BiopolymerClass.cpp:2584:54: required from ‘void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch&, ResidueStretchContainer&) [with ResidueStretchType = MobilizerStretch]’ /<>/src/BiopolymerClass.cpp:2588:181: required from here /<>/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 >/include/ResidueStretchContainer.h: In instantiation of ‘bool ResidueStretchContainer::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]’: /<>/include/ResidueStretchContainer.h:320:27: required from ‘void ResidueStretchContainer::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’ /<>/src/BiopolymerClass.cpp:4682:61: required from here /<>/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 >/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /<>/src/BiopolymerClass.cpp:4827:54: required from ‘void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer&, ResidueStretchContainer&) [with ResidueStretchType = DensityStretch]’ /<>/src/BiopolymerClass.cpp:4830:213: required from here /<>/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 >/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /usr/include/molmodel/molmodel/internal/Compound.h:36, from /<>/include/BiopolymerClass.h:16, from /<>/include/DisplacementContainer.h:14, from /<>/src/DisplacementContainer.cpp:12: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93, from /usr/include/simbody/SimTKcommon/Simmatrix.h:37: In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Kabsch78::superpose(std::vector > const&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Mat[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/include/Utils.h:23: /usr/include/molmodel/molmodel/internal/Superpose.h: In function ‘SimTK::Kabsch78::superpose(std::vector > const&)’: /usr/include/molmodel/molmodel/internal/Superpose.h:107:18: note: object ‘R’ of size 72 107 | Mat<3,3> R(0.0); | ^ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Kabsch78::superpose(std::vector > const&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Mat[1]’ [-Warray-bounds] 784 | { for(int i=0;i > const&)’: /usr/include/molmodel/molmodel/internal/Superpose.h:107:18: note: object ‘R’ of size 72 107 | Mat<3,3> R(0.0); | ^ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Kabsch78::superpose(std::vector > const&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Mat[1]’ [-Warray-bounds] 784 | { for(int i=0;i > const&)’: /usr/include/molmodel/molmodel/internal/Superpose.h:107:18: note: object ‘R’ of size 72 107 | Mat<3,3> R(0.0); | ^ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Kabsch78::superpose(std::vector > const&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:183:23: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Mat[1]’ [-Warray-bounds] 784 | { for(int i=0;i > const&)’: /usr/include/molmodel/molmodel/internal/Superpose.h:183:18: note: object ‘U’ of size 72 183 | Mat<3,3> U(0.0); // initialize 2-d array | ^ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Kabsch78::superpose(std::vector > const&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:183:23: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Mat[1]’ [-Warray-bounds] 784 | { for(int i=0;i > const&)’: /usr/include/molmodel/molmodel/internal/Superpose.h:183:18: note: object ‘U’ of size 72 183 | Mat<3,3> U(0.0); // initialize 2-d array | ^ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Kabsch78::superpose(std::vector > const&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:183:23: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Mat[1]’ [-Warray-bounds] 784 | { for(int i=0;i > const&)’: /usr/include/molmodel/molmodel/internal/Superpose.h:183:18: note: object ‘U’ of size 72 183 | Mat<3,3> U(0.0); // initialize 2-d array | ^ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘SimTK::Kabsch78::superpose(std::vector > const&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:201:24: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i > const&)’: /usr/include/molmodel/molmodel/internal/Superpose.h:201:33: note: object ‘’ of size 72 201 | rotation = Rotation(); | ^ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘SimTK::Kabsch78::superpose(std::vector > const&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:201:24: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i > const&)’: /usr/include/molmodel/molmodel/internal/Superpose.h:201:33: note: object ‘’ of size 72 201 | rotation = Rotation(); | ^ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘SimTK::Kabsch78::superpose(std::vector > const&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:201:24: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i > const&)’: /usr/include/molmodel/molmodel/internal/Superpose.h:201:33: note: object ‘’ of size 72 201 | rotation = Rotation(); | ^ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ In file included from /<>/include/Mutation.h:4, from /<>/include/BiopolymerClass.h:20: /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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); }; | ~~^~~~~~~~~~~~~~~~~ /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 [ 18%] Building CXX object CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -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 /<>/src/MobilizerContainer.cpp In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /<>/include/Utils.h:22, from /<>/src/MobilizerContainer.cpp:11: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ [ 21%] Building CXX object CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -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 /<>/src/MoleculeContainer.cpp In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/Simbody.h:38, from /usr/include/molmodel/SimTKmolmodel.h:47, from /<>/include/MoleculeContainer.h:6, from /<>/src/MoleculeContainer.cpp:3: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ [ 25%] Building CXX object CMakeFiles/MMB.dir/src/DensityContainer.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -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 /<>/src/DensityContainer.cpp /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /usr/include/molmodel/molmodel/internal/Compound.h:36, from /<>/include/BiopolymerClass.h:16, from /<>/include/ResidueStretchContainer.h:4, from /<>/include/DensityContainer.h:14, from /<>/src/DensityContainer.cpp:11: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ In file included from /<>/src/MobilizerContainer.cpp:12: /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /<>/src/MobilizerContainer.cpp: In member function ‘void MobilizerContainer::addMobilizerDomainsInterfacesToVector(const std::vector&, BiopolymerClassContainer&)’: /<>/src/MobilizerContainer.cpp:190:37: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 190 | if( (dist <= it->range) && | ~~~~~~~~~~~~~~~~~~~~^~ 191 | (it->domain1.contains(chain1, res1) && it->domain2.contains(chain2, res2)) || | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 In file included from /<>/include/ConstraintContainer.h:14, from /<>/include/MoleculeContainer.h:8: /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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); }; | ~~^~~~~~~~~~~~~~~~~ /<>/src/MoleculeContainer.cpp: In constructor ‘CustomMolecule::CustomMolecule(std::vector >, SimTK::DuMMForceFieldSubsystem&)’: /<>/src/MoleculeContainer.cpp:324:15: warning: unused variable ‘myAngle1’ [-Wunused-variable] 324 | Angle myAngle1 = 180*Deg2Rad; // this is a bond angle | ^~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ In file included from /<>/include/Mutation.h:4, from /<>/include/BiopolymerClass.h:20: /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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); }; | ~~^~~~~~~~~~~~~~~~~ /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /<>/src/DensityContainer.cpp: In member function ‘void DensityContainer::updateDensityStretch(int, const DensityStretch&, BiopolymerClassContainer&)’: /<>/src/DensityContainer.cpp:18:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 18 | if(id < 0 || id >= residueStretchVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 /<>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:22:59: required from here /<>/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 >/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:25:59: required from here /<>/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()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ [ 28%] 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/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o -MF CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o -c /<>/src/BasePairContainer.cpp In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/Simbody.h:38, from /usr/include/molmodel/SimTKmolmodel.h:47, from /<>/include/BasePairContainer.h:16, from /<>/src/BasePairContainer.cpp:11: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ [ 31%] Building CXX object CMakeFiles/MMB.dir/src/ContactContainer.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -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 /<>/src/ContactContainer.cpp In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /<>/include/Utils.h:22, from /<>/src/ContactContainer.cpp:11: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ In file included from /<>/include/Mutation.h:4, from /<>/include/BiopolymerClass.h:20, from /<>/include/BasePairContainer.h:17: /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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); }; | ~~^~~~~~~~~~~~~~~~~ /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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); }; | ~~^~~~~~~~~~~~~~~~~ [ 34%] Building CXX object CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o -MF CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o -c /<>/src/ConstraintContainer.cpp In file included from /<>/src/ContactContainer.cpp:12: /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /<>/src/ContactContainer.cpp: In member function ‘void ContactContainer::validateContact(ContactStretch, BiopolymerClassContainer&)’: /<>/src/ContactContainer.cpp:26:10: warning: variable ‘myEndCapsOn’ set but not used [-Wunused-but-set-variable] 26 | bool myEndCapsOn; | ^~~~~~~~~~~ /<>/src/ContactContainer.cpp: In member function ‘void ContactContainer::deleteContactWithin(int)’: /<>/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()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/ContactContainer.cpp: In member function ‘void ContactContainer::updateContactWithin(int, SimTK::String, int, double, SimTK::String, BiopolymerClassContainer&)’: /<>/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()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/ContactContainer.cpp: In member function ‘void ContactContainer::deleteContact(int)’: /<>/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()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/ContactContainer.cpp: In member function ‘void ContactContainer::updateContact(int, std::string, int, int, std::string, BiopolymerClassContainer&)’: /<>/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()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/ContactContainer.cpp: In member function ‘bool ContactContainer::hasSharedContact(SimTK::String, ResidueID, ResidueID, SimTK::String)’: /<>/src/ContactContainer.cpp:313:71: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 313 | ((tempContactStretch.getStartResidue() <= endResidueID) && (tempContactStretch.getEndResidue() >= endResidueID) || // the supplied end residue is in the range of this ContactStretch (with index $i). | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93, from /usr/include/simbody/SimTKcommon/Simmatrix.h:37: In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, std::vector > const&, double, double, std::vector > const&, std::map, std::allocator > const, std::shared_ptr, std::less, std::allocator > const>, std::allocator, std::allocator > const, std::shared_ptr > > >&)’ at /<>/src/BiopolymerClass.cpp:875:14: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClass.cpp: In member function ‘BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, std::vector > const&, double, double, std::vector > const&, std::map, std::allocator > const, std::shared_ptr, std::less, std::allocator > const>, std::allocator, std::allocator > const, std::shared_ptr > > >&)’: /<>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, std::vector > const&, double, double, std::vector > const&, std::map, std::allocator > const, std::shared_ptr, std::less, std::allocator > const>, std::allocator, std::allocator > const, std::shared_ptr > > >&)’ at /<>/src/BiopolymerClass.cpp:875:14: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClass.cpp: In member function ‘BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, std::vector > const&, double, double, std::vector > const&, std::map, std::allocator > const, std::shared_ptr, std::less, std::allocator > const>, std::allocator, std::allocator > const, std::shared_ptr > > >&)’: /<>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, std::vector > const&, double, double, std::vector > const&, std::map, std::allocator > const, std::shared_ptr, std::less, std::allocator > const>, std::allocator, std::allocator > const, std::shared_ptr > > >&)’ at /<>/src/BiopolymerClass.cpp:875:14: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClass.cpp: In member function ‘BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, std::vector > const&, double, double, std::vector > const&, std::map, std::allocator > const, std::shared_ptr, std::less, std::allocator > const>, std::allocator, std::allocator > const, std::shared_ptr > > >&)’: /<>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::scalarEq(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::operator=(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_::setRotationToIdentityMatrix()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, std::vector > const&, double, double, std::vector > const&, std::map, std::allocator > const, std::shared_ptr, std::less, std::allocator > const>, std::allocator, std::allocator > const, std::shared_ptr > > >&)’ at /<>/src/BiopolymerClass.cpp:876:44: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClass.cpp: In member function ‘BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, std::vector > const&, double, double, std::vector > const&, std::map, std::allocator > const, std::shared_ptr, std::less, std::allocator > const>, std::allocator, std::allocator > const, std::shared_ptr > > >&)’: /<>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::scalarEq(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::operator=(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_::setRotationToIdentityMatrix()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, std::vector > const&, double, double, std::vector > const&, std::map, std::allocator > const, std::shared_ptr, std::less, std::allocator > const>, std::allocator, std::allocator > const, std::shared_ptr > > >&)’ at /<>/src/BiopolymerClass.cpp:876:44: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClass.cpp: In member function ‘BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, std::vector > const&, double, double, std::vector > const&, std::map, std::allocator > const, std::shared_ptr, std::less, std::allocator > const>, std::allocator, std::allocator > const, std::shared_ptr > > >&)’: /<>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::scalarEq(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::operator=(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_::setRotationToIdentityMatrix()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, std::vector > const&, double, double, std::vector > const&, std::map, std::allocator > const, std::shared_ptr, std::less, std::allocator > const>, std::allocator, std::allocator > const, std::shared_ptr > > >&)’ at /<>/src/BiopolymerClass.cpp:876:44: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClass.cpp: In member function ‘BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, std::vector > const&, double, double, std::vector > const&, std::map, std::allocator > const, std::shared_ptr, std::less, std::allocator > const>, std::allocator, std::allocator > const, std::shared_ptr > > >&)’: /<>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /<>/include/Utils.h:22, from /<>/include/ConstraintContainer.h:14, from /<>/src/ConstraintContainer.cpp:10: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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 /<>/src/ConstraintContainer.cpp:11: /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /<>/src/ConstraintContainer.cpp: In member function ‘void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)’: /<>/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()) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/ConstraintContainer.cpp: In member function ‘void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)’: /<>/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()) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 [ 37%] Building CXX object CMakeFiles/MMB.dir/src/Repel.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/Repel.cpp.o -MF CMakeFiles/MMB.dir/src/Repel.cpp.o.d -o CMakeFiles/MMB.dir/src/Repel.cpp.o -c /<>/src/Repel.cpp In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/Simbody.h:38, from /usr/include/molmodel/SimTKmolmodel.h:47, from /<>/include/Repel.h:23, from /<>/src/Repel.cpp:12: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ [ 40%] Building CXX object CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o -MF CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o.d -o CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o -c /<>/src/MonoAtoms.cpp [ 43%] Building CXX object CMakeFiles/MMB.dir/src/Spiral.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/Spiral.cpp.o -MF CMakeFiles/MMB.dir/src/Spiral.cpp.o.d -o CMakeFiles/MMB.dir/src/Spiral.cpp.o -c /<>/src/Spiral.cpp /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /<>/include/Utils.h:22, from /<>/src/MonoAtoms.cpp:11: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/Simbody.h:38, from /usr/include/molmodel/SimTKmolmodel.h:47, from /<>/include/Spiral.h:14, from /<>/src/Spiral.cpp:11: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ In file included from /<>/include/AtomSpringContainer.h:14, from /<>/include/ParameterReader.h:20, from /<>/include/PeriodicScrubber.h:16, from /<>/include/Repel.h:24: /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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 /<>/include/Threading.h:2, from /<>/include/AtomSpringContainer.h:15: /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /<>/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();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 46%] Building CXX object CMakeFiles/MMB.dir/src/ParameterReader.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ParameterReader.cpp.o -MF CMakeFiles/MMB.dir/src/ParameterReader.cpp.o.d -o CMakeFiles/MMB.dir/src/ParameterReader.cpp.o -c /<>/src/ParameterReader.cpp /<>/src/Repel.cpp: In member function ‘void ConstrainedDynamics::constraintsAndRestraints(ParameterReader&, BiopolymerClassContainer&, SimTK::GeneralForceSubsystem&, SimTK::SimbodyMatterSubsystem&, SimTK::State&, SimTK::CompoundSystem&)’: /<>/src/Repel.cpp:172:31: warning: variable ‘myResidueID’ set but not used [-Wunused-but-set-variable] 172 | ResidueID myResidueID = myConstraintClass.getResidueID1(); | ^~~~~~~~~~~ /<>/include/Repel.h: In constructor ‘ConstrainedDynamics::ConstrainedDynamics(ParameterReader*)’: /<>/include/Repel.h:269:29: warning: ‘ConstrainedDynamics::_parameterReader’ will be initialized after [-Wreorder] 269 | ParameterReader * _parameterReader; | ^~~~~~~~~~~~~~~~ /<>/include/Repel.h:259:29: warning: ‘SimTK::SimbodyMatterSubsystem ConstrainedDynamics::_matter’ [-Wreorder] 259 | SimbodyMatterSubsystem _matter; | ^~~~~~~ /<>/src/Repel.cpp:342:1: warning: when initialized here [-Wreorder] 342 | ConstrainedDynamics::ConstrainedDynamics(ParameterReader * myParameterReader) : _parameterReader(myParameterReader), | ^~~~~~~~~~~~~~~~~~~ /<>/src/Repel.cpp: In member function ‘void ConstrainedDynamics::initializeBiopolymer(SimTK::String, SimTK::String)’: /<>/src/Repel.cpp:405:10: warning: variable ‘readFromFile’ set but not used [-Wunused-but-set-variable] 405 | bool readFromFile = false; | ^~~~~~~~~~~~ /<>/src/Repel.cpp: In member function ‘void ConstrainedDynamics::runAllSteps()’: /<>/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++){ | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /<>/include/Utils.h:22, from /<>/include/AtomSpringContainer.h:14, from /<>/include/ParameterReader.h:20, from /<>/src/ParameterReader.cpp:17: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ In file included from /<>/include/ContactContainer.h:15, from /<>/include/ParameterReader.h:21: /<>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:22:59: required from here /<>/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 >/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:25:59: required from here /<>/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 /<>/include/Spiral.h:16: /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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); }; | ~~^~~~~~~~~~~~~~~~~ /<>/src/Spiral.cpp: In member function ‘void Spiral::clear()’: /<>/src/Spiral.cpp:92:12: warning: unused variable ‘helixAdvancePerBasePair’ [-Wunused-variable] 92 | double helixAdvancePerBasePair = -11111. ; // in nm // should be user specified. | ^~~~~~~~~~~~~~~~~~~~~~~ /<>/src/Spiral.cpp: In member function ‘double Spiral::harmonicThetaAdjustment(double)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/src/Spiral.cpp: In member function ‘void Spiral::writeCylindricalSpiralCommandFile(MonoAtomsContainer&)’: /<>/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 ; | ^~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/src/Spiral.cpp: In member function ‘void Spiral::writeSphericalSpiralCommandFile(MonoAtomsContainer&)’: /<>/src/Spiral.cpp:238:16: warning: unused variable ‘currentPhi’ [-Wunused-variable] 238 | double currentPhi = priorPhi + deltaPhi ; // phiFromTheta(currentTheta, pitch, radius, phiOffset); | ^~~~~~~~~~ /<>/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 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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); }; | ~~^~~~~~~~~~~~~~~~~ /<>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::addAllMutualChainResidues(double, std::vector, std::vector, BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]’: /<>/include/ResidueStretchContainer.h:210:4: required from ‘void ResidueStretchContainer::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]’ /<>/src/Repel.cpp:470:84: required from here /<>/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++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/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++) { | ~~^~~~~~~~~~~~~~~~~~~~~ /<>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::addAllMutualChainResidues(double, std::vector, std::vector, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’: /<>/include/ResidueStretchContainer.h:210:4: required from ‘void ResidueStretchContainer::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’ /<>/src/Repel.cpp:573:84: required from here /<>/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++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/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++) { | ~~^~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 /<>/include/ResidueStretchContainer.h: In instantiation of ‘bool ResidueStretchContainer::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = MobilizerStretch]’: /<>/include/ResidueStretchContainer.h:264:27: required from ‘void ResidueStretchContainer::addAllMutualChainResidues(double, std::vector, std::vector, BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]’ /<>/include/ResidueStretchContainer.h:210:4: required from ‘void ResidueStretchContainer::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]’ /<>/src/Repel.cpp:470:84: required from here /<>/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 >/include/ResidueStretchContainer.h: In instantiation of ‘bool ResidueStretchContainer::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]’: /<>/include/ResidueStretchContainer.h:264:27: required from ‘void ResidueStretchContainer::addAllMutualChainResidues(double, std::vector, std::vector, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’ /<>/include/ResidueStretchContainer.h:210:4: required from ‘void ResidueStretchContainer::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’ /<>/src/Repel.cpp:573:84: required from here /<>/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] /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/src/Repel.cpp: At global scope: /<>/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 ) { | ^~~~~~~~~~~~ /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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 /<>/include/Threading.h:2, from /<>/include/AtomSpringContainer.h:15: /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /<>/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();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/ParameterReader.cpp: In member function ‘void ParameterReader::removeNonPriorityBasePairs(int)’: /<>/src/ParameterReader.cpp:727:9: warning: unused variable ‘oldDutyCyclePriority’ [-Wunused-variable] 727 | int oldDutyCyclePriority=0; | ^~~~~~~~~~~~~~~~~~~~ /<>/src/ParameterReader.cpp: In member function ‘void ParameterReader::updateAllResiduesWithin(int, SimTK::String, int, double)’: /<>/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()){ | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/ParameterReader.cpp: In member function ‘void ParameterReader::deleteAllResiduesWithin(int)’: /<>/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()){ | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ /<>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’: /<>/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. | ^~~~~~~~~~~~~~~ /<>/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)) | ^ /<>/src/ParameterReader.cpp:2658:27: warning: variable ‘residueID1’ set but not used [-Wunused-but-set-variable] 2658 | ResidueID residueID1 = ResidueID(-11111,'X'); | ^~~~~~~~~~ /<>/src/ParameterReader.cpp:2659:27: warning: variable ‘residueID2’ set but not used [-Wunused-but-set-variable] 2659 | ResidueID residueID2 = ResidueID(-11111,'X'); | ^~~~~~~~~~ /<>/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)) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 In file included from /<>/include/ContactContainer.h:15, from /<>/include/ParameterReader.h:21: /<>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:22:59: required from here /<>/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 >/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:25:59: required from here /<>/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()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = SingleResidue]’: /<>/src/ParameterReader.cpp:814:42: required from here /<>/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] [ 50%] Building CXX object CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o -MF CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o.d -o CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o -c /<>/src/BaseInteractionParameterReader.cpp In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /<>/src/BaseInteractionParameterReader.cpp:17: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ In file included from /<>/include/BaseInteractionParameterReader.h:22, from /<>/src/BaseInteractionParameterReader.cpp:18: /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); }; | ~~^~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 [ 53%] Building CXX object CMakeFiles/MMB.dir/src/TetherForce.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/TetherForce.cpp.o -MF CMakeFiles/MMB.dir/src/TetherForce.cpp.o.d -o CMakeFiles/MMB.dir/src/TetherForce.cpp.o -c /<>/src/TetherForce.cpp In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/Simbody.h:38, from /usr/include/molmodel/SimTKmolmodel.h:47, from /<>/include/TetherForce.h:18, from /<>/src/TetherForce.cpp:11: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ [ 56%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o -MF CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o.d -o CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o -c /<>/src/BiopolymerClassTwoTransformForces.cpp /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/Simbody.h:38, from /usr/include/molmodel/SimTKmolmodel.h:47, from /<>/include/BiopolymerClassTwoTransformForces.h:16, from /<>/src/BiopolymerClassTwoTransformForces.cpp:10: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ In file included from /<>/include/AtomSpringContainer.h:14, from /<>/include/ParameterReader.h:20, from /<>/include/TetherForce.h:19: /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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 /<>/include/Threading.h:2, from /<>/include/AtomSpringContainer.h:15: /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /<>/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();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 In file included from /<>/include/ContactContainer.h:15, from /<>/include/ParameterReader.h:21: /<>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:22:59: required from here /<>/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 >/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:25:59: required from here /<>/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()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 59%] Building CXX object CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -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 /<>/src/WaterDroplet.cpp In file included from /<>/include/AtomSpringContainer.h:14, from /<>/include/ParameterReader.h:20, from /<>/include/BiopolymerClassTwoTransformForces.h:17: /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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 /<>/include/Threading.h:2, from /<>/include/AtomSpringContainer.h:15: /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /<>/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();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’: /<>/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. | ^~~~~~~~~ /<>/src/BiopolymerClassTwoTransformForces.cpp:280:16: warning: variable ‘scrubberPeriod’ set but not used [-Wunused-but-set-variable] 280 | double scrubberPeriod; | ^~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/Simbody.h:38, from /usr/include/molmodel/SimTKmolmodel.h:47, from /<>/include/Water.h:1, from /<>/include/WaterDroplet.h:15, from /<>/src/WaterDroplet.cpp:11: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ In file included from /<>/include/ContactContainer.h:15, from /<>/include/ParameterReader.h:21: /<>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:22:59: required from here /<>/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 >/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:25:59: required from here /<>/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()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ [ 62%] Building CXX object CMakeFiles/MMB.dir/src/DensityMap.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DensityMap.cpp.o -MF CMakeFiles/MMB.dir/src/DensityMap.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityMap.cpp.o -c /<>/src/DensityMap.cpp In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /<>/include/Utils.h:22, from /<>/src/DensityMap.cpp:11: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ In file included from /<>/include/WaterDroplet.h:16: /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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 /<>/include/Threading.h:2, from /<>/include/AtomSpringContainer.h:15, from /<>/include/WaterDroplet.h:17: /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /<>/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 /usr/include/simbody/SimTKcommon/SmallMatrix.h:93, from /usr/include/simbody/SimTKcommon/Simmatrix.h:37: In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘AllTwoTransformLinearSprings::calcForce(SimTK::State const&, SimTK::Vector_, 1> >&, SimTK::Vector_ >&, SimTK::Vector_&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:116:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘AllTwoTransformLinearSprings::calcForce(SimTK::State const&, SimTK::Vector_, 1> >&, SimTK::Vector_ >&, SimTK::Vector_&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72 116 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘AllTwoTransformLinearSprings::calcForce(SimTK::State const&, SimTK::Vector_, 1> >&, SimTK::Vector_ >&, SimTK::Vector_&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:116:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘AllTwoTransformLinearSprings::calcForce(SimTK::State const&, SimTK::Vector_, 1> >&, SimTK::Vector_ >&, SimTK::Vector_&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72 116 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘AllTwoTransformLinearSprings::calcForce(SimTK::State const&, SimTK::Vector_, 1> >&, SimTK::Vector_ >&, SimTK::Vector_&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:116:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘AllTwoTransformLinearSprings::calcForce(SimTK::State const&, SimTK::Vector_, 1> >&, SimTK::Vector_ >&, SimTK::Vector_&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72 116 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::scalarEq(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::operator=(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_::setRotationToIdentityMatrix()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘AllTwoTransformLinearSprings::calcForce(SimTK::State const&, SimTK::Vector_, 1> >&, SimTK::Vector_ >&, SimTK::Vector_&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:117:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘AllTwoTransformLinearSprings::calcForce(SimTK::State const&, SimTK::Vector_, 1> >&, SimTK::Vector_ >&, SimTK::Vector_&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72 116 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::scalarEq(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::operator=(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_::setRotationToIdentityMatrix()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘AllTwoTransformLinearSprings::calcForce(SimTK::State const&, SimTK::Vector_, 1> >&, SimTK::Vector_ >&, SimTK::Vector_&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:117:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘AllTwoTransformLinearSprings::calcForce(SimTK::State const&, SimTK::Vector_, 1> >&, SimTK::Vector_ >&, SimTK::Vector_&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72 116 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::scalarEq(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::operator=(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_::setRotationToIdentityMatrix()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘AllTwoTransformLinearSprings::calcForce(SimTK::State const&, SimTK::Vector_, 1> >&, SimTK::Vector_ >&, SimTK::Vector_&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:117:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘AllTwoTransformLinearSprings::calcForce(SimTK::State const&, SimTK::Vector_, 1> >&, SimTK::Vector_ >&, SimTK::Vector_&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72 116 | Rotation rotation2; | ^~~~~~~~~ /<>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /<>/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();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/BiopolymerClassTwoTransformForces.cpp:254:29: warning: ‘myFrcScalar’ may be used uninitialized [-Wmaybe-uninitialized] 254 | myFrcScalar *= myParameterReader.twoTransformForceMultiplier; | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/BiopolymerClassTwoTransformForces.cpp:167:20: note: ‘myFrcScalar’ was declared here 167 | double myFrcScalar; | ^~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘AllTwoTransformLinearSprings::calcPotentialEnergy(SimTK::State const&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:319:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘AllTwoTransformLinearSprings::calcPotentialEnergy(SimTK::State const&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72 319 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘AllTwoTransformLinearSprings::calcPotentialEnergy(SimTK::State const&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:319:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘AllTwoTransformLinearSprings::calcPotentialEnergy(SimTK::State const&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72 319 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘AllTwoTransformLinearSprings::calcPotentialEnergy(SimTK::State const&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:319:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘AllTwoTransformLinearSprings::calcPotentialEnergy(SimTK::State const&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72 319 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::scalarEq(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::operator=(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_::setRotationToIdentityMatrix()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘AllTwoTransformLinearSprings::calcPotentialEnergy(SimTK::State const&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:320:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘AllTwoTransformLinearSprings::calcPotentialEnergy(SimTK::State const&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72 319 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::scalarEq(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::operator=(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_::setRotationToIdentityMatrix()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘AllTwoTransformLinearSprings::calcPotentialEnergy(SimTK::State const&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:320:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘AllTwoTransformLinearSprings::calcPotentialEnergy(SimTK::State const&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72 319 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::scalarEq(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::operator=(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_::setRotationToIdentityMatrix()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘AllTwoTransformLinearSprings::calcPotentialEnergy(SimTK::State const&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:320:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘AllTwoTransformLinearSprings::calcPotentialEnergy(SimTK::State const&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72 319 | Rotation rotation2; | ^~~~~~~~~ /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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); }; | ~~^~~~~~~~~~~~~~~~~ /<>/src/DensityMap.cpp: In member function ‘void DensityMap::resizeVectorOfAmplitudeAndRandomPhases()’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/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) ) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/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 )) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/DensityMap.cpp: In member function ‘void DensityMap::densityAutocorrelation(bool, bool) const’: /<>/src/DensityMap.cpp:209:12: warning: unused variable ‘ySquared’ [-Wunused-variable] 209 | double ySquared = 0.; | ^~~~~~~~ /<>/src/DensityMap.cpp:210:12: warning: unused variable ‘zSquared’ [-Wunused-variable] 210 | double zSquared = 0.; | ^~~~~~~~ /<>/src/DensityMap.cpp: In member function ‘void DensityMap::populateNoiseMap()’: /<>/src/DensityMap.cpp:307:12: warning: unused variable ‘groundFrequencyX’ [-Wunused-variable] 307 | double groundFrequencyX = 1/unitCellParameters.getNa()/unitCellParameters.geta()/2; | ^~~~~~~~~~~~~~~~ /<>/src/DensityMap.cpp:308:12: warning: unused variable ‘groundFrequencyY’ [-Wunused-variable] 308 | double groundFrequencyY = 1/unitCellParameters.getNb()/unitCellParameters.getb()/2; | ^~~~~~~~~~~~~~~~ /<>/src/DensityMap.cpp:309:12: warning: unused variable ‘groundFrequencyZ’ [-Wunused-variable] 309 | double groundFrequencyZ = 1/unitCellParameters.getNc()/unitCellParameters.getc()/2; | ^~~~~~~~~~~~~~~~ /<>/src/DensityMap.cpp:311:12: warning: unused variable ‘maxFrequencyX’ [-Wunused-variable] 311 | double maxFrequencyX = 1/unitCellParameters.geta()/2; | ^~~~~~~~~~~~~ /<>/src/DensityMap.cpp:312:12: warning: unused variable ‘maxFrequencyY’ [-Wunused-variable] 312 | double maxFrequencyY = 1/unitCellParameters.getb()/2; | ^~~~~~~~~~~~~ /<>/src/DensityMap.cpp:313:12: warning: unused variable ‘maxFrequencyZ’ [-Wunused-variable] 313 | double maxFrequencyZ = 1/unitCellParameters.getc()/2; | ^~~~~~~~~~~~~ /<>/src/DensityMap.cpp:318:12: warning: variable ‘signalToNoiseRatio’ set but not used [-Wunused-but-set-variable] 318 | double signalToNoiseRatio = 0.; | ^~~~~~~~~~~~~~~~~~ /<>/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. | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 65%] Building CXX object CMakeFiles/MMB.dir/src/DensityForce.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DensityForce.cpp.o -MF CMakeFiles/MMB.dir/src/DensityForce.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityForce.cpp.o -c /<>/src/DensityForce.cpp /<>/src/DensityMap.cpp: In member function ‘void DensityMap::loadParametersAndDensity_CCP4MAP()’: /<>/src/DensityMap.cpp:543:13: warning: unused variable ‘newU’ [-Wunused-variable] 543 | int newU, newV, newW; | ^~~~ /<>/src/DensityMap.cpp:543:19: warning: unused variable ‘newV’ [-Wunused-variable] 543 | int newU, newV, newW; | ^~~~ /<>/src/DensityMap.cpp:543:25: warning: unused variable ‘newW’ [-Wunused-variable] 543 | int newU, newV, newW; | ^~~~ /<>/src/DensityMap.cpp:507:9: warning: unused variable ‘xGridInds’ [-Wunused-variable] 507 | int xGridInds = xDimInds; | ^~~~~~~~~ /<>/src/DensityMap.cpp:508:9: warning: unused variable ‘yGridInds’ [-Wunused-variable] 508 | int yGridInds = yDimInds; | ^~~~~~~~~ /<>/src/DensityMap.cpp:509:9: warning: unused variable ‘zGridInds’ [-Wunused-variable] 509 | int zGridInds = zDimInds; | ^~~~~~~~~ /<>/src/DensityMap.cpp: In member function ‘void DensityMap::writeDensityMapXplor(SimTK::String, bool, bool)’: /<>/src/DensityMap.cpp:689:13: warning: unused variable ‘densitiesPerLine’ [-Wunused-variable] 689 | int densitiesPerLine = 6; | ^~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/Simbody.h:38, from /usr/include/molmodel/SimTKmolmodel.h:47, from /<>/include/DensityForce.h:19, from /<>/src/DensityForce.cpp:11: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ In file included from /<>/include/AtomSpringContainer.h:14, from /<>/include/ParameterReader.h:20, from /<>/include/DensityForce.h:20: /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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 /<>/include/Threading.h:2, from /<>/include/AtomSpringContainer.h:15: /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /<>/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();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 68%] Building CXX object CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o -MF CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o.d -o CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o -c /<>/src/ElectrostaticPotentialGridForce.cpp /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 In file included from /<>/include/ContactContainer.h:15, from /<>/include/ParameterReader.h:21: /<>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:22:59: required from here /<>/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 >/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:25:59: required from here /<>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/Simbody.h:38, from /usr/include/molmodel/SimTKmolmodel.h:47, from /<>/include/ElectrostaticPotentialGridForce.h:18, from /<>/src/ElectrostaticPotentialGridForce.cpp:11: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93, from /usr/include/simbody/SimTKcommon/Simmatrix.h:37: In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘Displacement::Displacement()’ at /<>/include/Utils.h:544:8, inlined from ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2223:19: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Displacement[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2223:26: note: at offset 56 into object ‘myDisplacement’ of size 128 2223 | Displacement myDisplacement; | ^~~~~~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘Displacement::Displacement()’ at /<>/include/Utils.h:544:8, inlined from ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2223:19: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Displacement[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2223:26: note: at offset 56 into object ‘myDisplacement’ of size 128 2223 | Displacement myDisplacement; | ^~~~~~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘Displacement::Displacement()’ at /<>/include/Utils.h:544:8, inlined from ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2223:19: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Displacement[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2223:26: note: at offset 56 into object ‘myDisplacement’ of size 128 2223 | Displacement myDisplacement; | ^~~~~~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2224:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72 2224 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2224:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72 2224 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2224:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72 2224 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::scalarEq(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::operator=(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_::setRotationToIdentityMatrix()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2225:52: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72 2224 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::scalarEq(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::operator=(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_::setRotationToIdentityMatrix()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2225:52: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72 2224 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::scalarEq(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::operator=(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_::setRotationToIdentityMatrix()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2225:52: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72 2224 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘Displacement::Displacement()’ at /<>/include/Utils.h:544:8, inlined from ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2207:30: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Displacement[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2207:30: note: at offset 56 into object ‘myDisplacement’ of size 128 2207 | Displacement myDisplacement; | ^~~~~~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘Displacement::Displacement()’ at /<>/include/Utils.h:544:8, inlined from ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2207:30: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Displacement[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2207:30: note: at offset 56 into object ‘myDisplacement’ of size 128 2207 | Displacement myDisplacement; | ^~~~~~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘Displacement::Displacement()’ at /<>/include/Utils.h:544:8, inlined from ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2207:30: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Displacement[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2207:30: note: at offset 56 into object ‘myDisplacement’ of size 128 2207 | Displacement myDisplacement; | ^~~~~~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2209:26: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72 2209 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2209:26: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72 2209 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Vec<3, double, 4>::operator=(double const&)SimTK::Vec<3, double, 4>&’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(double const&)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::Mat(int)’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_::Rotation_()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2209:26: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72 2209 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::scalarEq(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::operator=(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_::setRotationToIdentityMatrix()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2210:56: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72 2209 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::scalarEq(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::operator=(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_::setRotationToIdentityMatrix()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2210:56: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72 2209 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec<3, double, 4>::scalarEq(double const&)SimTK::Vec<3, double, 4>&’, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::scalarEq(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat<3, 3, double, 3, 1>::operator=(double const&)SimTK::Mat<3, 3, double, 3, 1>&’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_::setRotationToIdentityMatrix()’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2210:56: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘struct Vec[0]’ is partly outside array bounds of ‘struct Rotation[1]’ [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘ParameterReader::parameterStringInterpreter(ParameterStringClass const&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72 2209 | Rotation myRotation; | ^~~~~~~~~~ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ [ 71%] Building CXX object CMakeFiles/MMB.dir/src/MMBLogger.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/MMBLogger.cpp.o -MF CMakeFiles/MMB.dir/src/MMBLogger.cpp.o.d -o CMakeFiles/MMB.dir/src/MMBLogger.cpp.o -c /<>/src/MMBLogger.cpp [ 75%] Building CXX object CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -MF CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o.d -o CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -c /<>/src/PeriodicPdbAndEnergyWriter.cpp [ 78%] Building CXX object CMakeFiles/MMB.dir/src/CifOutput.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/CifOutput.cpp.o -MF CMakeFiles/MMB.dir/src/CifOutput.cpp.o.d -o CMakeFiles/MMB.dir/src/CifOutput.cpp.o -c /<>/src/CifOutput.cpp In file included from /<>/include/AtomSpringContainer.h:14, from /<>/include/ParameterReader.h:20, from /<>/include/ElectrostaticPotentialGridForce.h:19: /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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 /<>/include/Threading.h:2, from /<>/include/AtomSpringContainer.h:15: /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /<>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/gemmi/to_mmcif.hpp:81, from /<>/src/CifOutput.cpp:10: /usr/include/gemmi/sprintf.hpp:26:4: warning: #warning "Using system stb_sprintf.h, not the bundled one. It may not work." [-Wcpp] 26 | # warning "Using system stb_sprintf.h, not the bundled one. It may not work." | ^~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /<>/include/Utils.h:22, from /<>/include/AtomSpringContainer.h:14, from /<>/include/ParameterReader.h:20, from /<>/include/PeriodicPdbAndEnergyWriter.h:13, from /<>/src/PeriodicPdbAndEnergyWriter.cpp:18: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ In file included from /<>/include/ContactContainer.h:15, from /<>/include/ParameterReader.h:21: /<>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:22:59: required from here /<>/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 >/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:25:59: required from here /<>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /usr/include/molmodel/molmodel/internal/Compound.h:36, from /<>/include/BiopolymerClass.h:16, from /<>/include/CifOutput.h:5, from /<>/src/CifOutput.cpp:1: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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 /<>/include/Mutation.h:4, from /<>/include/BiopolymerClass.h:20: /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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); }; | ~~^~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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 /<>/include/Threading.h:2, from /<>/include/AtomSpringContainer.h:15: /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /<>/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 /<>/include/AtomSpringContainer.h:15, from /<>/include/ParameterReader.h:20, from /<>/include/PeriodicPdbAndEnergyWriter.h:13, from /<>/include/CifOutput.h:12: /<>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /<>/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();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/PeriodicPdbAndEnergyWriter.cpp: In member function ‘virtual void SimTK::PeriodicPdbAndEnergyWriter::handleEvent(SimTK::State&, SimTK::Real, bool&) const’: /<>/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) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/PeriodicPdbAndEnergyWriter.cpp:202:20: warning: unused variable ‘lastEnergy’ [-Wunused-variable] 202 | double lastEnergy = myEnergies.back(); | ^~~~~~~~~~ /<>/src/PeriodicPdbAndEnergyWriter.cpp:49:9: warning: unused variable ‘compoundNumber’ [-Wunused-variable] 49 | int compoundNumber = 1; | ^~~~~~~~~~~~~~ /<>/src/PeriodicPdbAndEnergyWriter.cpp:50:9: warning: unused variable ‘requiredPrecision’ [-Wunused-variable] 50 | int requiredPrecision = 12; | ^~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 [ 81%] Building CXX object CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -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 /<>/src/ProgressWriter.cpp In file included from /<>/include/ContactContainer.h:15, from /<>/include/ParameterReader.h:21: /<>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:22:59: required from here /<>/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 >/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:25:59: required from here /<>/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 /<>/include/ContactContainer.h:15, from /<>/include/ParameterReader.h:21: /<>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:22:59: required from here /<>/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 >/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:25:59: required from here /<>/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()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/src/ProgressWriter.cpp: In member function ‘void ProgressWriter::write(bool)’: /<>/src/ProgressWriter.cpp:202:18: warning: ignoring return value of ‘int ftruncate(int, __off_t)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 202 | ftruncate(_output, 0); | ~~~~~~~~~^~~~~~~~~~~~ [ 84%] Building CXX object CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -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 /<>/src/NTC_PARAMETER_READER.cpp In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /<>/src/NTC_PARAMETER_READER.cpp:15: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ In file included from /<>/include/NtC_Class_Container.h:14, from /<>/src/NTC_PARAMETER_READER.cpp:16: /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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 /<>/include/NTC_FORCE_CLASS.h:4, from /<>/src/NTC_PARAMETER_READER.cpp:17: /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Building CXX object CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -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 /<>/src/NtCClassContainer.cpp /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /usr/include/molmodel/molmodel/internal/Compound.h:36, from /<>/include/BiopolymerClass.h:16, from /<>/src/NtCClassContainer.cpp:13: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ In file included from /<>/include/Mutation.h:4, from /<>/include/BiopolymerClass.h:20: /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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); }; | ~~^~~~~~~~~~~~~~~~~ /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ [ 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/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -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 /<>/src/NtCForces.cpp /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/Simbody.h:38, from /usr/include/molmodel/SimTKmolmodel.h:47, from /<>/include/NtCForces.h:12, from /<>/src/NtCForces.cpp:11: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ In file included from /<>/include/AtomSpringContainer.h:14, from /<>/include/ParameterReader.h:20, from /<>/include/NtCForces.h:13: /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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 /<>/include/Threading.h:2, from /<>/include/AtomSpringContainer.h:15: /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /<>/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();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 In file included from /<>/include/ContactContainer.h:15, from /<>/include/ParameterReader.h:21: /<>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:22:59: required from here /<>/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 >/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:25:59: required from here /<>/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()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ [ 93%] Linking CXX shared library libMMB.so /usr/bin/cmake -E cmake_link_script CMakeFiles/MMB.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -shared -Wl,-soname,libMMB.so.4.0 -o libMMB.so.4.0 CMakeFiles/MMB.dir/src/Utils.cpp.o CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o CMakeFiles/MMB.dir/src/DensityContainer.cpp.o CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o CMakeFiles/MMB.dir/src/ContactContainer.cpp.o CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o CMakeFiles/MMB.dir/src/Repel.cpp.o CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o CMakeFiles/MMB.dir/src/Spiral.cpp.o CMakeFiles/MMB.dir/src/ParameterReader.cpp.o CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o CMakeFiles/MMB.dir/src/TetherForce.cpp.o CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o CMakeFiles/MMB.dir/src/DensityMap.cpp.o CMakeFiles/MMB.dir/src/DensityForce.cpp.o CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o CMakeFiles/MMB.dir/src/MMBLogger.cpp.o CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o CMakeFiles/MMB.dir/src/CifOutput.cpp.o CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o CMakeFiles/MMB.dir/src/NtCForces.cpp.o /usr/lib/powerpc64le-linux-gnu/libSimTKmolmodel.so.3.1 /usr/lib/powerpc64le-linux-gnu/libOpenMM.so /usr/lib/powerpc64le-linux-gnu/libz.so /usr/lib/powerpc64le-linux-gnu/libSimTKsimbody.so.3.7 /usr/lib/powerpc64le-linux-gnu/libSimTKmath.so.3.7 /usr/lib/powerpc64le-linux-gnu/libSimTKcommon.so.3.7 /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/liblapack.so /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/liblapack.so -lpthread -lrt -ldl -lm /usr/bin/cmake -E cmake_symlink_library libMMB.so.4.0 libMMB.so.4.0 libMMB.so make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' [ 93%] Built target MMB make -f CMakeFiles/MMB_EXEC.dir/build.make CMakeFiles/MMB_EXEC.dir/depend make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' cd /<>/obj-powerpc64le-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu /<>/obj-powerpc64le-linux-gnu/CMakeFiles/MMB_EXEC.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' make -f CMakeFiles/MMB_EXEC.dir/build.make CMakeFiles/MMB_EXEC.dir/build make[3]: Entering directory '/<>/obj-powerpc64le-linux-gnu' [ 96%] Building CXX object CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o /usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DUSE_MMB_CONSTEXPR -I/<>/obj-powerpc64le-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -MD -MT CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o -MF CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o.d -o CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o -c /<>/src/RNABuilder.cpp In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/Simbody.h:38, from /usr/include/molmodel/SimTKmolmodel.h:47, from /<>/src/RNABuilder.cpp:20: /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(double)’: /usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1169 | approxCompleteEllipticIntegralsKE(double m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1177 | approxCompleteEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::approxCompleteEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1186 | approxCompleteEllipticIntegralsKE(int m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(float)’: /usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1257 | inline std::pair completeEllipticIntegralsKE(float m) | ^ /usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair SimTK::completeEllipticIntegralsKE(int)’: /usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1265 | inline std::pair completeEllipticIntegralsKE(int m) | ^ In file included from /<>/include/AtomSpringContainer.h:14, from /<>/include/ParameterReader.h:20, from /<>/src/RNABuilder.cpp:22: /<>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /<>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 290 | if (derivComponents.size() == 1) | ^~ /<>/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; | ^~~~~~ /<>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’: /<>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable] 321 | char endChar = *(inputString.substr(stringLength-1, 1)).c_str(); | ^~~~~~~ /<>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /<>/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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void Interface::print()’: /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/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 ++) { | ~~^~~~~~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1308:9: warning: when initialized here [-Wreorder] 1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’: /<>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder] 1294 | String chain; | ^~~~~ /<>/include/Utils.h:1292:19: warning: ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder] 1292 | ResidueID residueID; | ^~~~~~~~~ /<>/include/Utils.h:1314:9: warning: when initialized here [-Wreorder] 1314 | MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) : | ^~~~~~~~~~~ /<>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector, double, SimTK::String)’: /<>/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 /<>/include/Threading.h:2, from /<>/include/AtomSpringContainer.h:15: /<>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /<>/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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /<>/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /<>/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();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1095 | static inline std::pair approxCompleteEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’: /usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1192 | static inline std::pair completeEllipticIntegralsKE_T(T m) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’: /usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here /usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 In file included from /<>/include/ContactContainer.h:15, from /<>/include/ParameterReader.h:21: /<>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:22:59: required from here /<>/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 >/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /<>/include/DensityContainer.h:25:59: required from here /<>/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()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/include/Utils.h: At global scope: /<>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 257 | const char* digits = "0123456789"; | ^~~~~~ /<>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 256 | const char* spaces = " \t"; | ^~~~~~ [100%] Linking CXX executable MMB /usr/bin/cmake -E cmake_link_script CMakeFiles/MMB_EXEC.dir/link.txt --verbose=1 /usr/bin/c++ -D BuildNtC -D USE_OPENMM -g -O3 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/macromoleculebuilder-4.0.0+dfsg-2 -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o -o MMB -Wl,-rpath,/<>/obj-powerpc64le-linux-gnu: libMMB.so.4.0 /usr/lib/powerpc64le-linux-gnu/libSimTKmolmodel.so.3.1 /usr/lib/powerpc64le-linux-gnu/libSimTKsimbody.so.3.7 /usr/lib/powerpc64le-linux-gnu/libSimTKmath.so.3.7 /usr/lib/powerpc64le-linux-gnu/libSimTKcommon.so.3.7 /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/liblapack.so /usr/lib/powerpc64le-linux-gnu/libblas.so /usr/lib/powerpc64le-linux-gnu/liblapack.so -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' [100%] Built target MMB_EXEC make[2]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-powerpc64le-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' dh_auto_test -a create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install -a cd obj-powerpc64le-linux-gnu && make -j4 install DESTDIR=/<>/macromoleculebuilder-4.0.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/obj-powerpc64le-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-powerpc64le-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-powerpc64le-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /<>/debian/tmp/usr/include/MMB/AddBackboneOxygenForces.h -- Installing: /<>/debian/tmp/usr/include/MMB/AddNASTForces.h -- Installing: /<>/debian/tmp/usr/include/MMB/AtomSpringContainer.h -- Installing: /<>/debian/tmp/usr/include/MMB/BaseInteractionParameterReader.h -- Installing: /<>/debian/tmp/usr/include/MMB/BasePairContainer.h -- Installing: /<>/debian/tmp/usr/include/MMB/BiopolymerClass.h -- Installing: /<>/debian/tmp/usr/include/MMB/BiopolymerClassTwoTransformForces.h -- Installing: /<>/debian/tmp/usr/include/MMB/CalcTransformCorrection.h -- Installing: /<>/debian/tmp/usr/include/MMB/CenterOfMass.h -- Installing: /<>/debian/tmp/usr/include/MMB/CifOutput.h -- Installing: /<>/debian/tmp/usr/include/MMB/Constexpr.h -- Installing: /<>/debian/tmp/usr/include/MMB/ConstraintContainer.h -- Installing: /<>/debian/tmp/usr/include/MMB/ContactContainer.h -- Installing: /<>/debian/tmp/usr/include/MMB/DensityContainer.h -- Installing: /<>/debian/tmp/usr/include/MMB/DensityForce.h -- Installing: /<>/debian/tmp/usr/include/MMB/DensityMap.h -- Installing: /<>/debian/tmp/usr/include/MMB/DisplacementContainer.h -- Installing: /<>/debian/tmp/usr/include/MMB/ElectrostaticPotentialGridForce.h -- 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Installing: /<>/debian/tmp/usr/include/MMB/NTC_PARAMETER_READER.h -- Installing: /<>/debian/tmp/usr/include/MMB/NtCBackboneTorsionForce.h -- Installing: /<>/debian/tmp/usr/include/MMB/NtCForces.h -- Installing: /<>/debian/tmp/usr/include/MMB/NtCInteractionParameterReader.h -- Installing: /<>/debian/tmp/usr/include/MMB/NtC_Class_Container.h -- Installing: /<>/debian/tmp/usr/include/MMB/ParameterReader.h -- Installing: /<>/debian/tmp/usr/include/MMB/ParameterReader_wrapper.h -- Installing: /<>/debian/tmp/usr/include/MMB/PeriodicParameterReaderUpdater.h -- Installing: /<>/debian/tmp/usr/include/MMB/PeriodicPdbAndCOMWriter.h -- Installing: /<>/debian/tmp/usr/include/MMB/PeriodicPdbAndEnergySingleFrameWriter.h -- Installing: /<>/debian/tmp/usr/include/MMB/PeriodicPdbAndEnergyWriter.h -- Installing: /<>/debian/tmp/usr/include/MMB/PeriodicPdbSingleFrameWriter.h -- Installing: /<>/debian/tmp/usr/include/MMB/PeriodicScrubber.h -- Installing: /<>/debian/tmp/usr/include/MMB/ProgressWriter.h -- Installing: /<>/debian/tmp/usr/include/MMB/RandomizeRNACoordinates.h -- Installing: /<>/debian/tmp/usr/include/MMB/Repel.h -- Installing: /<>/debian/tmp/usr/include/MMB/ResidueStretchContainer.h -- Installing: /<>/debian/tmp/usr/include/MMB/RigidifyFormedHelices.h -- Installing: /<>/debian/tmp/usr/include/MMB/SetChiMobility.h -- Installing: /<>/debian/tmp/usr/include/MMB/SetSingleBondMobility.h -- Installing: /<>/debian/tmp/usr/include/MMB/Spiral.h -- Installing: /<>/debian/tmp/usr/include/MMB/StackingForceSubsystem.h -- Installing: /<>/debian/tmp/usr/include/MMB/Sterics.h -- Installing: /<>/debian/tmp/usr/include/MMB/TetherForce.h -- Installing: /<>/debian/tmp/usr/include/MMB/Threading.h -- Installing: /<>/debian/tmp/usr/include/MMB/UnitCellParameters.h -- Installing: /<>/debian/tmp/usr/include/MMB/Utils.h -- Installing: /<>/debian/tmp/usr/include/MMB/WadleyKeatingDuartePyleTorsionForce.h -- Installing: /<>/debian/tmp/usr/include/MMB/Water.h -- Installing: /<>/debian/tmp/usr/include/MMB/WaterDroplet.h -- Installing: /<>/debian/tmp/usr/include/MMB/superimposer.h -- Installing: /<>/debian/tmp/usr/include/MMB/MMB_config.h -- Installing: /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/libMMB.so.4.0 -- Installing: /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/libMMB.so -- Installing: /<>/debian/tmp/usr/share/MMB/parameters.csv -- Installing: /<>/debian/tmp/usr/bin/MMB -- Set runtime path of "/<>/debian/tmp/usr/bin/MMB" to "" -- Installing: /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/cmake/mmb/MmbConfigVersion.cmake -- Installing: /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/cmake/mmb/MmbTargets.cmake -- Installing: /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/cmake/mmb/MmbTargets-release.cmake -- Installing: /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/pkgconfig/mmb.pc make[1]: Leaving directory '/<>/obj-powerpc64le-linux-gnu' dh_install -a dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman make[1]: Entering directory '/<>' a2x -d manpage -f manpage -D debian/tmp debian/MMB.1.asciidoc dh_installman make[1]: Leaving directory '/<>' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a 5fae48fa67505dafabe1786a9fb0276613096d77 71da0f60852baa6558968209ecc270399870a69e dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 151 INFO: pkgstriptranslations version 151 INFO: pkgstriptranslations version 151 pkgstriptranslations: processing libmmb4.0-dbgsym (in debian/.debhelper/libmmb4.0/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing libmmb-dev (in debian/libmmb-dev); do_strip: , oemstrip: pkgstriptranslations: processing mmb-dbgsym (in debian/.debhelper/mmb/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libmmb-dev/DEBIAN/control, package libmmb-dev, directory debian/libmmb-dev Searching for duplicated docs in dependency libmmb4.0... symlinking changelog.Debian.gz in libmmb-dev to file in libmmb4.0 pkgstripfiles: processing control file: debian/.debhelper/mmb/dbgsym-root/DEBIAN/control, package mmb-dbgsym, directory debian/.debhelper/mmb/dbgsym-root dpkg-deb: building package 'mmb-dbgsym' in 'debian/.debhelper/scratch-space/build-mmb/mmb-dbgsym_4.0.0+dfsg-2_ppc64el.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package libmmb-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libmmb-dev' in '../libmmb-dev_4.0.0+dfsg-2_ppc64el.deb'. Renaming mmb-dbgsym_4.0.0+dfsg-2_ppc64el.deb to mmb-dbgsym_4.0.0+dfsg-2_ppc64el.ddeb INFO: pkgstriptranslations version 151 pkgstriptranslations: processing libmmb4.0 (in debian/libmmb4.0); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libmmb4.0/DEBIAN/control, package libmmb4.0, directory debian/libmmb4.0 pkgstripfiles: Truncating usr/share/doc/libmmb4.0/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package libmmb4.0 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libmmb4.0' in '../libmmb4.0_4.0.0+dfsg-2_ppc64el.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/libmmb4.0/dbgsym-root/DEBIAN/control, package libmmb4.0-dbgsym, directory debian/.debhelper/libmmb4.0/dbgsym-root dpkg-deb: building package 'libmmb4.0-dbgsym' in 'debian/.debhelper/scratch-space/build-libmmb4.0/libmmb4.0-dbgsym_4.0.0+dfsg-2_ppc64el.deb'. Renaming libmmb4.0-dbgsym_4.0.0+dfsg-2_ppc64el.deb to libmmb4.0-dbgsym_4.0.0+dfsg-2_ppc64el.ddeb INFO: pkgstriptranslations version 151 pkgstriptranslations: processing mmb (in debian/mmb); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/mmb/DEBIAN/control, package mmb, directory debian/mmb Searching for duplicated docs in dependency libmmb4.0... symlinking changelog.Debian.gz in mmb to file in libmmb4.0 pkgstripfiles: Running PNG optimization (using 4 cpus) for package mmb ... pkgstripfiles: No PNG files. dpkg-deb: building package 'mmb' in '../mmb_4.0.0+dfsg-2_ppc64el.deb'. dpkg-genbuildinfo --build=any -O../macromoleculebuilder_4.0.0+dfsg-2_ppc64el.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../macromoleculebuilder_4.0.0+dfsg-2_ppc64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-02-04T01:58:45Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ macromoleculebuilder_4.0.0+dfsg-2_ppc64el.changes: -------------------------------------------------- Format: 1.8 Date: Mon, 12 Dec 2022 04:04:16 -0500 Source: macromoleculebuilder Binary: libmmb-dev libmmb4.0 mmb Built-For-Profiles: noudeb Architecture: ppc64el Version: 4.0.0+dfsg-2 Distribution: lunar-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andrius Merkys Description: libmmb-dev - development files of MacroMoleculeBuilder libmmb4.0 - shared library of MacroMoleculeBuilder mmb - model the structure and dynamics of macromolecules Changes: macromoleculebuilder (4.0.0+dfsg-2) unstable; urgency=medium . * No-changes source-only upload to unstable. Checksums-Sha1: 1a5e294568505ce47992181186b0e83810ae4662 77098 libmmb-dev_4.0.0+dfsg-2_ppc64el.deb ac3da77f75b8c38a1d39328ef652982c61f8e9cf 24211088 libmmb4.0-dbgsym_4.0.0+dfsg-2_ppc64el.ddeb 6e94db692f7f4868e47aa3ebe0fe154784a753e7 1126436 libmmb4.0_4.0.0+dfsg-2_ppc64el.deb 8afc24a46c370d223d560ce3e6b637de51959f41 10837 macromoleculebuilder_4.0.0+dfsg-2_ppc64el.buildinfo 9bfd0dc8c7d99aa1ba9981583aa218933c7e091e 1509392 mmb-dbgsym_4.0.0+dfsg-2_ppc64el.ddeb 00d35be20f71641bda1e4c67c29cc7faa10e885a 29360 mmb_4.0.0+dfsg-2_ppc64el.deb Checksums-Sha256: ddaabeca18ef7a6013798ee74f1eeb855e934d00c2d95431b7da2fef0b494df6 77098 libmmb-dev_4.0.0+dfsg-2_ppc64el.deb 1570808ad4eb85d4cda5c8c5b16bb87c2b8ab42813c7812a91d2d10474878bc5 24211088 libmmb4.0-dbgsym_4.0.0+dfsg-2_ppc64el.ddeb 346ad0d6a55efda9e2ffc9fb7c67dbc82b27fd38df23395dee4b93762652e806 1126436 libmmb4.0_4.0.0+dfsg-2_ppc64el.deb 03be626f6806b3bb01aa4fb52a57acad1978e989a260e8da1f12e10586d7b01b 10837 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field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: macromoleculebuilder Binary: libmmb-dev libmmb4.0 libmmb4.0-dbgsym mmb mmb-dbgsym Architecture: ppc64el Version: 4.0.0+dfsg-2 Checksums-Md5: 83afeaedf6fe87403f126445ce0672b5 77098 libmmb-dev_4.0.0+dfsg-2_ppc64el.deb 2793c2e61aa10de848b8654f61e6d37e 24211088 libmmb4.0-dbgsym_4.0.0+dfsg-2_ppc64el.ddeb b513508806f55297b805451d21aa40c4 1126436 libmmb4.0_4.0.0+dfsg-2_ppc64el.deb 544808ae064a6c5fa863fc94449237a2 1509392 mmb-dbgsym_4.0.0+dfsg-2_ppc64el.ddeb 6c008b65d5076cbfeac62b05b4981820 29360 mmb_4.0.0+dfsg-2_ppc64el.deb Checksums-Sha1: 1a5e294568505ce47992181186b0e83810ae4662 77098 libmmb-dev_4.0.0+dfsg-2_ppc64el.deb ac3da77f75b8c38a1d39328ef652982c61f8e9cf 24211088 libmmb4.0-dbgsym_4.0.0+dfsg-2_ppc64el.ddeb 6e94db692f7f4868e47aa3ebe0fe154784a753e7 1126436 libmmb4.0_4.0.0+dfsg-2_ppc64el.deb 9bfd0dc8c7d99aa1ba9981583aa218933c7e091e 1509392 mmb-dbgsym_4.0.0+dfsg-2_ppc64el.ddeb 00d35be20f71641bda1e4c67c29cc7faa10e885a 29360 mmb_4.0.0+dfsg-2_ppc64el.deb Checksums-Sha256: ddaabeca18ef7a6013798ee74f1eeb855e934d00c2d95431b7da2fef0b494df6 77098 libmmb-dev_4.0.0+dfsg-2_ppc64el.deb 1570808ad4eb85d4cda5c8c5b16bb87c2b8ab42813c7812a91d2d10474878bc5 24211088 libmmb4.0-dbgsym_4.0.0+dfsg-2_ppc64el.ddeb 346ad0d6a55efda9e2ffc9fb7c67dbc82b27fd38df23395dee4b93762652e806 1126436 libmmb4.0_4.0.0+dfsg-2_ppc64el.deb b3952390f253344ba0a2f5e63d26573272203775ab4406de03f14723e5d6ec17 1509392 mmb-dbgsym_4.0.0+dfsg-2_ppc64el.ddeb 3774a8e575718a13b7b6708b518e506ce8272c498868d7fd13959c8278827731 29360 mmb_4.0.0+dfsg-2_ppc64el.deb Build-Origin: Ubuntu Build-Architecture: ppc64el Build-Date: Sat, 04 Feb 2023 01:58:44 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: asciidoc-base (= 10.2.0-1), asciidoc-common (= 10.2.0-1), autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-11), autotools-dev (= 20220109.1), base-files (= 12.3ubuntu1), base-passwd (= 3.6.1), bash (= 5.2.15-2ubuntu1), binutils (= 2.40-2ubuntu1), binutils-common (= 2.40-2ubuntu1), binutils-powerpc64le-linux-gnu (= 2.40-2ubuntu1), bsdextrautils (= 2.38.1-4ubuntu1), bsdutils (= 1:2.38.1-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), cmake (= 3.25.1-1), cmake-data (= 3.25.1-1), coreutils (= 9.1-1ubuntu2), cpp (= 4:12.2.0-1ubuntu1), cpp-12 (= 12.2.0-14ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-9ubuntu1), debconf (= 1.5.82), debhelper (= 13.11.4ubuntu3), debianutils (= 5.7-0.4), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.8-3), docbook-xml (= 4.5-12), docbook-xsl (= 1.79.2+dfsg-2), dpkg (= 1.21.19ubuntu3), dpkg-dev (= 1.21.19ubuntu3), dwz (= 0.15-1), file (= 1:5.44-3), findutils (= 4.9.0-3ubuntu1), freeglut3-dev (= 3.4.0-1), g++ (= 4:12.2.0-1ubuntu1), g++-12 (= 12.2.0-14ubuntu1), gcc (= 4:12.2.0-1ubuntu1), gcc-12 (= 12.2.0-14ubuntu1), gcc-12-base (= 12.2.0-14ubuntu1), gemmi-dev (= 0.5.6+ds-2ubuntu2), gettext (= 0.21-11), gettext-base (= 0.21-11), grep (= 3.8-5), groff-base (= 1.22.4-9), gzip (= 1.12-1ubuntu1), hostname (= 3.23ubuntu2), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libarchive13 (= 3.6.2-1ubuntu1), libasan8 (= 12.2.0-14ubuntu1), libatomic1 (= 12.2.0-14ubuntu1), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.0.7-1.1), libaudit1 (= 1:3.0.7-1.1), libbinutils (= 2.40-2ubuntu1), libblas-dev (= 3.11.0-2), libblas3 (= 3.11.0-2), libblkid1 (= 2.38.1-4ubuntu1), libbrotli1 (= 1.0.9-2build7), libbsd0 (= 0.11.7-2), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.37-0ubuntu1), libc-dev-bin (= 2.37-0ubuntu1), libc6 (= 2.37-0ubuntu1), libc6-dev (= 2.37-0ubuntu1), libcap-ng0 (= 0.8.3-1build1), libcap2 (= 1:2.66-3ubuntu1), libcc1-0 (= 12.2.0-14ubuntu1), libcom-err2 (= 1.46.6~rc1-1ubuntu1), libcrypt-dev (= 1:4.4.33-2), libcrypt1 (= 1:4.4.33-2), libctf-nobfd0 (= 2.40-2ubuntu1), libctf0 (= 2.40-2ubuntu1), libcurl4 (= 7.87.0-2ubuntu1), libdb5.3 (= 5.3.28+dfsg2-1), libdebconfclient0 (= 0.264ubuntu1), libdebhelper-perl (= 13.11.4ubuntu3), libdpkg-perl (= 1.21.19ubuntu3), libdrm-amdgpu1 (= 2.4.114-1), libdrm-common (= 2.4.114-1), libdrm-nouveau2 (= 2.4.114-1), libdrm-radeon1 (= 2.4.114-1), libdrm2 (= 2.4.114-1), libdw1 (= 0.188-2.1), libedit2 (= 3.1-20221030-2), libegl-dev (= 1.6.0-1), libegl-mesa0 (= 22.2.5-0ubuntu1), libegl1 (= 1.6.0-1), libelf1 (= 0.188-2.1), libexpat1 (= 2.5.0-1), libffi8 (= 3.4.4-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libgbm1 (= 22.2.5-0ubuntu1), libgcc-12-dev (= 12.2.0-14ubuntu1), libgcc-s1 (= 12.2.0-14ubuntu1), libgcrypt20 (= 1.10.1-3ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgfortran5 (= 12.2.0-14ubuntu1), libgl-dev (= 1.6.0-1), libgl1 (= 1.6.0-1), libgl1-mesa-dev (= 22.2.5-0ubuntu1), libgl1-mesa-dri (= 22.2.5-0ubuntu1), libglapi-mesa (= 22.2.5-0ubuntu1), libgles-dev (= 1.6.0-1), libgles1 (= 1.6.0-1), libgles2 (= 1.6.0-1), libglu1-mesa (= 9.0.2-1.1), libglu1-mesa-dev (= 9.0.2-1.1), libglut-dev (= 3.4.0-1), libglut3.12 (= 3.4.0-1), libglvnd-core-dev (= 1.6.0-1), libglvnd-dev (= 1.6.0-1), libglvnd0 (= 1.6.0-1), libglx-dev (= 1.6.0-1), libglx-mesa0 (= 22.2.5-0ubuntu1), libglx0 (= 1.6.0-1), libgmp10 (= 2:6.2.1+dfsg1-1.1ubuntu1), libgnutls30 (= 3.7.8-4ubuntu1), libgomp1 (= 12.2.0-14ubuntu1), libgpg-error0 (= 1.46-1), libgssapi-krb5-2 (= 1.20.1-1build1), libhogweed6 (= 3.8.1-2), libice-dev (= 2:1.0.10-1build2), libice6 (= 2:1.0.10-1build2), libicu71 (= 71.1-3ubuntu1), libidn2-0 (= 2.3.3-1build1), libisl23 (= 0.25-1), libitm1 (= 12.2.0-14ubuntu1), libjansson4 (= 2.14-2), libjsoncpp25 (= 1.9.5-4), libk5crypto3 (= 1.20.1-1build1), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-1build1), libkrb5support0 (= 1.20.1-1build1), liblapack-dev (= 3.11.0-2), liblapack3 (= 3.11.0-2), libldap2 (= 2.6.3+dfsg-1~exp1ubuntu1), libllvm15 (= 1:15.0.7-1), liblsan0 (= 12.2.0-14ubuntu1), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.1-0.0), libmagic-mgc (= 1:5.44-3), libmagic1 (= 1:5.44-3), libmd0 (= 1.0.4-2), libmount1 (= 2.38.1-4ubuntu1), libmpc3 (= 1.3.1-1), libmpdec3 (= 2.5.1-2build2), libmpfr6 (= 4.2.0-1), libncurses6 (= 6.4-2), libncursesw6 (= 6.4-2), libnettle8 (= 3.8.1-2), libnghttp2-14 (= 1.51.0-1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libopengl-dev (= 1.6.0-1), libopengl0 (= 1.6.0-1), libopenmm-dev (= 7.7.0+dfsg-9build1), libopenmm7.7 (= 7.7.0+dfsg-9build1), libp11-kit0 (= 0.24.1-2ubuntu1), libpam-modules (= 1.5.2-5ubuntu1), libpam-modules-bin (= 1.5.2-5ubuntu1), libpam-runtime (= 1.5.2-5ubuntu1), libpam0g (= 1.5.2-5ubuntu1), libpcre2-8-0 (= 10.42-1), libperl5.36 (= 5.36.0-7), libpipeline1 (= 1.5.7-1), libprocps8 (= 2:3.3.17-7ubuntu1), libpsl5 (= 0.21.0-1.2build2), libpthread-stubs0-dev (= 0.4-1build2), libpython3-stdlib (= 3.11.1-0ubuntu1), libpython3.11-minimal (= 3.11.1-2), libpython3.11-stdlib (= 3.11.1-2), libquadmath0 (= 12.2.0-14ubuntu1), libreadline8 (= 8.2-1.3), librhash0 (= 1.4.3-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg-10), libsasl2-modules-db (= 2.1.28+dfsg-10), libseccomp2 (= 2.5.4-1ubuntu2), libselinux1 (= 3.4-1build3), libsensors-config (= 1:3.6.0-7ubuntu1), libsensors5 (= 1:3.6.0-7ubuntu1), libseqan2-dev (= 2.4.0+dfsg-15ubuntu1), libsimbody-dev (= 3.7+dfsg-3), libsimbody3.7 (= 3.7+dfsg-3), libsimtkmolmodel-dev (= 3.1.0-2build1), libsimtkmolmodel-plugins (= 3.1.0-2build1), libsimtkmolmodel3.1 (= 3.1.0-2build1), libsm-dev (= 2:1.2.3-1build2), libsm6 (= 2:1.2.3-1build2), libsmartcols1 (= 2.38.1-4ubuntu1), libsqlite3-0 (= 3.40.1-1), libssh-4 (= 0.10.4-2), libssl3 (= 3.0.7-1ubuntu1), libstb-dev (= 0.0~git20220908.8b5f1f3+ds-1), libstb0 (= 0.0~git20220908.8b5f1f3+ds-1), libstdc++-12-dev (= 12.2.0-14ubuntu1), libstdc++6 (= 12.2.0-14ubuntu1), libsub-override-perl (= 0.09-4), libsystemd0 (= 252.4-1ubuntu1), libtasn1-6 (= 4.19.0-2), libtinfo6 (= 6.4-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-5), libtsan2 (= 12.2.0-14ubuntu1), libubsan1 (= 12.2.0-14ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 252.4-1ubuntu1), libunistring2 (= 1.0-2), libuuid1 (= 2.38.1-4ubuntu1), libuv1 (= 1.44.2-1), libwayland-client0 (= 1.21.0-1), libwayland-server0 (= 1.21.0-1), libx11-6 (= 2:1.8.3-3), libx11-data (= 2:1.8.3-3), libx11-dev (= 2:1.8.3-3), libx11-xcb1 (= 2:1.8.3-3), libxau-dev (= 1:1.0.9-1build5), libxau6 (= 1:1.0.9-1build5), libxcb-dri2-0 (= 1.15-1), libxcb-dri3-0 (= 1.15-1), libxcb-glx0 (= 1.15-1), libxcb-present0 (= 1.15-1), libxcb-shm0 (= 1.15-1), libxcb-sync1 (= 1.15-1), libxcb-xfixes0 (= 1.15-1), libxcb1 (= 1.15-1), libxcb1-dev (= 1.15-1), libxdmcp-dev (= 1:1.1.3-0ubuntu5), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxext-dev (= 2:1.3.4-1build1), libxext6 (= 2:1.3.4-1build1), libxfixes-dev (= 1:6.0.0-2), libxfixes3 (= 1:6.0.0-2), libxi-dev (= 2:1.8-1build1), libxi6 (= 2:1.8-1build1), libxml2 (= 2.9.14+dfsg-1.1), libxml2-utils (= 2.9.14+dfsg-1.1), libxmu-dev (= 2:1.1.3-3), libxmu-headers (= 2:1.1.3-3), libxmu6 (= 2:1.1.3-3), libxshmfence1 (= 1.3-1build4), libxslt1.1 (= 1.1.35-1), libxt-dev (= 1:1.2.1-1), libxt6 (= 1:1.2.1-1), libxxf86vm1 (= 1:1.1.4-1build3), libzstd1 (= 1.5.2+dfsg2-3), linux-libc-dev (= 6.1.0-14.14), login (= 1:4.13+dfsg1-1ubuntu1), lsb-base (= 11.5), lto-disabled-list (= 37), m4 (= 1.4.19-2), make (= 4.3-4.1build1), man-db (= 2.11.2-1), mawk (= 1.3.4.20200120-3.1), media-types (= 8.0.0), ncurses-base (= 6.4-2), ncurses-bin (= 6.4-2), patch (= 2.7.6-7build2), perl (= 5.36.0-7), perl-base (= 5.36.0-7), perl-modules-5.36 (= 5.36.0-7), po-debconf (= 1.0.21+nmu1), procps (= 2:3.3.17-7ubuntu1), python3 (= 3.11.1-0ubuntu1), python3-minimal (= 3.11.1-0ubuntu1), python3.11 (= 3.11.1-2), python3.11-minimal (= 3.11.1-2), readline-common (= 8.2-1.3), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-1), sensible-utils (= 0.0.17+nmu1), sgml-base (= 1.31), sgml-data (= 2.0.11+nmu1), sysvinit-utils (= 3.05-7ubuntu2), tao-pegtl-dev (= 3.2.7-1), tar (= 1.34+dfsg-1.1), usrmerge (= 33ubuntu1), util-linux (= 2.38.1-4ubuntu1), util-linux-extra (= 2.38.1-4ubuntu1), x11-common (= 1:7.7+23ubuntu2), x11proto-dev (= 2022.1-1), xml-core (= 0.18+nmu1), xorg-sgml-doctools (= 1:1.11-1.1), xsltproc (= 1.1.35-1), xtrans-dev (= 1.4.0-1), xz-utils (= 5.4.1-0.0), zlib1g (= 1:1.2.13.dfsg-1ubuntu4), zlib1g-dev (= 1:1.2.13.dfsg-1ubuntu4) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1670835856" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libmmb-dev_4.0.0+dfsg-2_ppc64el.deb ----------------------------------- new Debian package, version 2.0. size 77098 bytes: control archive=2852 bytes. 855 bytes, 21 lines control 5050 bytes, 71 lines md5sums Package: libmmb-dev Source: macromoleculebuilder Version: 4.0.0+dfsg-2 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debichem Team Installed-Size: 559 Depends: libmmb4.0 (= 4.0.0+dfsg-2) Breaks: libmmblib-dev (<< 4.0.0) Replaces: libmmblib-dev (<< 4.0.0) Section: libdevel Priority: optional Multi-Arch: same Homepage: https://simtk.org/projects/rnatoolbox Description: development files of MacroMoleculeBuilder MacroMoleculeBuilder, previously known as RNABuilder, can be used for morphing, homology modeling, folding (e.g. using base pairing contacts), redesigning complexes, fitting to low-resolution density maps, predicting local rearrangements upon mutation, and many other applications. . This package contains the development files. drwxr-xr-x root/root 0 2022-12-12 09:04 ./ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/include/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/include/MMB/ -rw-r--r-- root/root 8108 2022-11-29 12:01 ./usr/include/MMB/AddBackboneOxygenForces.h -rw-r--r-- root/root 6293 2022-11-29 12:01 ./usr/include/MMB/AddNASTForces.h -rw-r--r-- root/root 5724 2022-11-29 12:01 ./usr/include/MMB/AtomSpringContainer.h -rw-r--r-- root/root 3559 2022-11-29 12:01 ./usr/include/MMB/BaseInteractionParameterReader.h -rw-r--r-- root/root 3477 2022-11-29 12:01 ./usr/include/MMB/BasePairContainer.h -rw-r--r-- root/root 42905 2022-11-29 12:01 ./usr/include/MMB/BiopolymerClass.h -rw-r--r-- root/root 2644 2022-11-29 12:01 ./usr/include/MMB/BiopolymerClassTwoTransformForces.h -rw-r--r-- root/root 19309 2022-11-29 12:01 ./usr/include/MMB/CalcTransformCorrection.h -rw-r--r-- root/root 3188 2022-11-29 12:01 ./usr/include/MMB/CenterOfMass.h -rw-r--r-- root/root 1328 2022-11-29 12:01 ./usr/include/MMB/CifOutput.h -rw-r--r-- root/root 188 2022-11-29 12:01 ./usr/include/MMB/Constexpr.h -rw-r--r-- root/root 3848 2022-11-29 12:01 ./usr/include/MMB/ConstraintContainer.h -rw-r--r-- root/root 3295 2022-11-29 12:01 ./usr/include/MMB/ContactContainer.h -rw-r--r-- root/root 1793 2022-11-29 12:01 ./usr/include/MMB/DensityContainer.h -rw-r--r-- root/root 2105 2022-11-29 12:01 ./usr/include/MMB/DensityForce.h -rw-r--r-- root/root 7794 2022-11-29 12:01 ./usr/include/MMB/DensityMap.h -rw-r--r-- root/root 1912 2022-11-29 12:01 ./usr/include/MMB/DisplacementContainer.h -rw-r--r-- root/root 2165 2022-11-29 12:01 ./usr/include/MMB/ElectrostaticPotentialGridForce.h -rw-r--r-- root/root 3001 2022-11-29 12:01 ./usr/include/MMB/ExportMacros.h -rw-r--r-- root/root 752 2022-11-29 12:01 ./usr/include/MMB/ExtraMath.h -rw-r--r-- root/root 1756 2022-11-29 12:01 ./usr/include/MMB/GeometricCenter.h -rw-r--r-- root/root 4613 2022-11-29 12:01 ./usr/include/MMB/HarmonicVelocityRescalingThermostat.h -rw-r--r-- root/root 227 2022-11-29 12:01 ./usr/include/MMB/Impossible.h -rw-r--r-- root/root 4871 2022-11-29 12:01 ./usr/include/MMB/KBBackboneTorsionForce.h -rw-r--r-- root/root 312 2022-11-29 12:01 ./usr/include/MMB/Lepton.h -rw-r--r-- root/root 8211 2022-11-29 12:01 ./usr/include/MMB/LigandDroplet.h -rw-r--r-- root/root 16881 2022-11-29 12:01 ./usr/include/MMB/Ligands.h -rw-r--r-- root/root 16712 2022-11-29 12:01 ./usr/include/MMB/Ligands.sam.h -rw-r--r-- root/root 3129 2022-11-29 12:01 ./usr/include/MMB/MMBLogger.h -rw-r--r-- root/root 91 2022-12-12 09:04 ./usr/include/MMB/MMB_config.h -rw-r--r-- root/root 5172 2022-11-29 12:01 ./usr/include/MMB/MobilizerContainer.h -rw-r--r-- root/root 3821 2022-11-29 12:01 ./usr/include/MMB/MoleculeContainer.h -rw-r--r-- root/root 4156 2022-11-29 12:01 ./usr/include/MMB/MonoAtoms.h -rw-r--r-- root/root 7486 2022-11-29 12:01 ./usr/include/MMB/Mutation.h -rw-r--r-- root/root 328 2022-11-29 12:01 ./usr/include/MMB/NTC_FORCE_CLASS.h -rw-r--r-- root/root 4598 2022-11-29 12:01 ./usr/include/MMB/NTC_PARAMETER_READER.h -rw-r--r-- root/root 4871 2022-11-29 12:01 ./usr/include/MMB/NtCBackboneTorsionForce.h -rw-r--r-- root/root 1747 2022-11-29 12:01 ./usr/include/MMB/NtCForces.h -rw-r--r-- root/root 4568 2022-11-29 12:01 ./usr/include/MMB/NtCInteractionParameterReader.h -rw-r--r-- root/root 2181 2022-11-29 12:01 ./usr/include/MMB/NtC_Class_Container.h -rw-r--r-- root/root 15506 2022-11-29 12:01 ./usr/include/MMB/ParameterReader.h -rw-r--r-- root/root 56249 2022-11-29 12:01 ./usr/include/MMB/ParameterReader_wrapper.h -rw-r--r-- root/root 5300 2022-11-29 12:01 ./usr/include/MMB/PeriodicParameterReaderUpdater.h -rw-r--r-- root/root 5408 2022-11-29 12:01 ./usr/include/MMB/PeriodicPdbAndCOMWriter.h -rw-r--r-- root/root 3151 2022-11-29 12:01 ./usr/include/MMB/PeriodicPdbAndEnergySingleFrameWriter.h -rw-r--r-- root/root 2002 2022-11-29 12:01 ./usr/include/MMB/PeriodicPdbAndEnergyWriter.h -rw-r--r-- root/root 4985 2022-11-29 12:01 ./usr/include/MMB/PeriodicPdbSingleFrameWriter.h -rw-r--r-- root/root 4299 2022-11-29 12:01 ./usr/include/MMB/PeriodicScrubber.h -rw-r--r-- root/root 1615 2022-11-29 12:01 ./usr/include/MMB/ProgressWriter.h -rw-r--r-- root/root 8487 2022-11-29 12:01 ./usr/include/MMB/RandomizeRNACoordinates.h -rw-r--r-- root/root 8587 2022-11-29 12:01 ./usr/include/MMB/Repel.h -rw-r--r-- root/root 23919 2022-11-29 12:01 ./usr/include/MMB/ResidueStretchContainer.h -rw-r--r-- root/root 12884 2022-11-29 12:01 ./usr/include/MMB/RigidifyFormedHelices.h -rw-r--r-- root/root 7179 2022-11-29 12:01 ./usr/include/MMB/SetChiMobility.h -rw-r--r-- root/root 3252 2022-11-29 12:01 ./usr/include/MMB/SetSingleBondMobility.h -rw-r--r-- root/root 3132 2022-11-29 12:01 ./usr/include/MMB/Spiral.h -rw-r--r-- root/root 2359 2022-11-29 12:01 ./usr/include/MMB/StackingForceSubsystem.h -rw-r--r-- root/root 15674 2022-11-29 12:01 ./usr/include/MMB/Sterics.h -rw-r--r-- root/root 1958 2022-11-29 12:01 ./usr/include/MMB/TetherForce.h -rw-r--r-- root/root 12675 2022-11-29 12:01 ./usr/include/MMB/Threading.h -rw-r--r-- root/root 5366 2022-11-29 12:01 ./usr/include/MMB/UnitCellParameters.h -rw-r--r-- root/root 63474 2022-11-29 12:01 ./usr/include/MMB/Utils.h -rw-r--r-- root/root 12299 2022-11-29 12:01 ./usr/include/MMB/WadleyKeatingDuartePyleTorsionForce.h -rw-r--r-- root/root 2817 2022-11-29 12:01 ./usr/include/MMB/Water.h -rw-r--r-- root/root 3544 2022-11-29 12:01 ./usr/include/MMB/WaterDroplet.h -rw-r--r-- root/root 845 2022-11-29 12:01 ./usr/include/MMB/superimposer.h drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/lib/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/lib/powerpc64le-linux-gnu/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/lib/powerpc64le-linux-gnu/cmake/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/lib/powerpc64le-linux-gnu/cmake/mmb/ -rw-r--r-- root/root 2872 2022-12-12 09:04 ./usr/lib/powerpc64le-linux-gnu/cmake/mmb/MmbConfigVersion.cmake -rw-r--r-- root/root 828 2022-12-12 09:04 ./usr/lib/powerpc64le-linux-gnu/cmake/mmb/MmbTargets-release.cmake -rw-r--r-- root/root 4462 2022-12-12 09:04 ./usr/lib/powerpc64le-linux-gnu/cmake/mmb/MmbTargets.cmake lrwxrwxrwx root/root 0 2022-12-12 09:04 ./usr/lib/powerpc64le-linux-gnu/libMMB.so -> libMMB.so.4.0 drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/lib/powerpc64le-linux-gnu/pkgconfig/ -rw-r--r-- root/root 199 2022-12-12 09:04 ./usr/lib/powerpc64le-linux-gnu/pkgconfig/mmb.pc drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/share/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/share/doc/libmmb-dev/ lrwxrwxrwx root/root 0 2022-12-12 09:04 ./usr/share/doc/libmmb-dev/changelog.Debian.gz -> ../libmmb4.0/changelog.Debian.gz -rw-r--r-- root/root 1550 2022-12-12 09:04 ./usr/share/doc/libmmb-dev/copyright libmmb4.0_4.0.0+dfsg-2_ppc64el.deb ---------------------------------- new Debian package, version 2.0. size 1126436 bytes: control archive=942 bytes. 920 bytes, 19 lines control 224 bytes, 3 lines md5sums 37 bytes, 1 lines shlibs 75 bytes, 2 lines triggers Package: libmmb4.0 Source: macromoleculebuilder Version: 4.0.0+dfsg-2 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debichem Team Installed-Size: 4630 Depends: libc6 (>= 2.33), libgcc-s1 (>= 3.4.4), libopenmm7.7 (>= 7.7.0+dfsg), libsimbody3.7 (>= 3.7+dfsg), libsimtkmolmodel3.1 (>= 3.1.0), libstdc++6 (>= 11), zlib1g (>= 1:1.2.6) Section: libs Priority: optional Multi-Arch: same Homepage: https://simtk.org/projects/rnatoolbox Description: shared library of MacroMoleculeBuilder MacroMoleculeBuilder, previously known as RNABuilder, can be used for morphing, homology modeling, folding (e.g. using base pairing contacts), redesigning complexes, fitting to low-resolution density maps, predicting local rearrangements upon mutation, and many other applications. . This package contains the shared library. drwxr-xr-x root/root 0 2022-12-12 09:04 ./ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/lib/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/lib/powerpc64le-linux-gnu/ -rw-r--r-- root/root 4725928 2022-12-12 09:04 ./usr/lib/powerpc64le-linux-gnu/libMMB.so.4.0 drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/share/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/share/doc/libmmb4.0/ -rw-r--r-- root/root 1126 2022-12-12 09:04 ./usr/share/doc/libmmb4.0/changelog.Debian.gz -rw-r--r-- root/root 1550 2022-12-12 09:04 ./usr/share/doc/libmmb4.0/copyright mmb_4.0.0+dfsg-2_ppc64el.deb ---------------------------- new Debian package, version 2.0. size 29360 bytes: control archive=772 bytes. 852 bytes, 16 lines control 170 bytes, 3 lines md5sums Package: mmb Source: macromoleculebuilder Version: 4.0.0+dfsg-2 Architecture: ppc64el Maintainer: Ubuntu Developers Original-Maintainer: Debichem Team Installed-Size: 145 Depends: mmb-common, libc6 (>= 2.34), libgcc-s1 (>= 3.4.4), libmmb4.0 (>= 4.0.0+dfsg), libsimbody3.7 (>= 3.7+dfsg), libsimtkmolmodel3.1 (>= 3.1.0), libstdc++6 (>= 9) Section: science Priority: optional Homepage: https://simtk.org/projects/rnatoolbox Description: model the structure and dynamics of macromolecules MacroMoleculeBuilder, previously known as RNABuilder, can be used for morphing, homology modeling, folding (e.g. using base pairing contacts), redesigning complexes, fitting to low-resolution density maps, predicting local rearrangements upon mutation, and many other applications. drwxr-xr-x root/root 0 2022-12-12 09:04 ./ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/bin/ -rwxr-xr-x root/root 133528 2022-12-12 09:04 ./usr/bin/MMB drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/share/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/share/doc/mmb/ lrwxrwxrwx root/root 0 2022-12-12 09:04 ./usr/share/doc/mmb/changelog.Debian.gz -> ../libmmb4.0/changelog.Debian.gz -rw-r--r-- root/root 1550 2022-12-12 09:04 ./usr/share/doc/mmb/copyright drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/share/man/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/share/man/man1/ -rw-r--r-- root/root 789 2022-12-12 09:04 ./usr/share/man/man1/MMB.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: ppc64el Build Type: any Build-Space: 880744 Build-Time: 276 Distribution: lunar-proposed Host Architecture: ppc64el Install-Time: 24 Job: macromoleculebuilder_4.0.0+dfsg-2.dsc Machine Architecture: ppc64el Package: macromoleculebuilder Package-Time: 302 Source-Version: 4.0.0+dfsg-2 Space: 880744 Status: successful Version: 4.0.0+dfsg-2 -------------------------------------------------------------------------------- Finished at 2023-02-04T01:58:45Z Build needed 00:05:02, 880744k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=ppc64el PACKAGEBUILD-24934404 Scanning for processes to kill in build PACKAGEBUILD-24934404