sbuild (Debian sbuild) 0.81.2+deb11u1 (31 August 2022) on debian-ci-siliconvalley +==============================================================================+ | macromoleculebuilder 4.0.0+dfsg-2 (arm64) Wed, 12 Apr 2023 11:46:13 +0000 | +==============================================================================+ Package: macromoleculebuilder Version: 4.0.0+dfsg-2 Source Version: 4.0.0+dfsg-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: arm64 Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-3d0ac0cc-71f6-4ee1-b339-e8c5f39c32b9' with '<>' I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-wzwDiR/resolver-ag5BW0' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian sid InRelease [184 kB] Get:2 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:3 http://localhost:3142/debian sid/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2023-04-12-0803.16-F-2023-04-12-0203.05.pdiff [21.1 kB] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2023-04-12-0803.16-F-2023-04-12-0203.05.pdiff [2198 B] Get:4 http://localhost:3142/debian sid/main Sources T-2023-04-12-0803.16-F-2023-04-12-0203.05.pdiff [21.1 kB] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2023-04-12-0803.16-F-2023-04-12-0203.05.pdiff [2198 B] Get:6 http://localhost:3142/debian sid/main arm64 Packages [9288 kB] Fetched 9622 kB in 2s (3984 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'macromoleculebuilder' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/macromoleculebuilder.git Please use: git clone https://salsa.debian.org/debichem-team/macromoleculebuilder.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2574 kB of source archives. Get:1 http://localhost:3142/debian sid/main macromoleculebuilder 4.0.0+dfsg-2 (dsc) [2434 B] Get:2 http://localhost:3142/debian sid/main macromoleculebuilder 4.0.0+dfsg-2 (tar) [2567 kB] Get:3 http://localhost:3142/debian sid/main macromoleculebuilder 4.0.0+dfsg-2 (diff) [4240 B] Fetched 2574 kB in 0s (42.5 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-wzwDiR/macromoleculebuilder-4.0.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-wzwDiR' 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, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 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, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 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 [499 B] Get:5 copy:/<>/apt_archive ./ Packages [588 B] Fetched 2044 B in 0s (0 B/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 binutils-aarch64-linux-gnu bsdextrautils cmake cmake-data cpp-12-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism docbook-xml docbook-xsl dpkg-cross dwz file freeglut3-dev:arm64 g++-12-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-11-base:arm64 gcc-12-aarch64-linux-gnu gcc-12-aarch64-linux-gnu-base gcc-12-base:arm64 gcc-12-cross-base gcc-aarch64-linux-gnu gemmi-dev:arm64 gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libasan6:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libblas-dev:arm64 libblas3:arm64 libbrotli1 libbsd0 libbsd0:arm64 libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libcom-err2:arm64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:arm64 libcrypt1:arm64 libcurl4 libdebhelper-perl libdebian-dpkgcross-perl libdrm-amdgpu1:arm64 libdrm-common libdrm-nouveau2:arm64 libdrm-radeon1:arm64 libdrm2:arm64 libedit2:arm64 libegl-dev:arm64 libegl-mesa0:arm64 libegl1:arm64 libelf1 libelf1:arm64 libexpat1 libexpat1:arm64 libffi8:arm64 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgbm1:arm64 libgcc-11-dev:arm64 libgcc-12-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgfortran5:arm64 libgl-dev:arm64 libgl1:arm64 libgl1-mesa-dev:arm64 libgl1-mesa-dri:arm64 libglapi-mesa:arm64 libgles-dev:arm64 libgles1:arm64 libgles2:arm64 libglu1-mesa:arm64 libglu1-mesa-dev:arm64 libglut-dev:arm64 libglut3.12:arm64 libglvnd-core-dev:arm64 libglvnd-dev:arm64 libglvnd0:arm64 libglx-dev:arm64 libglx-mesa0:arm64 libglx0:arm64 libgomp1:arm64 libgomp1-arm64-cross libgssapi-krb5-2:arm64 libhwasan0:arm64 libhwasan0-arm64-cross libice-dev:arm64 libice6:arm64 libicu72 libicu72:arm64 libio-string-perl libitm1:arm64 libitm1-arm64-cross libjsoncpp25 libk5crypto3:arm64 libkeyutils1:arm64 libkrb5-3:arm64 libkrb5support0:arm64 liblapack-dev:arm64 liblapack3:arm64 libldap-2.5-0 libllvm15:arm64 liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross liblzma5:arm64 libmagic-mgc libmagic1 libmd0:arm64 libncursesw6 libnghttp2-14 libnsl-dev:arm64 libnsl2:arm64 libopengl-dev:arm64 libopengl0:arm64 libopenmm-dev:arm64 libopenmm7.7:arm64 libpipeline1 libproc2-0 libpsl5 libpthread-stubs0-dev libpthread-stubs0-dev:arm64 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5:arm64 libseqan2-dev libsimbody-dev:arm64 libsimbody3.7:arm64 libsimtkmolmodel-dev:arm64 libsimtkmolmodel-plugins:arm64 libsimtkmolmodel3.1:arm64 libsm-dev:arm64 libsm6:arm64 libsqlite3-0 libssh2-1 libssl3:arm64 libstb-dev:arm64 libstb0:arm64 libstdc++-11-dev:arm64 libstdc++-12-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libtinfo6:arm64 libtirpc-dev:arm64 libtirpc3:arm64 libtool libtsan0:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libuuid1:arm64 libuv1 libwayland-client0:arm64 libwayland-server0:arm64 libx11-6 libx11-6:arm64 libx11-data libx11-dev libx11-dev:arm64 libx11-xcb1:arm64 libxau-dev libxau-dev:arm64 libxau6 libxau6:arm64 libxcb-dri2-0:arm64 libxcb-dri3-0:arm64 libxcb-glx0:arm64 libxcb-present0:arm64 libxcb-randr0:arm64 libxcb-shm0:arm64 libxcb-sync1:arm64 libxcb-xfixes0:arm64 libxcb1 libxcb1:arm64 libxcb1-dev libxcb1-dev:arm64 libxdmcp-dev libxdmcp-dev:arm64 libxdmcp6 libxdmcp6:arm64 libxext-dev:arm64 libxext6:arm64 libxfixes-dev:arm64 libxfixes3:arm64 libxi-dev:arm64 libxi6:arm64 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxml2:arm64 libxml2-utils libxmu-dev:arm64 libxmu-headers libxmu6:arm64 libxshmfence1:arm64 libxslt1.1 libxt-dev:arm64 libxt6:arm64 libxxf86vm1:arm64 libyaml-perl libz3-4:arm64 libzstd1:arm64 linux-libc-dev:arm64 linux-libc-dev-arm64-cross m4 man-db media-types po-debconf procps python3 python3-minimal python3.11 python3.11-minimal readline-common sensible-utils sgml-base sgml-data tao-pegtl-dev ucf x11-common x11proto-dev xml-core xorg-sgml-doctools xsltproc xtrans-dev zlib1g:arm64 zlib1g-dev:arm64 Suggested packages: asciidoc-doc docbook-utils source-highlight autoconf-archive gnu-standards autoconf-doc binutils-doc cmake-doc cmake-format elpa-cmake-mode ninja-build gcc-12-locales cpp-12-doc cpp-doc 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 binutils-multiarch gcc-12-doc manpages-dev flex bison gdb-aarch64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff lrzip liblapack-doc:arm64 glibc-doc:arm64 libc-l10n:arm64 locales:arm64 libnss-nis:arm64 libnss-nisplus:arm64 manpages-dev:arm64 krb5-doc:arm64 krb5-user:arm64 libice-doc:arm64 lm-sensors lm-sensors:arm64 libsm-doc:arm64 libstdc++-11-doc:arm64 libtool-doc gfortran | fortran95-compiler gcj-jdk libx11-doc libx11-doc:arm64 libxcb-doc libxcb-doc:arm64 libxext-doc:arm64 libxt-doc:arm64 libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.11-venv python3.11-doc binfmt-support readline-doc sgml-base-doc perlsgml w3-recs opensp Recommended packages: xmlto curl | wget | lynx libidn2-0:arm64 ca-certificates libarchive-cpio-perl krb5-locales:arm64 libldap-common libgpm2 publicsuffix libsasl2-modules libltdl-dev uuid-runtime:arm64 libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl psmisc The following NEW packages will be installed: asciidoc-base asciidoc-common autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdextrautils cmake cmake-data cpp-12-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism docbook-xml docbook-xsl dpkg-cross dwz file freeglut3-dev:arm64 g++-12-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-11-base:arm64 gcc-12-aarch64-linux-gnu gcc-12-aarch64-linux-gnu-base gcc-12-base:arm64 gcc-12-cross-base gcc-aarch64-linux-gnu gemmi-dev:arm64 gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libasan6:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libblas-dev:arm64 libblas3:arm64 libbrotli1 libbsd0 libbsd0:arm64 libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libcom-err2:arm64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:arm64 libcrypt1:arm64 libcurl4 libdebhelper-perl libdebian-dpkgcross-perl libdrm-amdgpu1:arm64 libdrm-common libdrm-nouveau2:arm64 libdrm-radeon1:arm64 libdrm2:arm64 libedit2:arm64 libegl-dev:arm64 libegl-mesa0:arm64 libegl1:arm64 libelf1 libelf1:arm64 libexpat1 libexpat1:arm64 libffi8:arm64 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgbm1:arm64 libgcc-11-dev:arm64 libgcc-12-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgfortran5:arm64 libgl-dev:arm64 libgl1:arm64 libgl1-mesa-dev:arm64 libgl1-mesa-dri:arm64 libglapi-mesa:arm64 libgles-dev:arm64 libgles1:arm64 libgles2:arm64 libglu1-mesa:arm64 libglu1-mesa-dev:arm64 libglut-dev:arm64 libglut3.12:arm64 libglvnd-core-dev:arm64 libglvnd-dev:arm64 libglvnd0:arm64 libglx-dev:arm64 libglx-mesa0:arm64 libglx0:arm64 libgomp1:arm64 libgomp1-arm64-cross libgssapi-krb5-2:arm64 libhwasan0:arm64 libhwasan0-arm64-cross libice-dev:arm64 libice6:arm64 libicu72 libicu72:arm64 libio-string-perl libitm1:arm64 libitm1-arm64-cross libjsoncpp25 libk5crypto3:arm64 libkeyutils1:arm64 libkrb5-3:arm64 libkrb5support0:arm64 liblapack-dev:arm64 liblapack3:arm64 libldap-2.5-0 libllvm15:arm64 liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross liblzma5:arm64 libmagic-mgc libmagic1 libmd0:arm64 libncursesw6 libnghttp2-14 libnsl-dev:arm64 libnsl2:arm64 libopengl-dev:arm64 libopengl0:arm64 libopenmm-dev:arm64 libopenmm7.7:arm64 libpipeline1 libproc2-0 libpsl5 libpthread-stubs0-dev libpthread-stubs0-dev:arm64 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5:arm64 libseqan2-dev libsimbody-dev:arm64 libsimbody3.7:arm64 libsimtkmolmodel-dev:arm64 libsimtkmolmodel-plugins:arm64 libsimtkmolmodel3.1:arm64 libsm-dev:arm64 libsm6:arm64 libsqlite3-0 libssh2-1 libssl3:arm64 libstb-dev:arm64 libstb0:arm64 libstdc++-11-dev:arm64 libstdc++-12-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libtinfo6:arm64 libtirpc-dev:arm64 libtirpc3:arm64 libtool libtsan0:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libuuid1:arm64 libuv1 libwayland-client0:arm64 libwayland-server0:arm64 libx11-6 libx11-6:arm64 libx11-data libx11-dev libx11-dev:arm64 libx11-xcb1:arm64 libxau-dev libxau-dev:arm64 libxau6 libxau6:arm64 libxcb-dri2-0:arm64 libxcb-dri3-0:arm64 libxcb-glx0:arm64 libxcb-present0:arm64 libxcb-randr0:arm64 libxcb-shm0:arm64 libxcb-sync1:arm64 libxcb-xfixes0:arm64 libxcb1 libxcb1:arm64 libxcb1-dev libxcb1-dev:arm64 libxdmcp-dev libxdmcp-dev:arm64 libxdmcp6 libxdmcp6:arm64 libxext-dev:arm64 libxext6:arm64 libxfixes-dev:arm64 libxfixes3:arm64 libxi-dev:arm64 libxi6:arm64 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxml2:arm64 libxml2-utils libxmu-dev:arm64 libxmu-headers libxmu6:arm64 libxshmfence1:arm64 libxslt1.1 libxt-dev:arm64 libxt6:arm64 libxxf86vm1:arm64 libyaml-perl libz3-4:arm64 libzstd1:arm64 linux-libc-dev:arm64 linux-libc-dev-arm64-cross m4 man-db media-types po-debconf procps python3 python3-minimal python3.11 python3.11-minimal readline-common sbuild-build-depends-main-dummy:arm64 sensible-utils sgml-base sgml-data tao-pegtl-dev ucf x11-common x11proto-dev xml-core xorg-sgml-doctools xsltproc xtrans-dev zlib1g:arm64 zlib1g-dev:arm64 0 upgraded, 259 newly installed, 0 to remove and 0 not upgraded. Need to get 188 MB of archives. After this operation, 809 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1016 B] Get:2 http://localhost:3142/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB] Get:3 http://localhost:3142/debian sid/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get:4 http://localhost:3142/debian sid/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:5 http://localhost:3142/debian sid/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get:6 http://localhost:3142/debian sid/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:7 http://localhost:3142/debian sid/main amd64 media-types all 10.0.0 [26.1 kB] Get:8 http://localhost:3142/debian sid/main amd64 libncursesw6 amd64 6.4-2 [134 kB] Get:9 http://localhost:3142/debian sid/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:10 http://localhost:3142/debian sid/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:11 http://localhost:3142/debian sid/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:12 http://localhost:3142/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get:13 http://localhost:3142/debian sid/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get:14 http://localhost:3142/debian sid/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:15 http://localhost:3142/debian sid/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:16 http://localhost:3142/debian sid/main amd64 sgml-base all 1.31 [15.4 kB] Get:17 http://localhost:3142/debian sid/main amd64 libproc2-0 amd64 2:4.0.3-1 [63.2 kB] Get:18 http://localhost:3142/debian sid/main amd64 procps amd64 2:4.0.3-1 [762 kB] Get:19 http://localhost:3142/debian sid/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get:20 http://localhost:3142/debian sid/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get:21 http://localhost:3142/debian sid/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get:22 http://localhost:3142/debian sid/main amd64 file amd64 1:5.44-3 [42.5 kB] Get:23 http://localhost:3142/debian sid/main amd64 gettext-base amd64 0.21-12 [160 kB] Get:24 http://localhost:3142/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:25 http://localhost:3142/debian sid/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get:26 http://localhost:3142/debian sid/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get:27 http://localhost:3142/debian sid/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get:28 http://localhost:3142/debian sid/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get:29 http://localhost:3142/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:30 http://localhost:3142/debian sid/main amd64 asciidoc-common all 10.2.0-1 [109 kB] Get:31 http://localhost:3142/debian sid/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get:32 http://localhost:3142/debian sid/main amd64 docbook-xsl all 1.79.2+dfsg-2 [1237 kB] Get:33 http://localhost:3142/debian sid/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:34 http://localhost:3142/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get:35 http://localhost:3142/debian sid/main amd64 libxml2-utils amd64 2.9.14+dfsg-1.1+b3 [99.0 kB] Get:36 http://localhost:3142/debian sid/main amd64 libxslt1.1 amd64 1.1.35-1 [242 kB] Get:37 http://localhost:3142/debian sid/main amd64 xsltproc amd64 1.1.35-1 [126 kB] Get:38 http://localhost:3142/debian sid/main amd64 asciidoc-base all 10.2.0-1 [89.5 kB] Get:39 http://localhost:3142/debian sid/main amd64 m4 amd64 1.4.19-3 [287 kB] Get:40 http://localhost:3142/debian sid/main amd64 autoconf all 2.71-3 [332 kB] Get:41 http://localhost:3142/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:42 http://localhost:3142/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:43 http://localhost:3142/debian sid/main amd64 autopoint all 0.21-12 [495 kB] Get:44 http://localhost:3142/debian sid/main amd64 binutils-aarch64-linux-gnu amd64 2.40-2 [3353 kB] Get:45 http://localhost:3142/debian sid/main amd64 libarchive13 amd64 3.6.2-1 [343 kB] Get:46 http://localhost:3142/debian sid/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:47 http://localhost:3142/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-11 [20.1 kB] Get:48 http://localhost:3142/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg-11 [59.5 kB] Get:49 http://localhost:3142/debian sid/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:50 http://localhost:3142/debian sid/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get:51 http://localhost:3142/debian sid/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:52 http://localhost:3142/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:53 http://localhost:3142/debian sid/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:54 http://localhost:3142/debian sid/main amd64 libcurl4 amd64 7.88.1-8 [386 kB] Get:55 http://localhost:3142/debian sid/main amd64 libjsoncpp25 amd64 1.9.5-4 [78.6 kB] Get:56 http://localhost:3142/debian sid/main amd64 librhash0 amd64 1.4.3-3 [134 kB] Get:57 http://localhost:3142/debian sid/main amd64 libuv1 amd64 1.44.2-1 [140 kB] Get:58 http://localhost:3142/debian sid/main amd64 cmake-data all 3.25.1-1 [2026 kB] Get:59 http://localhost:3142/debian sid/main amd64 cmake amd64 3.25.1-1 [8692 kB] Get:60 http://localhost:3142/debian sid/main amd64 gcc-12-aarch64-linux-gnu-base amd64 12.2.0-14cross1 [37.7 kB] Get:61 http://localhost:3142/debian sid/main amd64 cpp-12-aarch64-linux-gnu amd64 12.2.0-14cross1 [9150 kB] Get:62 http://localhost:3142/debian sid/main amd64 cpp-aarch64-linux-gnu amd64 4:12.2.0-3 [3980 B] Get:63 http://localhost:3142/debian sid/main amd64 cross-config all 2.6.20 [16.3 kB] Get:64 http://localhost:3142/debian sid/main amd64 gcc-12-cross-base all 12.2.0-14cross1 [33.2 kB] Get:65 http://localhost:3142/debian sid/main amd64 libc6-arm64-cross all 2.36-8cross1 [1005 kB] Get:66 http://localhost:3142/debian sid/main amd64 libgcc-s1-arm64-cross all 12.2.0-14cross1 [34.8 kB] Get:67 http://localhost:3142/debian sid/main amd64 libgomp1-arm64-cross all 12.2.0-14cross1 [102 kB] Get:68 http://localhost:3142/debian sid/main amd64 libitm1-arm64-cross all 12.2.0-14cross1 [23.5 kB] Get:69 http://localhost:3142/debian sid/main amd64 libatomic1-arm64-cross all 12.2.0-14cross1 [9292 B] Get:70 http://localhost:3142/debian sid/main amd64 libasan8-arm64-cross all 12.2.0-14cross1 [2097 kB] Get:71 http://localhost:3142/debian sid/main amd64 liblsan0-arm64-cross all 12.2.0-14cross1 [926 kB] Get:72 http://localhost:3142/debian sid/main amd64 libtsan2-arm64-cross all 12.2.0-14cross1 [2179 kB] Get:73 http://localhost:3142/debian sid/main amd64 libstdc++6-arm64-cross all 12.2.0-14cross1 [514 kB] Get:74 http://localhost:3142/debian sid/main amd64 libubsan1-arm64-cross all 12.2.0-14cross1 [861 kB] Get:75 http://localhost:3142/debian sid/main amd64 libhwasan0-arm64-cross all 12.2.0-14cross1 [998 kB] Get:76 http://localhost:3142/debian sid/main amd64 libgcc-12-dev-arm64-cross all 12.2.0-14cross1 [961 kB] Get:77 http://localhost:3142/debian sid/main amd64 gcc-12-aarch64-linux-gnu amd64 12.2.0-14cross1 [18.0 MB] Get:78 http://localhost:3142/debian sid/main amd64 gcc-aarch64-linux-gnu amd64 4:12.2.0-3 [1468 B] Get:79 http://localhost:3142/debian sid/main amd64 linux-libc-dev-arm64-cross all 6.1.4-1cross1 [1815 kB] Get:80 http://localhost:3142/debian sid/main amd64 libc6-dev-arm64-cross all 2.36-8cross1 [1424 kB] Get:81 http://localhost:3142/debian sid/main amd64 libstdc++-12-dev-arm64-cross all 12.2.0-14cross1 [1975 kB] Get:82 http://localhost:3142/debian sid/main amd64 g++-12-aarch64-linux-gnu amd64 12.2.0-14cross1 [10.1 MB] Get:83 http://localhost:3142/debian sid/main amd64 g++-aarch64-linux-gnu amd64 4:12.2.0-3 [1176 B] Get:84 http://localhost:3142/debian sid/main amd64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB] Get:85 http://localhost:3142/debian sid/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:86 http://localhost:3142/debian sid/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:87 http://localhost:3142/debian sid/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:88 http://localhost:3142/debian sid/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:89 http://localhost:3142/debian sid/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b1 [322 kB] Get:90 http://localhost:3142/debian sid/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:91 http://localhost:3142/debian sid/main amd64 libyaml-perl all 1.30-2 [63.4 kB] Get:92 http://localhost:3142/debian sid/main amd64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:93 http://localhost:3142/debian sid/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get:94 http://localhost:3142/debian sid/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get:95 http://localhost:3142/debian sid/main amd64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB] Get:96 http://localhost:3142/debian sid/main amd64 dpkg-cross all 2.6.20 [25.8 kB] Get:97 http://localhost:3142/debian sid/main amd64 crossbuild-essential-arm64 all 12.9 [6708 B] Get:98 http://localhost:3142/debian sid/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get:99 http://localhost:3142/debian sid/main amd64 libtool all 2.4.7-5 [517 kB] Get:100 http://localhost:3142/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB] Get:101 http://localhost:3142/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:102 http://localhost:3142/debian sid/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get:103 http://localhost:3142/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get:104 http://localhost:3142/debian sid/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get:105 http://localhost:3142/debian sid/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get:106 http://localhost:3142/debian sid/main amd64 dwz amd64 0.15-1 [109 kB] Get:107 http://localhost:3142/debian sid/main amd64 gettext amd64 0.21-12 [1300 kB] Get:108 http://localhost:3142/debian sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:109 http://localhost:3142/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:110 http://localhost:3142/debian sid/main amd64 debhelper all 13.11.4 [942 kB] Get:111 http://localhost:3142/debian sid/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get:112 http://localhost:3142/debian sid/main amd64 docbook-xml all 4.5-12 [85.2 kB] Get:113 http://localhost:3142/debian sid/main arm64 gcc-12-base arm64 12.2.0-14 [37.5 kB] Get:114 http://localhost:3142/debian sid/main arm64 libgcc-s1 arm64 12.2.0-14 [34.8 kB] Get:115 http://localhost:3142/debian sid/main arm64 libc6 arm64 2.36-9 [2313 kB] Get:116 http://localhost:3142/debian sid/main arm64 libglvnd0 arm64 1.6.0-1 [41.4 kB] Get:117 http://localhost:3142/debian sid/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get:118 http://localhost:3142/debian sid/main arm64 libmd0 arm64 1.0.4-2 [29.4 kB] Get:119 http://localhost:3142/debian sid/main arm64 libbsd0 arm64 0.11.7-4 [113 kB] Get:120 http://localhost:3142/debian sid/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get:121 http://localhost:3142/debian sid/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get:122 http://localhost:3142/debian sid/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get:123 http://localhost:3142/debian sid/main arm64 libx11-6 arm64 2:1.8.4-2 [736 kB] Get:124 http://localhost:3142/debian sid/main amd64 libdrm-common all 2.4.114-1 [7112 B] Get:125 http://localhost:3142/debian sid/main arm64 libdrm2 arm64 2.4.114-1+b1 [36.7 kB] Get:126 http://localhost:3142/debian sid/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get:127 http://localhost:3142/debian sid/main arm64 libglapi-mesa arm64 22.3.6-1+deb12u1 [44.7 kB] Get:128 http://localhost:3142/debian sid/main arm64 libx11-xcb1 arm64 2:1.8.4-2 [192 kB] Get:129 http://localhost:3142/debian sid/main arm64 libxcb-dri2-0 arm64 1.15-1 [107 kB] Get:130 http://localhost:3142/debian sid/main arm64 libxcb-dri3-0 arm64 1.15-1 [107 kB] Get:131 http://localhost:3142/debian sid/main arm64 libxcb-glx0 arm64 1.15-1 [123 kB] Get:132 http://localhost:3142/debian sid/main arm64 libxcb-present0 arm64 1.15-1 [106 kB] Get:133 http://localhost:3142/debian sid/main arm64 libxcb-randr0 arm64 1.15-1 [117 kB] Get:134 http://localhost:3142/debian sid/main arm64 libxcb-shm0 arm64 1.15-1 [106 kB] Get:135 http://localhost:3142/debian sid/main arm64 libxcb-sync1 arm64 1.15-1 [109 kB] Get:136 http://localhost:3142/debian sid/main arm64 libxcb-xfixes0 arm64 1.15-1 [110 kB] Get:137 http://localhost:3142/debian sid/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get:138 http://localhost:3142/debian sid/main arm64 libxfixes3 arm64 1:6.0.0-2 [22.9 kB] Get:139 http://localhost:3142/debian sid/main arm64 libxshmfence1 arm64 1.3-1 [8712 B] Get:140 http://localhost:3142/debian sid/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b2 [20.1 kB] Get:141 http://localhost:3142/debian sid/main arm64 libdrm-amdgpu1 arm64 2.4.114-1+b1 [20.4 kB] Get:142 http://localhost:3142/debian sid/main arm64 libdrm-nouveau2 arm64 2.4.114-1+b1 [18.4 kB] Get:143 http://localhost:3142/debian sid/main arm64 libdrm-radeon1 arm64 2.4.114-1+b1 [20.9 kB] Get:144 http://localhost:3142/debian sid/main arm64 zlib1g arm64 1:1.2.13.dfsg-1 [82.7 kB] Get:145 http://localhost:3142/debian sid/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get:146 http://localhost:3142/debian sid/main arm64 libtinfo6 arm64 6.4-2 [324 kB] Get:147 http://localhost:3142/debian sid/main arm64 libedit2 arm64 3.1-20221030-2 [88.1 kB] Get:148 http://localhost:3142/debian sid/main arm64 libffi8 arm64 3.4.4-1 [20.5 kB] Get:149 http://localhost:3142/debian sid/main arm64 libstdc++6 arm64 12.2.0-14 [557 kB] Get:150 http://localhost:3142/debian sid/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get:151 http://localhost:3142/debian sid/main arm64 liblzma5 arm64 5.4.1-0.2 [199 kB] Get:152 http://localhost:3142/debian sid/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB] Get:153 http://localhost:3142/debian sid/main arm64 libz3-4 arm64 4.8.12-3.1 [6282 kB] Get:154 http://localhost:3142/debian sid/main arm64 libllvm15 arm64 1:15.0.7-4 [20.7 MB] Get:155 http://localhost:3142/debian sid/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get:156 http://localhost:3142/debian sid/main arm64 libsensors5 arm64 1:3.6.0-7.1 [33.3 kB] Get:157 http://localhost:3142/debian sid/main arm64 libzstd1 arm64 1.5.4+dfsg2-5 [251 kB] Get:158 http://localhost:3142/debian sid/main arm64 libgl1-mesa-dri arm64 22.3.6-1+deb12u1 [6278 kB] Get:159 http://localhost:3142/debian sid/main arm64 libglx-mesa0 arm64 22.3.6-1+deb12u1 [146 kB] Get:160 http://localhost:3142/debian sid/main arm64 libglx0 arm64 1.6.0-1 [30.8 kB] Get:161 http://localhost:3142/debian sid/main arm64 libgl1 arm64 1.6.0-1 [90.2 kB] Get:162 http://localhost:3142/debian sid/main arm64 libxi6 arm64 2:1.8-1+b1 [82.3 kB] Get:163 http://localhost:3142/debian sid/main arm64 libglut3.12 arm64 3.4.0-1 [133 kB] Get:164 http://localhost:3142/debian sid/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get:165 http://localhost:3142/debian sid/main amd64 x11proto-dev all 2022.1-1 [599 kB] Get:166 http://localhost:3142/debian sid/main arm64 libxau-dev arm64 1:1.0.9-1 [23.2 kB] Get:167 http://localhost:3142/debian sid/main arm64 libxdmcp-dev arm64 1:1.1.2-3 [41.2 kB] Get:168 http://localhost:3142/debian sid/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get:169 http://localhost:3142/debian sid/main arm64 libpthread-stubs0-dev arm64 0.4-1 [5336 B] Get:170 http://localhost:3142/debian sid/main arm64 libxcb1-dev arm64 1.15-1 [182 kB] Get:171 http://localhost:3142/debian sid/main arm64 libx11-dev arm64 2:1.8.4-2 [817 kB] Get:172 http://localhost:3142/debian sid/main arm64 libglx-dev arm64 1.6.0-1 [15.3 kB] Get:173 http://localhost:3142/debian sid/main arm64 libgl-dev arm64 1.6.0-1 [100 kB] Get:174 http://localhost:3142/debian sid/main arm64 libglvnd-core-dev arm64 1.6.0-1 [12.9 kB] Get:175 http://localhost:3142/debian sid/main arm64 libwayland-server0 arm64 1.21.0-1 [34.9 kB] Get:176 http://localhost:3142/debian sid/main arm64 libgbm1 arm64 22.3.6-1+deb12u1 [37.0 kB] Get:177 http://localhost:3142/debian sid/main arm64 libwayland-client0 arm64 1.21.0-1 [27.6 kB] Get:178 http://localhost:3142/debian sid/main arm64 libegl-mesa0 arm64 22.3.6-1+deb12u1 [107 kB] Get:179 http://localhost:3142/debian sid/main arm64 libegl1 arm64 1.6.0-1 [33.1 kB] Get:180 http://localhost:3142/debian sid/main arm64 libegl-dev arm64 1.6.0-1 [19.1 kB] Get:181 http://localhost:3142/debian sid/main arm64 libgles1 arm64 1.6.0-1 [12.1 kB] Get:182 http://localhost:3142/debian sid/main arm64 libgles2 arm64 1.6.0-1 [17.5 kB] Get:183 http://localhost:3142/debian sid/main arm64 libgles-dev arm64 1.6.0-1 [50.4 kB] Get:184 http://localhost:3142/debian sid/main arm64 libopengl0 arm64 1.6.0-1 [31.7 kB] Get:185 http://localhost:3142/debian sid/main arm64 libopengl-dev arm64 1.6.0-1 [4932 B] Get:186 http://localhost:3142/debian sid/main arm64 libglvnd-dev arm64 1.6.0-1 [4696 B] Get:187 http://localhost:3142/debian sid/main arm64 libgl1-mesa-dev arm64 22.3.6-1+deb12u1 [14.5 kB] Get:188 http://localhost:3142/debian sid/main arm64 libglu1-mesa arm64 9.0.2-1.1 [153 kB] Get:189 http://localhost:3142/debian sid/main arm64 libglu1-mesa-dev arm64 9.0.2-1.1 [193 kB] Get:190 http://localhost:3142/debian sid/main arm64 libxext-dev arm64 2:1.3.4-1+b1 [107 kB] Get:191 http://localhost:3142/debian sid/main amd64 x11-common all 1:7.7+23 [252 kB] Get:192 http://localhost:3142/debian sid/main arm64 libice6 arm64 2:1.0.10-1 [55.6 kB] Get:193 http://localhost:3142/debian sid/main arm64 libuuid1 arm64 2.38.1-5+b1 [28.5 kB] Get:194 http://localhost:3142/debian sid/main arm64 libsm6 arm64 2:1.2.3-1 [34.0 kB] Get:195 http://localhost:3142/debian sid/main arm64 libxt6 arm64 1:1.2.1-1.1 [172 kB] Get:196 http://localhost:3142/debian sid/main arm64 libice-dev arm64 2:1.0.10-1 [66.0 kB] Get:197 http://localhost:3142/debian sid/main arm64 libsm-dev arm64 2:1.2.3-1 [37.4 kB] Get:198 http://localhost:3142/debian sid/main arm64 libxt-dev arm64 1:1.2.1-1.1 [402 kB] Get:199 http://localhost:3142/debian sid/main arm64 libglut-dev arm64 3.4.0-1 [160 kB] Get:200 http://localhost:3142/debian sid/main arm64 freeglut3-dev arm64 3.4.0-1 [53.1 kB] Get:201 http://localhost:3142/debian sid/main arm64 gcc-11-base arm64 11.3.0-12 [38.4 kB] Get:202 http://localhost:3142/debian sid/main arm64 gemmi-dev arm64 0.5.7+ds-2+b1 [404 kB] Get:203 http://localhost:3142/debian sid/main arm64 libasan6 arm64 11.3.0-12 [1952 kB] Get:204 http://localhost:3142/debian sid/main arm64 libatomic1 arm64 12.2.0-14 [9536 B] Get:205 http://localhost:3142/debian sid/main arm64 libblas3 arm64 3.11.0-2 [91.4 kB] Get:206 http://localhost:3142/debian sid/main arm64 libblas-dev arm64 3.11.0-2 [97.6 kB] Get:207 http://localhost:3142/debian sid/main amd64 libbsd0 amd64 0.11.7-4 [115 kB] Get:208 http://localhost:3142/debian sid/main arm64 linux-libc-dev arm64 6.1.20-2 [1733 kB] Get:209 http://localhost:3142/debian sid/main arm64 libcrypt1 arm64 1:4.4.33-2 [90.0 kB] Get:210 http://localhost:3142/debian sid/main arm64 libcrypt-dev arm64 1:4.4.33-2 [121 kB] Get:211 http://localhost:3142/debian sid/main arm64 libcom-err2 arm64 1.47.0-2 [19.6 kB] Get:212 http://localhost:3142/debian sid/main arm64 libkrb5support0 arm64 1.20.1-1+b1 [31.7 kB] Get:213 http://localhost:3142/debian sid/main arm64 libk5crypto3 arm64 1.20.1-1+b1 [79.2 kB] Get:214 http://localhost:3142/debian sid/main arm64 libkeyutils1 arm64 1.6.3-2 [8844 B] Get:215 http://localhost:3142/debian sid/main arm64 libssl3 arm64 3.0.8-1 [1801 kB] Get:216 http://localhost:3142/debian sid/main arm64 libkrb5-3 arm64 1.20.1-1+b1 [313 kB] Get:217 http://localhost:3142/debian sid/main arm64 libgssapi-krb5-2 arm64 1.20.1-1+b1 [123 kB] Get:218 http://localhost:3142/debian sid/main arm64 libtirpc3 arm64 1.3.3+ds-1 [80.9 kB] Get:219 http://localhost:3142/debian sid/main arm64 libnsl2 arm64 1.3.0-2 [36.9 kB] Get:220 http://localhost:3142/debian sid/main arm64 libtirpc-dev arm64 1.3.3+ds-1 [194 kB] Get:221 http://localhost:3142/debian sid/main arm64 libnsl-dev arm64 1.3.0-2 [66.1 kB] Get:222 http://localhost:3142/debian sid/main arm64 libc6-dev arm64 2.36-9 [1428 kB] Get:223 http://localhost:3142/debian sid/main arm64 libgomp1 arm64 12.2.0-14 [104 kB] Get:224 http://localhost:3142/debian sid/main arm64 libitm1 arm64 12.2.0-14 [23.9 kB] Get:225 http://localhost:3142/debian sid/main arm64 liblsan0 arm64 12.2.0-14 [926 kB] Get:226 http://localhost:3142/debian sid/main arm64 libtsan0 arm64 11.3.0-12 [1957 kB] Get:227 http://localhost:3142/debian sid/main arm64 libubsan1 arm64 12.2.0-14 [862 kB] Get:228 http://localhost:3142/debian sid/main arm64 libhwasan0 arm64 12.2.0-14 [998 kB] Get:229 http://localhost:3142/debian sid/main arm64 libgcc-11-dev arm64 11.3.0-12 [929 kB] Get:230 http://localhost:3142/debian sid/main arm64 libgfortran5 arm64 12.2.0-14 [340 kB] Get:231 http://localhost:3142/debian sid/main arm64 liblapack3 arm64 3.11.0-2 [1664 kB] Get:232 http://localhost:3142/debian sid/main arm64 liblapack-dev arm64 3.11.0-2 [3065 kB] Get:233 http://localhost:3142/debian sid/main arm64 libopenmm7.7 arm64 7.7.0+dfsg-9+b1 [632 kB] Get:234 http://localhost:3142/debian sid/main arm64 libopenmm-dev arm64 7.7.0+dfsg-9+b1 [313 kB] Get:235 http://localhost:3142/debian sid/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B] Get:236 http://localhost:3142/debian sid/main amd64 libseqan2-dev all 2.4.0+dfsg-15 [1215 kB] Get:237 http://localhost:3142/debian sid/main arm64 libxfixes-dev arm64 1:6.0.0-2 [25.2 kB] Get:238 http://localhost:3142/debian sid/main arm64 libxi-dev arm64 2:1.8-1+b1 [244 kB] Get:239 http://localhost:3142/debian sid/main arm64 libxmu6 arm64 2:1.1.3-3 [57.2 kB] Get:240 http://localhost:3142/debian sid/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:241 http://localhost:3142/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:242 http://localhost:3142/debian sid/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:243 http://localhost:3142/debian sid/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get:244 http://localhost:3142/debian sid/main amd64 libxau-dev amd64 1:1.0.9-1 [22.9 kB] Get:245 http://localhost:3142/debian sid/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [42.2 kB] Get:246 http://localhost:3142/debian sid/main amd64 libxcb1-dev amd64 1.15-1 [181 kB] Get:247 http://localhost:3142/debian sid/main amd64 libx11-dev amd64 2:1.8.4-2 [836 kB] Get:248 http://localhost:3142/debian sid/main amd64 libxmu-headers all 2:1.1.3-3 [68.5 kB] Get:249 http://localhost:3142/debian sid/main arm64 libxmu-dev arm64 2:1.1.3-3 [65.0 kB] Get:250 http://localhost:3142/debian sid/main arm64 libsimbody3.7 arm64 3.7+dfsg-3 [2638 kB] Get:251 http://localhost:3142/debian sid/main arm64 libsimbody-dev arm64 3.7+dfsg-3 [2727 kB] Get:252 http://localhost:3142/debian sid/main arm64 libsimtkmolmodel3.1 arm64 3.1.0-2 [579 kB] Get:253 http://localhost:3142/debian sid/main arm64 libsimtkmolmodel-dev arm64 3.1.0-2 [1863 kB] Get:254 http://localhost:3142/debian sid/main arm64 libsimtkmolmodel-plugins arm64 3.1.0-2 [16.3 kB] Get:255 http://localhost:3142/debian sid/main arm64 libstb0 arm64 0.0~git20220908.8b5f1f3+ds-1 [194 kB] Get:256 http://localhost:3142/debian sid/main arm64 libstb-dev arm64 0.0~git20220908.8b5f1f3+ds-1 [576 kB] Get:257 http://localhost:3142/debian sid/main arm64 libstdc++-11-dev arm64 11.3.0-12 [1927 kB] Get:258 http://localhost:3142/debian sid/main amd64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] Get:259 http://localhost:3142/debian sid/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 188 MB in 1s (172 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 15279 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-5_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... 15609 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../2-libncursesw6_6.4-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.4-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../3-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../4-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../5-libsqlite3-0_3.40.1-2_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.40.1-2) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... 16060 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../002-libproc2-0_2%3a4.0.3-1_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.3-1) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.3-1_amd64.deb ... Unpacking procps (2:4.0.3-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../006-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../009-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../012-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package ucf. Preparing to unpack .../014-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package asciidoc-common. Preparing to unpack .../015-asciidoc-common_10.2.0-1_all.deb ... Unpacking asciidoc-common (10.2.0-1) ... Selecting previously unselected package xml-core. Preparing to unpack .../016-xml-core_0.18+nmu1_all.deb ... Unpacking xml-core (0.18+nmu1) ... Selecting previously unselected package docbook-xsl. Preparing to unpack .../017-docbook-xsl_1.79.2+dfsg-2_all.deb ... Unpacking docbook-xsl (1.79.2+dfsg-2) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../018-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../019-libxml2_2.9.14+dfsg-1.1+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package libxml2-utils. Preparing to unpack .../020-libxml2-utils_2.9.14+dfsg-1.1+b3_amd64.deb ... Unpacking libxml2-utils (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package libxslt1.1:amd64. Preparing to unpack .../021-libxslt1.1_1.1.35-1_amd64.deb ... Unpacking libxslt1.1:amd64 (1.1.35-1) ... Selecting previously unselected package xsltproc. Preparing to unpack .../022-xsltproc_1.1.35-1_amd64.deb ... Unpacking xsltproc (1.1.35-1) ... Selecting previously unselected package asciidoc-base. Preparing to unpack .../023-asciidoc-base_10.2.0-1_all.deb ... Unpacking asciidoc-base (10.2.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../024-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../025-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../026-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../027-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../028-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package binutils-aarch64-linux-gnu. Preparing to unpack .../029-binutils-aarch64-linux-gnu_2.40-2_amd64.deb ... Unpacking binutils-aarch64-linux-gnu (2.40-2) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../030-libarchive13_3.6.2-1_amd64.deb ... Unpacking libarchive13:amd64 (3.6.2-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../031-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../032-libsasl2-modules-db_2.1.28+dfsg-11_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-11) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../033-libsasl2-2_2.1.28+dfsg-11_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-11) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../034-libldap-2.5-0_2.5.13+dfsg-5_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../035-libnghttp2-14_1.52.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.52.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../036-libpsl5_0.21.2-1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.2-1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../037-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../038-libssh2-1_1.10.0-3+b1_amd64.deb ... Unpacking libssh2-1:amd64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../039-libcurl4_7.88.1-8_amd64.deb ... Unpacking libcurl4:amd64 (7.88.1-8) ... Selecting previously unselected package libjsoncpp25:amd64. Preparing to unpack .../040-libjsoncpp25_1.9.5-4_amd64.deb ... Unpacking libjsoncpp25:amd64 (1.9.5-4) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../041-librhash0_1.4.3-3_amd64.deb ... Unpacking librhash0:amd64 (1.4.3-3) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../042-libuv1_1.44.2-1_amd64.deb ... Unpacking libuv1:amd64 (1.44.2-1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../043-cmake-data_3.25.1-1_all.deb ... Unpacking cmake-data (3.25.1-1) ... Selecting previously unselected package cmake. Preparing to unpack .../044-cmake_3.25.1-1_amd64.deb ... Unpacking cmake (3.25.1-1) ... Selecting previously unselected package gcc-12-aarch64-linux-gnu-base:amd64. Preparing to unpack .../045-gcc-12-aarch64-linux-gnu-base_12.2.0-14cross1_amd64.deb ... Unpacking gcc-12-aarch64-linux-gnu-base:amd64 (12.2.0-14cross1) ... Selecting previously unselected package cpp-12-aarch64-linux-gnu. Preparing to unpack .../046-cpp-12-aarch64-linux-gnu_12.2.0-14cross1_amd64.deb ... Unpacking cpp-12-aarch64-linux-gnu (12.2.0-14cross1) ... Selecting previously unselected package cpp-aarch64-linux-gnu. Preparing to unpack .../047-cpp-aarch64-linux-gnu_4%3a12.2.0-3_amd64.deb ... Unpacking cpp-aarch64-linux-gnu (4:12.2.0-3) ... Selecting previously unselected package cross-config. Preparing to unpack .../048-cross-config_2.6.20_all.deb ... Unpacking cross-config (2.6.20) ... Selecting previously unselected package gcc-12-cross-base. Preparing to unpack .../049-gcc-12-cross-base_12.2.0-14cross1_all.deb ... Unpacking gcc-12-cross-base (12.2.0-14cross1) ... Selecting previously unselected package libc6-arm64-cross. Preparing to unpack .../050-libc6-arm64-cross_2.36-8cross1_all.deb ... Unpacking libc6-arm64-cross (2.36-8cross1) ... Selecting previously unselected package libgcc-s1-arm64-cross. Preparing to unpack .../051-libgcc-s1-arm64-cross_12.2.0-14cross1_all.deb ... Unpacking libgcc-s1-arm64-cross (12.2.0-14cross1) ... Selecting previously unselected package libgomp1-arm64-cross. Preparing to unpack .../052-libgomp1-arm64-cross_12.2.0-14cross1_all.deb ... Unpacking libgomp1-arm64-cross (12.2.0-14cross1) ... Selecting previously unselected package libitm1-arm64-cross. Preparing to unpack .../053-libitm1-arm64-cross_12.2.0-14cross1_all.deb ... Unpacking libitm1-arm64-cross (12.2.0-14cross1) ... Selecting previously unselected package libatomic1-arm64-cross. Preparing to unpack .../054-libatomic1-arm64-cross_12.2.0-14cross1_all.deb ... Unpacking libatomic1-arm64-cross (12.2.0-14cross1) ... Selecting previously unselected package libasan8-arm64-cross. Preparing to unpack .../055-libasan8-arm64-cross_12.2.0-14cross1_all.deb ... Unpacking libasan8-arm64-cross (12.2.0-14cross1) ... Selecting previously unselected package liblsan0-arm64-cross. Preparing to unpack .../056-liblsan0-arm64-cross_12.2.0-14cross1_all.deb ... Unpacking liblsan0-arm64-cross (12.2.0-14cross1) ... Selecting previously unselected package libtsan2-arm64-cross. Preparing to unpack .../057-libtsan2-arm64-cross_12.2.0-14cross1_all.deb ... Unpacking libtsan2-arm64-cross (12.2.0-14cross1) ... Selecting previously unselected package libstdc++6-arm64-cross. Preparing to unpack .../058-libstdc++6-arm64-cross_12.2.0-14cross1_all.deb ... Unpacking libstdc++6-arm64-cross (12.2.0-14cross1) ... Selecting previously unselected package libubsan1-arm64-cross. Preparing to unpack .../059-libubsan1-arm64-cross_12.2.0-14cross1_all.deb ... Unpacking libubsan1-arm64-cross (12.2.0-14cross1) ... Selecting previously unselected package libhwasan0-arm64-cross. Preparing to unpack .../060-libhwasan0-arm64-cross_12.2.0-14cross1_all.deb ... Unpacking libhwasan0-arm64-cross (12.2.0-14cross1) ... Selecting previously unselected package libgcc-12-dev-arm64-cross. Preparing to unpack .../061-libgcc-12-dev-arm64-cross_12.2.0-14cross1_all.deb ... Unpacking libgcc-12-dev-arm64-cross (12.2.0-14cross1) ... Selecting previously unselected package gcc-12-aarch64-linux-gnu. Preparing to unpack .../062-gcc-12-aarch64-linux-gnu_12.2.0-14cross1_amd64.deb ... Unpacking gcc-12-aarch64-linux-gnu (12.2.0-14cross1) ... Selecting previously unselected package gcc-aarch64-linux-gnu. Preparing to unpack .../063-gcc-aarch64-linux-gnu_4%3a12.2.0-3_amd64.deb ... Unpacking gcc-aarch64-linux-gnu (4:12.2.0-3) ... Selecting previously unselected package linux-libc-dev-arm64-cross. Preparing to unpack .../064-linux-libc-dev-arm64-cross_6.1.4-1cross1_all.deb ... Unpacking linux-libc-dev-arm64-cross (6.1.4-1cross1) ... Selecting previously unselected package libc6-dev-arm64-cross. Preparing to unpack .../065-libc6-dev-arm64-cross_2.36-8cross1_all.deb ... Unpacking libc6-dev-arm64-cross (2.36-8cross1) ... Selecting previously unselected package libstdc++-12-dev-arm64-cross. Preparing to unpack .../066-libstdc++-12-dev-arm64-cross_12.2.0-14cross1_all.deb ... Unpacking libstdc++-12-dev-arm64-cross (12.2.0-14cross1) ... Selecting previously unselected package g++-12-aarch64-linux-gnu. Preparing to unpack .../067-g++-12-aarch64-linux-gnu_12.2.0-14cross1_amd64.deb ... Unpacking g++-12-aarch64-linux-gnu (12.2.0-14cross1) ... Selecting previously unselected package g++-aarch64-linux-gnu. Preparing to unpack .../068-g++-aarch64-linux-gnu_4%3a12.2.0-3_amd64.deb ... Unpacking g++-aarch64-linux-gnu (4:12.2.0-3) ... Selecting previously unselected package libconfig-inifiles-perl. Preparing to unpack .../069-libconfig-inifiles-perl_3.000003-2_all.deb ... Unpacking libconfig-inifiles-perl (3.000003-2) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../070-libio-string-perl_1.08-4_all.deb ... Unpacking libio-string-perl (1.08-4) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../071-libxml-namespacesupport-perl_1.12-2_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-2) ... Selecting previously unselected package libxml-sax-base-perl. Preparing to unpack .../072-libxml-sax-base-perl_1.09-3_all.deb ... Unpacking libxml-sax-base-perl (1.09-3) ... Selecting previously unselected package libxml-sax-perl. Preparing to unpack .../073-libxml-sax-perl_1.02+dfsg-3_all.deb ... Unpacking libxml-sax-perl (1.02+dfsg-3) ... Selecting previously unselected package libxml-libxml-perl. Preparing to unpack .../074-libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b1_amd64.deb ... Unpacking libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b1) ... Selecting previously unselected package libxml-simple-perl. Preparing to unpack .../075-libxml-simple-perl_2.25-2_all.deb ... Unpacking libxml-simple-perl (2.25-2) ... Selecting previously unselected package libyaml-perl. Preparing to unpack .../076-libyaml-perl_1.30-2_all.deb ... Unpacking libyaml-perl (1.30-2) ... Selecting previously unselected package libconfig-auto-perl. Preparing to unpack .../077-libconfig-auto-perl_0.44-2_all.deb ... Unpacking libconfig-auto-perl (0.44-2) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../078-libfile-which-perl_1.27-2_all.deb ... Unpacking libfile-which-perl (1.27-2) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../079-libfile-homedir-perl_1.006-2_all.deb ... Unpacking libfile-homedir-perl (1.006-2) ... Selecting previously unselected package libdebian-dpkgcross-perl. Preparing to unpack .../080-libdebian-dpkgcross-perl_2.6.20_all.deb ... Unpacking libdebian-dpkgcross-perl (2.6.20) ... Selecting previously unselected package dpkg-cross. Preparing to unpack .../081-dpkg-cross_2.6.20_all.deb ... Unpacking dpkg-cross (2.6.20) ... Selecting previously unselected package crossbuild-essential-arm64. Preparing to unpack .../082-crossbuild-essential-arm64_12.9_all.deb ... Unpacking crossbuild-essential-arm64 (12.9) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../083-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../084-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../085-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../086-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../087-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../088-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../089-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../090-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../091-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package gettext. Preparing to unpack .../092-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../093-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../094-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../095-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package sgml-data. Preparing to unpack .../096-sgml-data_2.0.11+nmu1_all.deb ... Unpacking sgml-data (2.0.11+nmu1) ... Selecting previously unselected package docbook-xml. Preparing to unpack .../097-docbook-xml_4.5-12_all.deb ... Unpacking docbook-xml (4.5-12) ... Selecting previously unselected package gcc-12-base:arm64. Preparing to unpack .../098-gcc-12-base_12.2.0-14_arm64.deb ... Unpacking gcc-12-base:arm64 (12.2.0-14) ... Selecting previously unselected package libgcc-s1:arm64. Preparing to unpack .../099-libgcc-s1_12.2.0-14_arm64.deb ... Unpacking libgcc-s1:arm64 (12.2.0-14) ... Selecting previously unselected package libc6:arm64. Preparing to unpack .../100-libc6_2.36-9_arm64.deb ... Unpacking libc6:arm64 (2.36-9) ... Selecting previously unselected package libglvnd0:arm64. Preparing to unpack .../101-libglvnd0_1.6.0-1_arm64.deb ... Unpacking libglvnd0:arm64 (1.6.0-1) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../102-libxau6_1%3a1.0.9-1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.9-1) ... Selecting previously unselected package libmd0:arm64. Preparing to unpack .../103-libmd0_1.0.4-2_arm64.deb ... Unpacking libmd0:arm64 (1.0.4-2) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../104-libbsd0_0.11.7-4_arm64.deb ... Unpacking libbsd0:arm64 (0.11.7-4) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../105-libxdmcp6_1%3a1.1.2-3_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../106-libxcb1_1.15-1_arm64.deb ... Unpacking libxcb1:arm64 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../107-libx11-data_2%3a1.8.4-2_all.deb ... Unpacking libx11-data (2:1.8.4-2) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../108-libx11-6_2%3a1.8.4-2_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.4-2) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../109-libdrm-common_2.4.114-1_all.deb ... Unpacking libdrm-common (2.4.114-1) ... Selecting previously unselected package libdrm2:arm64. Preparing to unpack .../110-libdrm2_2.4.114-1+b1_arm64.deb ... Unpacking libdrm2:arm64 (2.4.114-1+b1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../111-libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package libglapi-mesa:arm64. Preparing to unpack .../112-libglapi-mesa_22.3.6-1+deb12u1_arm64.deb ... Unpacking libglapi-mesa:arm64 (22.3.6-1+deb12u1) ... Selecting previously unselected package libx11-xcb1:arm64. Preparing to unpack .../113-libx11-xcb1_2%3a1.8.4-2_arm64.deb ... Unpacking libx11-xcb1:arm64 (2:1.8.4-2) ... Selecting previously unselected package libxcb-dri2-0:arm64. Preparing to unpack .../114-libxcb-dri2-0_1.15-1_arm64.deb ... Unpacking libxcb-dri2-0:arm64 (1.15-1) ... Selecting previously unselected package libxcb-dri3-0:arm64. Preparing to unpack .../115-libxcb-dri3-0_1.15-1_arm64.deb ... Unpacking libxcb-dri3-0:arm64 (1.15-1) ... Selecting previously unselected package libxcb-glx0:arm64. Preparing to unpack .../116-libxcb-glx0_1.15-1_arm64.deb ... Unpacking libxcb-glx0:arm64 (1.15-1) ... Selecting previously unselected package libxcb-present0:arm64. Preparing to unpack .../117-libxcb-present0_1.15-1_arm64.deb ... Unpacking libxcb-present0:arm64 (1.15-1) ... Selecting previously unselected package libxcb-randr0:arm64. Preparing to unpack .../118-libxcb-randr0_1.15-1_arm64.deb ... Unpacking libxcb-randr0:arm64 (1.15-1) ... Selecting previously unselected package libxcb-shm0:arm64. Preparing to unpack .../119-libxcb-shm0_1.15-1_arm64.deb ... Unpacking libxcb-shm0:arm64 (1.15-1) ... Selecting previously unselected package libxcb-sync1:arm64. Preparing to unpack .../120-libxcb-sync1_1.15-1_arm64.deb ... Unpacking libxcb-sync1:arm64 (1.15-1) ... Selecting previously unselected package libxcb-xfixes0:arm64. Preparing to unpack .../121-libxcb-xfixes0_1.15-1_arm64.deb ... Unpacking libxcb-xfixes0:arm64 (1.15-1) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../122-libxext6_2%3a1.3.4-1+b1_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxfixes3:arm64. Preparing to unpack .../123-libxfixes3_1%3a6.0.0-2_arm64.deb ... Unpacking libxfixes3:arm64 (1:6.0.0-2) ... Selecting previously unselected package libxshmfence1:arm64. Preparing to unpack .../124-libxshmfence1_1.3-1_arm64.deb ... Unpacking libxshmfence1:arm64 (1.3-1) ... Selecting previously unselected package libxxf86vm1:arm64. Preparing to unpack .../125-libxxf86vm1_1%3a1.1.4-1+b2_arm64.deb ... Unpacking libxxf86vm1:arm64 (1:1.1.4-1+b2) ... Selecting previously unselected package libdrm-amdgpu1:arm64. Preparing to unpack .../126-libdrm-amdgpu1_2.4.114-1+b1_arm64.deb ... Unpacking libdrm-amdgpu1:arm64 (2.4.114-1+b1) ... Selecting previously unselected package libdrm-nouveau2:arm64. Preparing to unpack .../127-libdrm-nouveau2_2.4.114-1+b1_arm64.deb ... Unpacking libdrm-nouveau2:arm64 (2.4.114-1+b1) ... Selecting previously unselected package libdrm-radeon1:arm64. Preparing to unpack .../128-libdrm-radeon1_2.4.114-1+b1_arm64.deb ... Unpacking libdrm-radeon1:arm64 (2.4.114-1+b1) ... Selecting previously unselected package zlib1g:arm64. Preparing to unpack .../129-zlib1g_1%3a1.2.13.dfsg-1_arm64.deb ... Unpacking zlib1g:arm64 (1:1.2.13.dfsg-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../130-libelf1_0.188-2.1_arm64.deb ... Unpacking libelf1:arm64 (0.188-2.1) ... Selecting previously unselected package libtinfo6:arm64. Preparing to unpack .../131-libtinfo6_6.4-2_arm64.deb ... Unpacking libtinfo6:arm64 (6.4-2) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../132-libedit2_3.1-20221030-2_arm64.deb ... Unpacking libedit2:arm64 (3.1-20221030-2) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../133-libffi8_3.4.4-1_arm64.deb ... Unpacking libffi8:arm64 (3.4.4-1) ... Selecting previously unselected package libstdc++6:arm64. Preparing to unpack .../134-libstdc++6_12.2.0-14_arm64.deb ... Unpacking libstdc++6:arm64 (12.2.0-14) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../135-libicu72_72.1-3_arm64.deb ... Unpacking libicu72:arm64 (72.1-3) ... Selecting previously unselected package liblzma5:arm64. Preparing to unpack .../136-liblzma5_5.4.1-0.2_arm64.deb ... Unpacking liblzma5:arm64 (5.4.1-0.2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../137-libxml2_2.9.14+dfsg-1.1+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package libz3-4:arm64. Preparing to unpack .../138-libz3-4_4.8.12-3.1_arm64.deb ... Unpacking libz3-4:arm64 (4.8.12-3.1) ... Selecting previously unselected package libllvm15:arm64. Preparing to unpack .../139-libllvm15_1%3a15.0.7-4_arm64.deb ... Unpacking libllvm15:arm64 (1:15.0.7-4) ... Selecting previously unselected package libsensors-config. Preparing to unpack .../140-libsensors-config_1%3a3.6.0-7.1_all.deb ... Unpacking libsensors-config (1:3.6.0-7.1) ... Selecting previously unselected package libsensors5:arm64. Preparing to unpack .../141-libsensors5_1%3a3.6.0-7.1_arm64.deb ... Unpacking libsensors5:arm64 (1:3.6.0-7.1) ... Selecting previously unselected package libzstd1:arm64. Preparing to unpack .../142-libzstd1_1.5.4+dfsg2-5_arm64.deb ... Unpacking libzstd1:arm64 (1.5.4+dfsg2-5) ... Selecting previously unselected package libgl1-mesa-dri:arm64. Preparing to unpack .../143-libgl1-mesa-dri_22.3.6-1+deb12u1_arm64.deb ... Unpacking libgl1-mesa-dri:arm64 (22.3.6-1+deb12u1) ... Selecting previously unselected package libglx-mesa0:arm64. Preparing to unpack .../144-libglx-mesa0_22.3.6-1+deb12u1_arm64.deb ... Unpacking libglx-mesa0:arm64 (22.3.6-1+deb12u1) ... Selecting previously unselected package libglx0:arm64. Preparing to unpack .../145-libglx0_1.6.0-1_arm64.deb ... Unpacking libglx0:arm64 (1.6.0-1) ... Selecting previously unselected package libgl1:arm64. Preparing to unpack .../146-libgl1_1.6.0-1_arm64.deb ... Unpacking libgl1:arm64 (1.6.0-1) ... Selecting previously unselected package libxi6:arm64. Preparing to unpack .../147-libxi6_2%3a1.8-1+b1_arm64.deb ... Unpacking libxi6:arm64 (2:1.8-1+b1) ... Selecting previously unselected package libglut3.12:arm64. Preparing to unpack .../148-libglut3.12_3.4.0-1_arm64.deb ... Unpacking libglut3.12:arm64 (3.4.0-1) ... Selecting previously unselected package xorg-sgml-doctools. Preparing to unpack .../149-xorg-sgml-doctools_1%3a1.11-1.1_all.deb ... Unpacking xorg-sgml-doctools (1:1.11-1.1) ... Selecting previously unselected package x11proto-dev. Preparing to unpack .../150-x11proto-dev_2022.1-1_all.deb ... Unpacking x11proto-dev (2022.1-1) ... Selecting previously unselected package libxau-dev:arm64. Preparing to unpack .../151-libxau-dev_1%3a1.0.9-1_arm64.deb ... Unpacking libxau-dev:arm64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp-dev:arm64. Preparing to unpack .../152-libxdmcp-dev_1%3a1.1.2-3_arm64.deb ... Unpacking libxdmcp-dev:arm64 (1:1.1.2-3) ... Selecting previously unselected package xtrans-dev. Preparing to unpack .../153-xtrans-dev_1.4.0-1_all.deb ... Unpacking xtrans-dev (1.4.0-1) ... Selecting previously unselected package libpthread-stubs0-dev:arm64. Preparing to unpack .../154-libpthread-stubs0-dev_0.4-1_arm64.deb ... Unpacking libpthread-stubs0-dev:arm64 (0.4-1) ... Selecting previously unselected package libxcb1-dev:arm64. Preparing to unpack .../155-libxcb1-dev_1.15-1_arm64.deb ... Unpacking libxcb1-dev:arm64 (1.15-1) ... Selecting previously unselected package libx11-dev:arm64. Preparing to unpack .../156-libx11-dev_2%3a1.8.4-2_arm64.deb ... Unpacking libx11-dev:arm64 (2:1.8.4-2) ... Selecting previously unselected package libglx-dev:arm64. Preparing to unpack .../157-libglx-dev_1.6.0-1_arm64.deb ... Unpacking libglx-dev:arm64 (1.6.0-1) ... Selecting previously unselected package libgl-dev:arm64. Preparing to unpack .../158-libgl-dev_1.6.0-1_arm64.deb ... Unpacking libgl-dev:arm64 (1.6.0-1) ... Selecting previously unselected package libglvnd-core-dev:arm64. Preparing to unpack .../159-libglvnd-core-dev_1.6.0-1_arm64.deb ... Unpacking libglvnd-core-dev:arm64 (1.6.0-1) ... Selecting previously unselected package libwayland-server0:arm64. Preparing to unpack .../160-libwayland-server0_1.21.0-1_arm64.deb ... Unpacking libwayland-server0:arm64 (1.21.0-1) ... Selecting previously unselected package libgbm1:arm64. Preparing to unpack .../161-libgbm1_22.3.6-1+deb12u1_arm64.deb ... Unpacking libgbm1:arm64 (22.3.6-1+deb12u1) ... Selecting previously unselected package libwayland-client0:arm64. Preparing to unpack .../162-libwayland-client0_1.21.0-1_arm64.deb ... Unpacking libwayland-client0:arm64 (1.21.0-1) ... Selecting previously unselected package libegl-mesa0:arm64. Preparing to unpack .../163-libegl-mesa0_22.3.6-1+deb12u1_arm64.deb ... Unpacking libegl-mesa0:arm64 (22.3.6-1+deb12u1) ... Selecting previously unselected package libegl1:arm64. Preparing to unpack .../164-libegl1_1.6.0-1_arm64.deb ... Unpacking libegl1:arm64 (1.6.0-1) ... Selecting previously unselected package libegl-dev:arm64. Preparing to unpack .../165-libegl-dev_1.6.0-1_arm64.deb ... Unpacking libegl-dev:arm64 (1.6.0-1) ... Selecting previously unselected package libgles1:arm64. Preparing to unpack .../166-libgles1_1.6.0-1_arm64.deb ... Unpacking libgles1:arm64 (1.6.0-1) ... Selecting previously unselected package libgles2:arm64. Preparing to unpack .../167-libgles2_1.6.0-1_arm64.deb ... Unpacking libgles2:arm64 (1.6.0-1) ... Selecting previously unselected package libgles-dev:arm64. Preparing to unpack .../168-libgles-dev_1.6.0-1_arm64.deb ... Unpacking libgles-dev:arm64 (1.6.0-1) ... Selecting previously unselected package libopengl0:arm64. Preparing to unpack .../169-libopengl0_1.6.0-1_arm64.deb ... Unpacking libopengl0:arm64 (1.6.0-1) ... Selecting previously unselected package libopengl-dev:arm64. Preparing to unpack .../170-libopengl-dev_1.6.0-1_arm64.deb ... Unpacking libopengl-dev:arm64 (1.6.0-1) ... Selecting previously unselected package libglvnd-dev:arm64. Preparing to unpack .../171-libglvnd-dev_1.6.0-1_arm64.deb ... Unpacking libglvnd-dev:arm64 (1.6.0-1) ... Selecting previously unselected package libgl1-mesa-dev:arm64. Preparing to unpack .../172-libgl1-mesa-dev_22.3.6-1+deb12u1_arm64.deb ... Unpacking libgl1-mesa-dev:arm64 (22.3.6-1+deb12u1) ... Selecting previously unselected package libglu1-mesa:arm64. Preparing to unpack .../173-libglu1-mesa_9.0.2-1.1_arm64.deb ... Unpacking libglu1-mesa:arm64 (9.0.2-1.1) ... Selecting previously unselected package libglu1-mesa-dev:arm64. Preparing to unpack .../174-libglu1-mesa-dev_9.0.2-1.1_arm64.deb ... Unpacking libglu1-mesa-dev:arm64 (9.0.2-1.1) ... Selecting previously unselected package libxext-dev:arm64. Preparing to unpack .../175-libxext-dev_2%3a1.3.4-1+b1_arm64.deb ... Unpacking libxext-dev:arm64 (2:1.3.4-1+b1) ... Selecting previously unselected package x11-common. Preparing to unpack .../176-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package libice6:arm64. Preparing to unpack .../177-libice6_2%3a1.0.10-1_arm64.deb ... Unpacking libice6:arm64 (2:1.0.10-1) ... Selecting previously unselected package libuuid1:arm64. Preparing to unpack .../178-libuuid1_2.38.1-5+b1_arm64.deb ... Unpacking libuuid1:arm64 (2.38.1-5+b1) ... Selecting previously unselected package libsm6:arm64. Preparing to unpack .../179-libsm6_2%3a1.2.3-1_arm64.deb ... Unpacking libsm6:arm64 (2:1.2.3-1) ... Selecting previously unselected package libxt6:arm64. Preparing to unpack .../180-libxt6_1%3a1.2.1-1.1_arm64.deb ... Unpacking libxt6:arm64 (1:1.2.1-1.1) ... Selecting previously unselected package libice-dev:arm64. Preparing to unpack .../181-libice-dev_2%3a1.0.10-1_arm64.deb ... Unpacking libice-dev:arm64 (2:1.0.10-1) ... Selecting previously unselected package libsm-dev:arm64. Preparing to unpack .../182-libsm-dev_2%3a1.2.3-1_arm64.deb ... Unpacking libsm-dev:arm64 (2:1.2.3-1) ... Selecting previously unselected package libxt-dev:arm64. Preparing to unpack .../183-libxt-dev_1%3a1.2.1-1.1_arm64.deb ... Unpacking libxt-dev:arm64 (1:1.2.1-1.1) ... Selecting previously unselected package libglut-dev:arm64. Preparing to unpack .../184-libglut-dev_3.4.0-1_arm64.deb ... Unpacking libglut-dev:arm64 (3.4.0-1) ... Selecting previously unselected package freeglut3-dev:arm64. Preparing to unpack .../185-freeglut3-dev_3.4.0-1_arm64.deb ... Unpacking freeglut3-dev:arm64 (3.4.0-1) ... Selecting previously unselected package gcc-11-base:arm64. Preparing to unpack .../186-gcc-11-base_11.3.0-12_arm64.deb ... Unpacking gcc-11-base:arm64 (11.3.0-12) ... Selecting previously unselected package gemmi-dev:arm64. Preparing to unpack .../187-gemmi-dev_0.5.7+ds-2+b1_arm64.deb ... Unpacking gemmi-dev:arm64 (0.5.7+ds-2+b1) ... Selecting previously unselected package libasan6:arm64. Preparing to unpack .../188-libasan6_11.3.0-12_arm64.deb ... Unpacking libasan6:arm64 (11.3.0-12) ... Selecting previously unselected package libatomic1:arm64. Preparing to unpack .../189-libatomic1_12.2.0-14_arm64.deb ... Unpacking libatomic1:arm64 (12.2.0-14) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../190-libblas3_3.11.0-2_arm64.deb ... Unpacking libblas3:arm64 (3.11.0-2) ... Selecting previously unselected package libblas-dev:arm64. Preparing to unpack .../191-libblas-dev_3.11.0-2_arm64.deb ... Unpacking libblas-dev:arm64 (3.11.0-2) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../192-libbsd0_0.11.7-4_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-4) ... Selecting previously unselected package linux-libc-dev:arm64. Preparing to unpack .../193-linux-libc-dev_6.1.20-2_arm64.deb ... Unpacking linux-libc-dev:arm64 (6.1.20-2) ... Selecting previously unselected package libcrypt1:arm64. Preparing to unpack .../194-libcrypt1_1%3a4.4.33-2_arm64.deb ... Unpacking libcrypt1:arm64 (1:4.4.33-2) ... Selecting previously unselected package libcrypt-dev:arm64. Preparing to unpack .../195-libcrypt-dev_1%3a4.4.33-2_arm64.deb ... Unpacking libcrypt-dev:arm64 (1:4.4.33-2) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../196-libcom-err2_1.47.0-2_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.0-2) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../197-libkrb5support0_1.20.1-1+b1_arm64.deb ... Unpacking libkrb5support0:arm64 (1.20.1-1+b1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../198-libk5crypto3_1.20.1-1+b1_arm64.deb ... Unpacking libk5crypto3:arm64 (1.20.1-1+b1) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../199-libkeyutils1_1.6.3-2_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-2) ... Selecting previously unselected package libssl3:arm64. Preparing to unpack .../200-libssl3_3.0.8-1_arm64.deb ... Unpacking libssl3:arm64 (3.0.8-1) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../201-libkrb5-3_1.20.1-1+b1_arm64.deb ... Unpacking libkrb5-3:arm64 (1.20.1-1+b1) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../202-libgssapi-krb5-2_1.20.1-1+b1_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.20.1-1+b1) ... Selecting previously unselected package libtirpc3:arm64. Preparing to unpack .../203-libtirpc3_1.3.3+ds-1_arm64.deb ... Unpacking libtirpc3:arm64 (1.3.3+ds-1) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../204-libnsl2_1.3.0-2_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-2) ... Selecting previously unselected package libtirpc-dev:arm64. Preparing to unpack .../205-libtirpc-dev_1.3.3+ds-1_arm64.deb ... Unpacking libtirpc-dev:arm64 (1.3.3+ds-1) ... Selecting previously unselected package libnsl-dev:arm64. Preparing to unpack .../206-libnsl-dev_1.3.0-2_arm64.deb ... Unpacking libnsl-dev:arm64 (1.3.0-2) ... Selecting previously unselected package libc6-dev:arm64. Preparing to unpack .../207-libc6-dev_2.36-9_arm64.deb ... Unpacking libc6-dev:arm64 (2.36-9) ... Selecting previously unselected package libgomp1:arm64. Preparing to unpack .../208-libgomp1_12.2.0-14_arm64.deb ... Unpacking libgomp1:arm64 (12.2.0-14) ... Selecting previously unselected package libitm1:arm64. Preparing to unpack .../209-libitm1_12.2.0-14_arm64.deb ... Unpacking libitm1:arm64 (12.2.0-14) ... Selecting previously unselected package liblsan0:arm64. Preparing to unpack .../210-liblsan0_12.2.0-14_arm64.deb ... Unpacking liblsan0:arm64 (12.2.0-14) ... Selecting previously unselected package libtsan0:arm64. Preparing to unpack .../211-libtsan0_11.3.0-12_arm64.deb ... Unpacking libtsan0:arm64 (11.3.0-12) ... Selecting previously unselected package libubsan1:arm64. Preparing to unpack .../212-libubsan1_12.2.0-14_arm64.deb ... Unpacking libubsan1:arm64 (12.2.0-14) ... Selecting previously unselected package libhwasan0:arm64. Preparing to unpack .../213-libhwasan0_12.2.0-14_arm64.deb ... Unpacking libhwasan0:arm64 (12.2.0-14) ... Selecting previously unselected package libgcc-11-dev:arm64. Preparing to unpack .../214-libgcc-11-dev_11.3.0-12_arm64.deb ... Unpacking libgcc-11-dev:arm64 (11.3.0-12) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../215-libgfortran5_12.2.0-14_arm64.deb ... Unpacking libgfortran5:arm64 (12.2.0-14) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../216-liblapack3_3.11.0-2_arm64.deb ... Unpacking liblapack3:arm64 (3.11.0-2) ... Selecting previously unselected package liblapack-dev:arm64. Preparing to unpack .../217-liblapack-dev_3.11.0-2_arm64.deb ... Unpacking liblapack-dev:arm64 (3.11.0-2) ... Selecting previously unselected package libopenmm7.7:arm64. Preparing to unpack .../218-libopenmm7.7_7.7.0+dfsg-9+b1_arm64.deb ... Unpacking libopenmm7.7:arm64 (7.7.0+dfsg-9+b1) ... Selecting previously unselected package libopenmm-dev:arm64. Preparing to unpack .../219-libopenmm-dev_7.7.0+dfsg-9+b1_arm64.deb ... Unpacking libopenmm-dev:arm64 (7.7.0+dfsg-9+b1) ... Selecting previously unselected package libpthread-stubs0-dev:amd64. Preparing to unpack .../220-libpthread-stubs0-dev_0.4-1_amd64.deb ... Unpacking libpthread-stubs0-dev:amd64 (0.4-1) ... Selecting previously unselected package libseqan2-dev. Preparing to unpack .../221-libseqan2-dev_2.4.0+dfsg-15_all.deb ... Unpacking libseqan2-dev (2.4.0+dfsg-15) ... Selecting previously unselected package libxfixes-dev:arm64. Preparing to unpack .../222-libxfixes-dev_1%3a6.0.0-2_arm64.deb ... Unpacking libxfixes-dev:arm64 (1:6.0.0-2) ... Selecting previously unselected package libxi-dev:arm64. Preparing to unpack .../223-libxi-dev_2%3a1.8-1+b1_arm64.deb ... Unpacking libxi-dev:arm64 (2:1.8-1+b1) ... Selecting previously unselected package libxmu6:arm64. Preparing to unpack .../224-libxmu6_2%3a1.1.3-3_arm64.deb ... Unpacking libxmu6:arm64 (2:1.1.3-3) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../225-libxau6_1%3a1.0.9-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../226-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../227-libxcb1_1.15-1_amd64.deb ... Unpacking libxcb1:amd64 (1.15-1) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../228-libx11-6_2%3a1.8.4-2_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.4-2) ... Selecting previously unselected package libxau-dev:amd64. Preparing to unpack .../229-libxau-dev_1%3a1.0.9-1_amd64.deb ... Unpacking libxau-dev:amd64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp-dev:amd64. Preparing to unpack .../230-libxdmcp-dev_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp-dev:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1-dev:amd64. Preparing to unpack .../231-libxcb1-dev_1.15-1_amd64.deb ... Unpacking libxcb1-dev:amd64 (1.15-1) ... Selecting previously unselected package libx11-dev:amd64. Preparing to unpack .../232-libx11-dev_2%3a1.8.4-2_amd64.deb ... Unpacking libx11-dev:amd64 (2:1.8.4-2) ... Selecting previously unselected package libxmu-headers. Preparing to unpack .../233-libxmu-headers_2%3a1.1.3-3_all.deb ... Unpacking libxmu-headers (2:1.1.3-3) ... Selecting previously unselected package libxmu-dev:arm64. Preparing to unpack .../234-libxmu-dev_2%3a1.1.3-3_arm64.deb ... Unpacking libxmu-dev:arm64 (2:1.1.3-3) ... Selecting previously unselected package libsimbody3.7:arm64. Preparing to unpack .../235-libsimbody3.7_3.7+dfsg-3_arm64.deb ... Unpacking libsimbody3.7:arm64 (3.7+dfsg-3) ... Selecting previously unselected package libsimbody-dev:arm64. Preparing to unpack .../236-libsimbody-dev_3.7+dfsg-3_arm64.deb ... Unpacking libsimbody-dev:arm64 (3.7+dfsg-3) ... Selecting previously unselected package libsimtkmolmodel3.1:arm64. Preparing to unpack .../237-libsimtkmolmodel3.1_3.1.0-2_arm64.deb ... Unpacking libsimtkmolmodel3.1:arm64 (3.1.0-2) ... Selecting previously unselected package libsimtkmolmodel-dev:arm64. Preparing to unpack .../238-libsimtkmolmodel-dev_3.1.0-2_arm64.deb ... Unpacking libsimtkmolmodel-dev:arm64 (3.1.0-2) ... Selecting previously unselected package libsimtkmolmodel-plugins:arm64. Preparing to unpack .../239-libsimtkmolmodel-plugins_3.1.0-2_arm64.deb ... Unpacking libsimtkmolmodel-plugins:arm64 (3.1.0-2) ... Selecting previously unselected package libstb0:arm64. Preparing to unpack .../240-libstb0_0.0~git20220908.8b5f1f3+ds-1_arm64.deb ... Unpacking libstb0:arm64 (0.0~git20220908.8b5f1f3+ds-1) ... Selecting previously unselected package libstb-dev:arm64. Preparing to unpack .../241-libstb-dev_0.0~git20220908.8b5f1f3+ds-1_arm64.deb ... Unpacking libstb-dev:arm64 (0.0~git20220908.8b5f1f3+ds-1) ... Selecting previously unselected package libstdc++-11-dev:arm64. Preparing to unpack .../242-libstdc++-11-dev_11.3.0-12_arm64.deb ... Unpacking libstdc++-11-dev:arm64 (11.3.0-12) ... Selecting previously unselected package tao-pegtl-dev. Preparing to unpack .../243-tao-pegtl-dev_3.2.7-1_all.deb ... Unpacking tao-pegtl-dev (3.2.7-1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../244-zlib1g-dev_1%3a1.2.13.dfsg-1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Selecting previously unselected package sbuild-build-depends-main-dummy:arm64. Preparing to unpack .../245-sbuild-build-depends-main-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-main-dummy:arm64 (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000003-2) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up gcc-11-base:arm64 (11.3.0-12) ... Setting up libfile-which-perl (1.27-2) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up gcc-12-cross-base (12.2.0-14cross1) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libglvnd-core-dev:arm64 (1.6.0-1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up gcc-12-aarch64-linux-gnu-base:amd64 (12.2.0-14cross1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up gemmi-dev:arm64 (0.5.7+ds-2+b1) ... Setting up libsqlite3-0:amd64 (3.40.1-2) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of restart. Setting up libsensors-config (1:3.6.0-7.1) ... Setting up libnghttp2-14:amd64 (1.52.0-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up linux-libc-dev:arm64 (6.1.20-2) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up binutils-aarch64-linux-gnu (2.40-2) ... Setting up file (1:5.44-3) ... Setting up libyaml-perl (1.30-2) ... Setting up libpthread-stubs0-dev:amd64 (0.4-1) ... Setting up libpthread-stubs0-dev:arm64 (0.4-1) ... Setting up gcc-12-base:arm64 (12.2.0-14) ... Setting up libseqan2-dev (2.4.0+dfsg-15) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-11) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up cross-config (2.6.20) ... Setting up libuv1:amd64 (1.44.2-1) ... Setting up libx11-data (2:1.8.4-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libc6-arm64-cross (2.36-8cross1) ... Setting up libproc2-0:amd64 (2:4.0.3-1) ... Setting up autopoint (0.21-12) ... Setting up libjsoncpp25:amd64 (1.9.5-4) ... Setting up libitm1-arm64-cross (12.2.0-14cross1) ... Setting up libncursesw6:amd64 (6.4-2) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-11) ... Setting up autoconf (2.71-3) ... Setting up linux-libc-dev-arm64-cross (6.1.4-1cross1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up librhash0:amd64 (1.4.3-3) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up procps (2:4.0.3-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... 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 libfile-homedir-perl (1.006-2) ... Setting up libbsd0:amd64 (0.11.7-4) ... Setting up libdrm-common (2.4.114-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Setting up liblocale-gettext-perl (1.07-5) ... Setting up tao-pegtl-dev (3.2.7-1) ... Setting up libgcc-s1-arm64-cross (12.2.0-14cross1) ... Setting up libatomic1-arm64-cross (12.2.0-14cross1) ... 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 liblsan0-arm64-cross (12.2.0-14cross1) ... Setting up libgomp1-arm64-cross (12.2.0-14cross1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up cpp-12-aarch64-linux-gnu (12.2.0-14cross1) ... Setting up libxau-dev:amd64 (1:1.0.9-1) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:amd64 (3.6.2-1) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libhwasan0-arm64-cross (12.2.0-14cross1) ... Setting up libc6-dev-arm64-cross (2.36-8cross1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libstdc++6-arm64-cross (12.2.0-14cross1) ... Setting up dh-autoreconf (20) ... Setting up libxdmcp-dev:amd64 (1:1.1.2-3) ... Setting up cpp-aarch64-linux-gnu (4:12.2.0-3) ... Setting up ucf (3.0043+nmu1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up xml-core (0.18+nmu1) ... Setting up libxslt1.1:amd64 (1.1.35-1) ... Setting up libcurl4:amd64 (7.88.1-8) ... Setting up libx11-6:amd64 (2:1.8.4-2) ... Setting up libasan8-arm64-cross (12.2.0-14cross1) ... Setting up libxml2-utils (2.9.14+dfsg-1.1+b3) ... Setting up libtsan2-arm64-cross (12.2.0-14cross1) ... Setting up libxcb1-dev:amd64 (1.15-1) ... Setting up libubsan1-arm64-cross (12.2.0-14cross1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up xsltproc (1.1.35-1) ... Setting up libx11-dev:amd64 (2:1.8.4-2) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libgcc-12-dev-arm64-cross (12.2.0-14cross1) ... Setting up gcc-12-aarch64-linux-gnu (12.2.0-14cross1) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up cmake (3.25.1-1) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up gcc-aarch64-linux-gnu (4:12.2.0-3) ... Setting up python3.11 (3.11.2-6) ... Setting up libxmu-headers (2:1.1.3-3) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libstdc++-12-dev-arm64-cross (12.2.0-14cross1) ... Setting up asciidoc-common (10.2.0-1) ... Setting up libxml-simple-perl (2.25-2) ... Setting up g++-12-aarch64-linux-gnu (12.2.0-14cross1) ... Setting up libconfig-auto-perl (0.44-2) ... Setting up g++-aarch64-linux-gnu (4:12.2.0-3) ... Setting up libdebian-dpkgcross-perl (2.6.20) ... Setting up dpkg-cross (2.6.20) ... Setting up crossbuild-essential-arm64 (12.9) ... Setting up libgcc-s1:arm64 (12.2.0-14) ... Setting up libc6:arm64 (2.36-9) ... Setting up libffi8:arm64 (3.4.4-1) ... Setting up libdrm2:arm64 (2.4.114-1+b1) ... Setting up libmd0:arm64 (1.0.4-2) ... Setting up libxshmfence1:arm64 (1.3-1) ... Setting up libhwasan0:arm64 (12.2.0-14) ... Setting up libbsd0:arm64 (0.11.7-4) ... Setting up libstdc++6:arm64 (12.2.0-14) ... Setting up liblsan0:arm64 (12.2.0-14) ... Setting up libitm1:arm64 (12.2.0-14) ... Setting up libtinfo6:arm64 (6.4-2) ... Setting up libdrm-amdgpu1:arm64 (2.4.114-1+b1) ... Setting up libtsan0:arm64 (11.3.0-12) ... Setting up libwayland-client0:arm64 (1.21.0-1) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up libwayland-server0:arm64 (1.21.0-1) ... Setting up libzstd1:arm64 (1.5.4+dfsg2-5) ... Setting up libice6:arm64 (2:1.0.10-1) ... Setting up libxau6:arm64 (1:1.0.9-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3) ... Setting up libkeyutils1:arm64 (1.6.3-2) ... Setting up libdrm-nouveau2:arm64 (2.4.114-1+b1) ... Setting up libxcb1:arm64 (1.15-1) ... Setting up libicu72:arm64 (72.1-3) ... Setting up libxcb-xfixes0:arm64 (1.15-1) ... Setting up libxau-dev:arm64 (1:1.0.9-1) ... Setting up liblzma5:arm64 (5.4.1-0.2) ... Setting up libopenmm7.7:arm64 (7.7.0+dfsg-9+b1) ... Setting up libice-dev:arm64 (2:1.0.10-1) ... Setting up libgbm1:arm64 (22.3.6-1+deb12u1) ... Setting up libdrm-radeon1:arm64 (2.4.114-1+b1) ... Setting up libglvnd0:arm64 (1.6.0-1) ... Setting up libxcb-glx0:arm64 (1.15-1) ... Setting up libedit2:arm64 (3.1-20221030-2) ... Setting up libssl3:arm64 (3.0.8-1) ... Setting up zlib1g:arm64 (1:1.2.13.dfsg-1) ... Setting up libcrypt1:arm64 (1:4.4.33-2) ... Setting up libxcb-shm0:arm64 (1.15-1) ... Setting up libcom-err2:arm64 (1.47.0-2) ... Setting up libgomp1:arm64 (12.2.0-14) ... Setting up libopenmm-dev:arm64 (7.7.0+dfsg-9+b1) ... Setting up libopengl0:arm64 (1.6.0-1) ... Setting up libasan6:arm64 (11.3.0-12) ... Setting up libkrb5support0:arm64 (1.20.1-1+b1) ... Setting up libxcb-present0:arm64 (1.15-1) ... Setting up libxdmcp-dev:arm64 (1:1.1.2-3) ... Setting up libz3-4:arm64 (4.8.12-3.1) ... Setting up libblas3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libgles2:arm64 (1.6.0-1) ... Setting up libxcb-sync1:arm64 (1.15-1) ... Setting up libgles1:arm64 (1.6.0-1) ... Setting up libstb0:arm64 (0.0~git20220908.8b5f1f3+ds-1) ... Setting up libatomic1:arm64 (12.2.0-14) ... Setting up libuuid1:arm64 (2.38.1-5+b1) ... Setting up libsensors5:arm64 (1:3.6.0-7.1) ... Setting up libk5crypto3:arm64 (1.20.1-1+b1) ... Setting up libglapi-mesa:arm64 (22.3.6-1+deb12u1) ... Setting up libgfortran5:arm64 (12.2.0-14) ... Setting up libubsan1:arm64 (12.2.0-14) ... Setting up libxcb-dri2-0:arm64 (1.15-1) ... Setting up libgcc-11-dev:arm64 (11.3.0-12) ... Setting up libstb-dev:arm64 (0.0~git20220908.8b5f1f3+ds-1) ... Setting up libcrypt-dev:arm64 (1:4.4.33-2) ... Setting up libxcb-randr0:arm64 (1.15-1) ... Setting up libx11-6:arm64 (2:1.8.4-2) ... Setting up libkrb5-3:arm64 (1.20.1-1+b1) ... Setting up libglu1-mesa:arm64 (9.0.2-1.1) ... Setting up libopengl-dev:arm64 (1.6.0-1) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up libsm6:arm64 (2:1.2.3-1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Setting up libblas-dev:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up libxcb-dri3-0:arm64 (1.15-1) ... Setting up libx11-xcb1:arm64 (2:1.8.4-2) ... Setting up liblapack3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1-dev:arm64 (1.15-1) ... Setting up libsm-dev:arm64 (2:1.2.3-1) ... Setting up libx11-dev:arm64 (2:1.8.4-2) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up libxxf86vm1:arm64 (1:1.1.4-1+b2) ... Setting up libegl-mesa0:arm64 (22.3.6-1+deb12u1) ... Setting up libxfixes3:arm64 (1:6.0.0-2) ... Setting up liblapack-dev:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:arm64 (1.20.1-1+b1) ... Setting up libxt6:arm64 (1:1.2.1-1.1) ... Setting up libxext-dev:arm64 (2:1.3.4-1+b1) ... Setting up libllvm15:arm64 (1:15.0.7-4) ... Setting up libegl1:arm64 (1.6.0-1) ... Setting up libtirpc3:arm64 (1.3.3+ds-1) ... Setting up libxmu6:arm64 (2:1.1.3-3) ... Setting up libxi6:arm64 (2:1.8-1+b1) ... Setting up libgl1-mesa-dri:arm64 (22.3.6-1+deb12u1) ... Setting up libxfixes-dev:arm64 (1:6.0.0-2) ... Setting up libtirpc-dev:arm64 (1.3.3+ds-1) ... Setting up libxt-dev:arm64 (1:1.2.1-1.1) ... Setting up libnsl2:arm64 (1.3.0-2) ... Setting up libxi-dev:arm64 (2:1.8-1+b1) ... Setting up libglx-mesa0:arm64 (22.3.6-1+deb12u1) ... Setting up libglx0:arm64 (1.6.0-1) ... Setting up libxmu-dev:arm64 (2:1.1.3-3) ... Setting up libgl1:arm64 (1.6.0-1) ... Setting up libglut3.12:arm64 (3.4.0-1) ... Setting up libnsl-dev:arm64 (1.3.0-2) ... Setting up libsimbody3.7:arm64 (3.7+dfsg-3) ... Setting up libc6-dev:arm64 (2.36-9) ... Setting up libglx-dev:arm64 (1.6.0-1) ... Setting up libgl-dev:arm64 (1.6.0-1) ... Setting up libsimtkmolmodel3.1:arm64 (3.1.0-2) ... Setting up libegl-dev:arm64 (1.6.0-1) ... Setting up libglu1-mesa-dev:arm64 (9.0.2-1.1) ... Setting up libstdc++-11-dev:arm64 (11.3.0-12) ... Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Setting up libgles-dev:arm64 (1.6.0-1) ... Setting up libsimtkmolmodel-plugins:arm64 (3.1.0-2) ... Setting up libsimtkmolmodel-dev:arm64 (3.1.0-2) ... Setting up libglvnd-dev:arm64 (1.6.0-1) ... Setting up libgl1-mesa-dev:arm64 (22.3.6-1+deb12u1) ... Setting up libglut-dev:arm64 (3.4.0-1) ... Setting up freeglut3-dev:arm64 (3.4.0-1) ... Setting up libsimbody-dev:arm64 (3.7+dfsg-3) ... Processing triggers for libc-bin (2.36-9) ... 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:arm64 (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) amd64 (x86_64) Toolchain package versions: binutils_2.40-2 dpkg-dev_1.21.21 g++-11_11.3.0-12 g++-12_12.2.0-14 gcc-11_11.3.0-12 gcc-12_12.2.0-14 libc6-dev_2.36-9 libstdc++-11-dev_11.3.0-12 libstdc++-12-dev_12.2.0-14 libstdc++-12-dev-arm64-cross_12.2.0-14cross1 libstdc++6_12.2.0-14 libstdc++6-arm64-cross_12.2.0-14cross1 linux-libc-dev_6.1.20-2 Package versions: adduser_3.132 apt_2.6.0 asciidoc-base_10.2.0-1 asciidoc-common_10.2.0-1 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-12 autotools-dev_20220109.1 base-files_12.4 base-passwd_3.6.1 bash_5.2.15-2+b1 binutils_2.40-2 binutils-aarch64-linux-gnu_2.40-2 binutils-common_2.40-2 binutils-x86-64-linux-gnu_2.40-2 bsdextrautils_2.38.1-5+b1 bsdutils_1:2.38.1-5+b1 build-essential_12.9 bzip2_1.0.8-5+b1 cmake_3.25.1-1 cmake-data_3.25.1-1 coreutils_9.1-1 cpp_4:12.2.0-3 cpp-11_11.3.0-12 cpp-12_12.2.0-14 cpp-12-aarch64-linux-gnu_12.2.0-14cross1 cpp-aarch64-linux-gnu_4:12.2.0-3 cross-config_2.6.20 crossbuild-essential-arm64_12.9 dash_0.5.12-2 debconf_1.5.82 debhelper_13.11.4 debian-archive-keyring_2023.3 debianutils_5.7-0.4 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 docbook-xml_4.5-12 docbook-xsl_1.79.2+dfsg-2 dpkg_1.21.21 dpkg-cross_2.6.20 dpkg-dev_1.21.21 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.31-1.2 file_1:5.44-3 findutils_4.9.0-4 freeglut3-dev_3.4.0-1 g++_4:12.2.0-3 g++-11_11.3.0-12 g++-12_12.2.0-14 g++-12-aarch64-linux-gnu_12.2.0-14cross1 g++-aarch64-linux-gnu_4:12.2.0-3 gcc_4:12.2.0-3 gcc-11_11.3.0-12 gcc-11-base_11.3.0-12 gcc-12_12.2.0-14 gcc-12-aarch64-linux-gnu_12.2.0-14cross1 gcc-12-aarch64-linux-gnu-base_12.2.0-14cross1 gcc-12-base_12.2.0-14 gcc-12-cross-base_12.2.0-14cross1 gcc-9-base_9.5.0-3 gcc-aarch64-linux-gnu_4:12.2.0-3 gemmi-dev_0.5.7+ds-2+b1 gettext_0.21-12 gettext-base_0.21-12 gpgv_2.2.40-1.1 grep_3.8-5 groff-base_1.22.4-10 gzip_1.12-1 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapt-pkg6.0_2.6.0 libarchive-zip-perl_1.68-1 libarchive13_3.6.2-1 libasan6_11.3.0-12 libasan8_12.2.0-14 libasan8-arm64-cross_12.2.0-14cross1 libatomic1_12.2.0-14 libatomic1-arm64-cross_12.2.0-14cross1 libattr1_1:2.5.1-4 libaudit-common_1:3.0.9-1 libaudit1_1:3.0.9-1 libbinutils_2.40-2 libblas-dev_3.11.0-2 libblas3_3.11.0-2 libblkid1_2.38.1-5+b1 libbrotli1_1.0.9-2+b6 libbsd0_0.11.7-4 libbz2-1.0_1.0.8-5+b1 libc-bin_2.36-9 libc-dev-bin_2.36-9 libc6_2.36-9 libc6-arm64-cross_2.36-8cross1 libc6-dev_2.36-9 libc6-dev-arm64-cross_2.36-8cross1 libcap-ng0_0.8.3-1+b3 libcap2_1:2.66-3 libcc1-0_12.2.0-14 libcom-err2_1.47.0-2 libconfig-auto-perl_0.44-2 libconfig-inifiles-perl_3.000003-2 libcrypt-dev_1:4.4.33-2 libcrypt1_1:4.4.33-2 libctf-nobfd0_2.40-2 libctf0_2.40-2 libcurl4_7.88.1-8 libdb5.3_5.3.28+dfsg2-1 libdebconfclient0_0.268 libdebhelper-perl_13.11.4 libdebian-dpkgcross-perl_2.6.20 libdpkg-perl_1.21.21 libdrm-amdgpu1_2.4.114-1+b1 libdrm-common_2.4.114-1 libdrm-nouveau2_2.4.114-1+b1 libdrm-radeon1_2.4.114-1+b1 libdrm2_2.4.114-1+b1 libedit2_3.1-20221030-2 libegl-dev_1.6.0-1 libegl-mesa0_22.3.6-1+deb12u1 libegl1_1.6.0-1 libelf1_0.188-2.1 libexpat1_2.5.0-1 libext2fs2_1.47.0-2 libfakeroot_1.31-1.2 libffi8_3.4.4-1 libfile-find-rule-perl_0.34-3 libfile-homedir-perl_1.006-2 libfile-stripnondeterminism-perl_1.13.1-1 libfile-which-perl_1.27-2 libgbm1_22.3.6-1+deb12u1 libgcc-11-dev_11.3.0-12 libgcc-12-dev_12.2.0-14 libgcc-12-dev-arm64-cross_12.2.0-14cross1 libgcc-s1_12.2.0-14 libgcc-s1-arm64-cross_12.2.0-14cross1 libgcrypt20_1.10.1-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_12.2.0-14 libgl-dev_1.6.0-1 libgl1_1.6.0-1 libgl1-mesa-dev_22.3.6-1+deb12u1 libgl1-mesa-dri_22.3.6-1+deb12u1 libglapi-mesa_22.3.6-1+deb12u1 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_22.3.6-1+deb12u1 libglx0_1.6.0-1 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.9-1 libgomp1_12.2.0-14 libgomp1-arm64-cross_12.2.0-14cross1 libgpg-error0_1.46-1 libgprofng0_2.40-2 libgssapi-krb5-2_1.20.1-1+b1 libhogweed6_3.8.1-2 libhwasan0_12.2.0-14 libhwasan0-arm64-cross_12.2.0-14cross1 libice-dev_2:1.0.10-1 libice6_2:1.0.10-1 libicu72_72.1-3 libidn2-0_2.3.3-1+b1 libio-string-perl_1.08-4 libisl23_0.25-1 libitm1_12.2.0-14 libitm1-arm64-cross_12.2.0-14cross1 libjansson4_2.14-2 libjsoncpp25_1.9.5-4 libk5crypto3_1.20.1-1+b1 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-1+b1 libkrb5support0_1.20.1-1+b1 liblapack-dev_3.11.0-2 liblapack3_3.11.0-2 libldap-2.5-0_2.5.13+dfsg-5 libllvm15_1:15.0.7-4 liblocale-gettext-perl_1.07-5 liblsan0_12.2.0-14 liblsan0-arm64-cross_12.2.0-14cross1 liblz4-1_1.9.4-1 liblzma5_5.4.1-0.2 libmagic-mgc_1:5.44-3 libmagic1_1:5.44-3 libmd0_1.0.4-2 libmount1_2.38.1-5+b1 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libncursesw6_6.4-2 libnettle8_3.8.1-2 libnghttp2-14_1.52.0-1 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnumber-compare-perl_0.03-3 libopengl-dev_1.6.0-1 libopengl0_1.6.0-1 libopenmm-dev_7.7.0+dfsg-9+b1 libopenmm7.7_7.7.0+dfsg-9+b1 libp11-kit0_0.24.1-2 libpam-modules_1.5.2-6 libpam-modules-bin_1.5.2-6 libpam-runtime_1.5.2-6 libpam0g_1.5.2-6 libpcre2-8-0_10.42-1 libpcre3_2:8.39-15 libperl5.34_5.34.0-5 libperl5.36_5.36.0-7 libpipeline1_1.5.7-1 libproc2-0_2:4.0.3-1 libpsl5_0.21.2-1 libpthread-stubs0-dev_0.4-1 libpython3-stdlib_3.11.2-1+b1 libpython3.11-minimal_3.11.2-6 libpython3.11-stdlib_3.11.2-6 libquadmath0_12.2.0-14 libreadline8_8.2-1.3 librhash0_1.4.3-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-11 libsasl2-modules-db_2.1.28+dfsg-11 libseccomp2_2.5.4-1+b3 libselinux1_3.4-1+b5 libsemanage-common_3.4-1 libsemanage2_3.4-1+b5 libsensors-config_1:3.6.0-7.1 libsensors5_1:3.6.0-7.1 libsepol2_3.4-2 libseqan2-dev_2.4.0+dfsg-15 libsimbody-dev_3.7+dfsg-3 libsimbody3.7_3.7+dfsg-3 libsimtkmolmodel-dev_3.1.0-2 libsimtkmolmodel-plugins_3.1.0-2 libsimtkmolmodel3.1_3.1.0-2 libsm-dev_2:1.2.3-1 libsm6_2:1.2.3-1 libsmartcols1_2.38.1-5+b1 libsqlite3-0_3.40.1-2 libss2_1.47.0-2 libssh2-1_1.10.0-3+b1 libssl3_3.0.8-1 libstb-dev_0.0~git20220908.8b5f1f3+ds-1 libstb0_0.0~git20220908.8b5f1f3+ds-1 libstdc++-11-dev_11.3.0-12 libstdc++-12-dev_12.2.0-14 libstdc++-12-dev-arm64-cross_12.2.0-14cross1 libstdc++6_12.2.0-14 libstdc++6-arm64-cross_12.2.0-14cross1 libsub-override-perl_0.09-4 libsystemd0_252.6-1 libtasn1-6_4.19.0-2 libtext-glob-perl_0.11-3 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 libtsan0_11.3.0-12 libtsan2_12.2.0-14 libtsan2-arm64-cross_12.2.0-14cross1 libubsan1_12.2.0-14 libubsan1-arm64-cross_12.2.0-14cross1 libuchardet0_0.0.7-1 libudev1_252.6-1 libunistring2_1.0-2 libuuid1_2.38.1-5+b1 libuv1_1.44.2-1 libwayland-client0_1.21.0-1 libwayland-server0_1.21.0-1 libx11-6_2:1.8.4-2 libx11-data_2:1.8.4-2 libx11-dev_2:1.8.4-2 libx11-xcb1_2:1.8.4-2 libxau-dev_1:1.0.9-1 libxau6_1:1.0.9-1 libxcb-dri2-0_1.15-1 libxcb-dri3-0_1.15-1 libxcb-glx0_1.15-1 libxcb-present0_1.15-1 libxcb-randr0_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_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext-dev_2:1.3.4-1+b1 libxext6_2:1.3.4-1+b1 libxfixes-dev_1:6.0.0-2 libxfixes3_1:6.0.0-2 libxi-dev_2:1.8-1+b1 libxi6_2:1.8-1+b1 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b1 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-2 libxml2_2.9.14+dfsg-1.1+b3 libxml2-utils_2.9.14+dfsg-1.1+b3 libxmu-dev_2:1.1.3-3 libxmu-headers_2:1.1.3-3 libxmu6_2:1.1.3-3 libxshmfence1_1.3-1 libxslt1.1_1.1.35-1 libxt-dev_1:1.2.1-1.1 libxt6_1:1.2.1-1.1 libxxf86vm1_1:1.1.4-1+b2 libxxhash0_0.8.1-1 libyaml-perl_1.30-2 libz3-4_4.8.12-3.1 libzstd1_1.5.4+dfsg2-5 linux-libc-dev_6.1.20-2 linux-libc-dev-arm64-cross_6.1.4-1cross1 login_1:4.13+dfsg1-1+b1 logsave_1.47.0-2 m4_1.4.19-3 make_4.3-4.1 man-db_2.11.2-2 mawk_1.3.4.20200120-3.1 media-types_10.0.0 mount_2.38.1-5+b1 ncurses-base_6.4-2 ncurses-bin_6.4-2 passwd_1:4.13+dfsg1-1+b1 patch_2.7.6-7 perl_5.36.0-7 perl-base_5.36.0-7 perl-modules-5.34_5.34.0-5 perl-modules-5.36_5.36.0-7 po-debconf_1.0.21+nmu1 procps_2:4.0.3-1 python3_3.11.2-1+b1 python3-minimal_3.11.2-1+b1 python3.11_3.11.2-6 python3.11-minimal_3.11.2-6 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.17+nmu1 sgml-base_1.31 sgml-data_2.0.11+nmu1 sysvinit-utils_3.06-4 tao-pegtl-dev_3.2.7-1 tar_1.34+dfsg-1.2 tzdata_2023c-2 ucf_3.0043+nmu1 usrmerge_35 util-linux_2.38.1-5+b1 util-linux-extra_2.38.1-5+b1 x11-common_1:7.7+23 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_5.4.1-0.2 zlib1g_1:1.2.13.dfsg-1 zlib1g-dev_1:1.2.13.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: macromoleculebuilder Binary: libmmb-dev, libmmb4.0, mmb, mmb-common Architecture: any all Version: 4.0.0+dfsg-2 Maintainer: Debichem Team Uploaders: Andrius Merkys , Homepage: https://simtk.org/projects/rnatoolbox Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/debichem-team/macromoleculebuilder Vcs-Git: https://salsa.debian.org/debichem-team/macromoleculebuilder.git 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 Package-List: libmmb-dev deb libdevel optional arch=any libmmb4.0 deb libs optional arch=any mmb deb science optional arch=any mmb-common deb science optional arch=all Checksums-Sha1: c37eccceb961f3e78d5b7145faf79ce425cf104e 2567256 macromoleculebuilder_4.0.0+dfsg.orig.tar.xz b50806d1a7f0dcf9c2987b1419b63757365a490d 4240 macromoleculebuilder_4.0.0+dfsg-2.debian.tar.xz Checksums-Sha256: 2f50d11c886c36fd18476f942d7521536ded599584e0d83462a63ba5f9ccc449 2567256 macromoleculebuilder_4.0.0+dfsg.orig.tar.xz ba82afa6469b21a3668baab8b8fa19e7354fadddde38b601e8977aab43512430 4240 macromoleculebuilder_4.0.0+dfsg-2.debian.tar.xz Files: 951370d06adf03fb858edccdee43c075 2567256 macromoleculebuilder_4.0.0+dfsg.orig.tar.xz 173b7de595d3165989f43175a22a73f5 4240 macromoleculebuilder_4.0.0+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmOW7zISHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKHfTwP/jJTXmAoUwIHrjUxPTfgMk8K/q8xIYtv quZPN/OmA/Hur/9Px4W/XBW5Ra8e5rfse7KT4nqHg4wT+d5oN0PZq/s+0xVhvGL0 2MwLay63LrwsZxXtpak8YNiczuewHt2CdJf9E4MhgKeIIVSRVr+euBxIj7YupxAb 1maEqm67DjcbhNJHmnxQgEi5GkTNb85OOJakQGPuX6zw6dJit1MLOZ+88wKnYZSz CyM7T5fELyk9FVXrV9NYaVfcWccx0l6uvSfABobPGQWq93G1md1G9yI+KEVrxnAR y4/XQ4zOiSC9wRiB85tVxR7WO7+5K0o8/YKUeBl7avcaB9rEKLU3s8vJHxsSc/Dd E/hbMlExycJNzNcJ6GGbTocsagp7TfQ8jdMoN/BKdfFHdivc9gXhVtGl1WKiGKyp ZqT73cfsEHYbo2C4tlYuOEwtgZSYsHwhmB7cOf03QTvIqr1a2OkUPlPywtsjNEAl gQBGjkjgDK46io9Ew2M3otAsKRstMgXSJX8ZPQtma82YUZB8D7ip+LTDDeaXwGMb uYdjLyxvRO4oqmLh2svNrGxbmiz7Jl4kqaNcggSJIjgsoDJorz/MypUiHyLEXjal 4/H4rOiYeixHlaeJk9a4x5YHn+qM+3zZV9lbBa7Q2VaOoHspU76JnPV6Q/hkH+q8 fhH2wJrD0rgL =0Rl3 -----END PGP SIGNATURE----- gpgv: Signature made Mon Dec 12 09:06:58 2022 UTC gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./macromoleculebuilder_4.0.0+dfsg-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 CONFIG_SITE=/etc/dpkg-cross/cross-config.arm64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=crossqa PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=crossqa SCHROOT_SESSION_ID=sid-amd64-sbuild-3d0ac0cc-71f6-4ee1-b339-e8c5f39c32b9 SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aarm64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package macromoleculebuilder dpkg-buildpackage: info: source version 4.0.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-architecture: warning: specified GNU system type aarch64-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0" cd obj-aarch64-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_SYSTEM_NAME=Linux -DCMAKE_SYSTEM_PROCESSOR=aarch64 -DCMAKE_C_COMPILER=aarch64-linux-gnu-gcc -DCMAKE_CXX_COMPILER=aarch64-linux-gnu-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/aarch64-linux-gnu-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/aarch64-linux-gnu-pkg-config -DQMAKE_EXECUTABLE=/usr/bin/aarch64-linux-gnu-qmake -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DCMAKE_BUILD_TYPE=Release -DENABLE_LEPTON=OFF -DGEMMI_DIR=/usr -DOpenMM_INCLUDE_DIR=/usr/include -DSimTKmolmodel=/usr "-DCMAKE_CXX_FLAGS=-D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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/aarch64-linux-gnu-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMM: /usr/include -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.2.13") -- Found gemmi version 0.5.7 -- 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_C_COMPILER CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED PKGCONFIG_EXECUTABLE PKG_CONFIG_EXECUTABLE QMAKE_EXECUTABLE SimTKmolmodel -- Build files have been written to: /<>/obj-aarch64-linux-gnu make[1]: Leaving directory '/<>' dh_auto_build -a cd obj-aarch64-linux-gnu && make -j1 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<>/obj-aarch64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-aarch64-linux-gnu/CMakeFiles /<>/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-aarch64-linux-gnu' make -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/CMakeFiles/MMB.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 3%] Building CXX object CMakeFiles/MMB.dir/src/Utils.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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) | ^ /<>/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 [ 6%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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 /<>/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/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/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/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/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() ; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/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++) { | ~~^~~~~~~~~~~~~~~~~~~~~ /<>/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/SmallMatrix.h:93, from /usr/include/simbody/SimTKcommon/Simmatrix.h:37: In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)’ at /<>/src/BiopolymerClass.cpp:875:14: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)’: /<>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)’ at /<>/src/BiopolymerClass.cpp:875:14: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)’: /<>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)’ at /<>/src/BiopolymerClass.cpp:875:14: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)’: /<>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)’ at /<>/src/BiopolymerClass.cpp:876:44: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)’: /<>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)’ at /<>/src/BiopolymerClass.cpp:876:44: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)’: /<>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)’ at /<>/src/BiopolymerClass.cpp:876:44: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)’: /<>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ [ 9%] Building CXX object CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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) | ^ /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 [ 12%] Building CXX object CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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/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) | ^ /<>/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/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/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/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 /<>/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/SmallMatrix.h:93, from /usr/include/simbody/SimTKcommon/Simmatrix.h:37: In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Mat<3, 3> [1]’ [-Warray-bounds] 784 | { for(int i=0;i>/include/Utils.h:23: /usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’: /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& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Mat<3, 3> [1]’ [-Warray-bounds] 784 | { for(int i=0;i R(0.0); | ^ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Mat<3, 3> [1]’ [-Warray-bounds] 784 | { for(int i=0;i R(0.0); | ^ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:183:23: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Mat<3, 3> [1]’ [-Warray-bounds] 784 | { for(int i=0;i U(0.0); // initialize 2-d array | ^ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:183:23: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Mat<3, 3> [1]’ [-Warray-bounds] 784 | { for(int i=0;i U(0.0); // initialize 2-d array | ^ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:183:23: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Mat<3, 3> [1]’ [-Warray-bounds] 784 | { for(int i=0;i U(0.0); // initialize 2-d array | ^ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:201:24: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i’ of size 72 201 | rotation = Rotation(); | ^ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:201:24: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i’ of size 72 201 | rotation = Rotation(); | ^ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:201:24: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i’ of size 72 201 | rotation = Rotation(); | ^ [ 15%] Building CXX object CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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 /<>/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 /<>/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"; | ^~~~~~ [ 18%] Building CXX object CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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: 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/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 /<>/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/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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) | ^ 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"; | ^~~~~~ [ 25%] Building CXX object CMakeFiles/MMB.dir/src/DensityContainer.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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 /<>/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"; | ^~~~~~ [ 28%] Building CXX object CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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) | ^ 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: 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"; | ^~~~~~ [ 31%] Building CXX object CMakeFiles/MMB.dir/src/ContactContainer.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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) | ^ /<>/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/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 /<>/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"; | ^~~~~~ [ 34%] Building CXX object CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 /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: 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 /<>/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"; | ^~~~~~ [ 37%] Building CXX object CMakeFiles/MMB.dir/src/Repel.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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) | ^ 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();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/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 /<>/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::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++) { | ~~^~~~~~~~~~~~~~~~~~~~~ /<>/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] /<>/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"; | ^~~~~~ [ 40%] Building CXX object CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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) | ^ /<>/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 /<>/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"; | ^~~~~~ [ 43%] Building CXX object CMakeFiles/MMB.dir/src/Spiral.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/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 ; | ^~~~~~ /<>/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 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /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"; | ^~~~~~ [ 46%] Building CXX object CMakeFiles/MMB.dir/src/ParameterReader.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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) | ^ /<>/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/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()){ | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/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] /<>/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/SmallMatrix.h:93, from /usr/include/simbody/SimTKcommon/Simmatrix.h:37: In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

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

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

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

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2224:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72 2224 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2224:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72 2224 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2224:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72 2224 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2225:52: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72 2224 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2225:52: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72 2224 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2225:52: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72 2224 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

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

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

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

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2209:26: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72 2209 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2209:26: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72 2209 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2209:26: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72 2209 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2210:56: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72 2209 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2210:56: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72 2209 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<>/src/ParameterReader.cpp:2210:56: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’: /<>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72 2209 | Rotation myRotation; | ^~~~~~~~~~ [ 50%] Building CXX object CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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) | ^ 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 /<>/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"; | ^~~~~~ [ 53%] Building CXX object CMakeFiles/MMB.dir/src/TetherForce.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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) | ^ 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()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/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"; | ^~~~~~ [ 56%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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/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 /<>/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"; | ^~~~~~ In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93, from /usr/include/simbody/SimTKcommon/Simmatrix.h:37: In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

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

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

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

& SimTK::Rotation_

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

& SimTK::Rotation_

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

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:117:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72 116 | Rotation rotation2; | ^~~~~~~~~ /<>/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; | ^~~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:319:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72 319 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:319:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72 319 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:319:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72 319 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:320:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72 319 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:320:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72 319 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’ at /<>/src/BiopolymerClassTwoTransformForces.cpp:320:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds] 784 | { for(int i=0;i>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’: /<>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72 319 | Rotation rotation2; | ^~~~~~~~~ [ 59%] Building CXX object CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 /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/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++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/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 /<>/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/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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: 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. | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/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 /<>/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"; | ^~~~~~ [ 65%] Building CXX object CMakeFiles/MMB.dir/src/DensityForce.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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) | ^ 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();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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"; | ^~~~~~ [ 68%] Building CXX object CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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 /<>/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();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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"; | ^~~~~~ [ 71%] Building CXX object CMakeFiles/MMB.dir/src/MMBLogger.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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) | ^ /<>/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/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 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"; | ^~~~~~ [ 78%] Building CXX object CMakeFiles/MMB.dir/src/CifOutput.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 /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." | ^~~~~~~ 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) | ^ 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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ 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();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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"; | ^~~~~~ [ 81%] Building CXX object CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 [ 84%] Building CXX object CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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) | ^ 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(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /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"; | ^~~~~~ [ 87%] Building CXX object CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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) | ^ 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 /<>/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"; | ^~~~~~ [ 90%] Building CXX object CMakeFiles/MMB.dir/src/NtCForces.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 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) | ^ 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/aarch64-linux-gnu-g++ -fPIC -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -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/aarch64-linux-gnu/libSimTKmolmodel.so.3.1 /usr/lib/aarch64-linux-gnu/libOpenMM.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libSimTKsimbody.so.3.7 /usr/lib/aarch64-linux-gnu/libSimTKmath.so.3.7 /usr/lib/aarch64-linux-gnu/libSimTKcommon.so.3.7 /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-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-aarch64-linux-gnu' [ 93%] Built target MMB make -f CMakeFiles/MMB_EXEC.dir/build.make CMakeFiles/MMB_EXEC.dir/depend make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' cd /<>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu /<>/obj-aarch64-linux-gnu/CMakeFiles/MMB_EXEC.dir/DependInfo.cmake --color= make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' make -f CMakeFiles/MMB_EXEC.dir/build.make CMakeFiles/MMB_EXEC.dir/build make[3]: Entering directory '/<>/obj-aarch64-linux-gnu' [ 96%] Building CXX object CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o /usr/bin/aarch64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DUSE_MMB_CONSTEXPR -I/<>/obj-aarch64-linux-gnu -I/<> -I/<>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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/aarch64-linux-gnu-g++ -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -Wl,-z,relro CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o -o MMB -Wl,-rpath,/<>/obj-aarch64-linux-gnu: libMMB.so.4.0 /usr/lib/aarch64-linux-gnu/libSimTKmolmodel.so.3.1 /usr/lib/aarch64-linux-gnu/libSimTKsimbody.so.3.7 /usr/lib/aarch64-linux-gnu/libSimTKmath.so.3.7 /usr/lib/aarch64-linux-gnu/libSimTKcommon.so.3.7 /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lpthread -lrt -ldl -lm make[3]: Leaving directory '/<>/obj-aarch64-linux-gnu' [100%] Built target MMB_EXEC make[2]: Leaving directory '/<>/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/<>/obj-aarch64-linux-gnu' dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install -a cd obj-aarch64-linux-gnu && make -j1 install DESTDIR=/<>/macromoleculebuilder-4.0.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/obj-aarch64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-aarch64-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 -- Installing: /<>/debian/tmp/usr/include/MMB/ExportMacros.h -- Installing: /<>/debian/tmp/usr/include/MMB/ExtraMath.h -- Installing: /<>/debian/tmp/usr/include/MMB/GeometricCenter.h -- Installing: /<>/debian/tmp/usr/include/MMB/HarmonicVelocityRescalingThermostat.h -- Installing: /<>/debian/tmp/usr/include/MMB/Impossible.h -- Installing: /<>/debian/tmp/usr/include/MMB/KBBackboneTorsionForce.h -- Installing: /<>/debian/tmp/usr/include/MMB/Lepton.h -- Installing: /<>/debian/tmp/usr/include/MMB/LigandDroplet.h -- Installing: /<>/debian/tmp/usr/include/MMB/Ligands.h -- Installing: /<>/debian/tmp/usr/include/MMB/Ligands.sam.h -- Installing: /<>/debian/tmp/usr/include/MMB/MMBLogger.h -- Installing: /<>/debian/tmp/usr/include/MMB/MobilizerContainer.h -- Installing: /<>/debian/tmp/usr/include/MMB/MoleculeContainer.h -- Installing: /<>/debian/tmp/usr/include/MMB/MonoAtoms.h -- Installing: /<>/debian/tmp/usr/include/MMB/Mutation.h -- Installing: /<>/debian/tmp/usr/include/MMB/NTC_FORCE_CLASS.h -- 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/aarch64-linux-gnu/libMMB.so.4.0 -- Installing: /<>/debian/tmp/usr/lib/aarch64-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/aarch64-linux-gnu/cmake/mmb/MmbConfigVersion.cmake -- Installing: /<>/debian/tmp/usr/lib/aarch64-linux-gnu/cmake/mmb/MmbTargets.cmake -- Installing: /<>/debian/tmp/usr/lib/aarch64-linux-gnu/cmake/mmb/MmbTargets-release.cmake -- Installing: /<>/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig/mmb.pc make[1]: Leaving directory '/<>/obj-aarch64-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 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'libmmb-dev' in '../libmmb-dev_4.0.0+dfsg-2_arm64.deb'. dpkg-deb: building package 'libmmb4.0' in '../libmmb4.0_4.0.0+dfsg-2_arm64.deb'. dpkg-deb: building package 'libmmb4.0-dbgsym' in '../libmmb4.0-dbgsym_4.0.0+dfsg-2_arm64.deb'. dpkg-deb: building package 'mmb' in '../mmb_4.0.0+dfsg-2_arm64.deb'. dpkg-deb: building package 'mmb-dbgsym' in '../mmb-dbgsym_4.0.0+dfsg-2_arm64.deb'. dpkg-genbuildinfo --build=any -O../macromoleculebuilder_4.0.0+dfsg-2_arm64.buildinfo dpkg-genchanges --build=any -O../macromoleculebuilder_4.0.0+dfsg-2_arm64.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 2023-04-12T11:55:52Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ macromoleculebuilder_4.0.0+dfsg-2_arm64.changes: ------------------------------------------------ Format: 1.8 Date: Mon, 12 Dec 2022 04:04:16 -0500 Source: macromoleculebuilder Binary: libmmb-dev libmmb4.0 libmmb4.0-dbgsym mmb mmb-dbgsym Built-For-Profiles: cross nocheck Architecture: arm64 Version: 4.0.0+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debichem Team 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: 141a577b3d71ee2c5ac430146787de4b9be5804e 76384 libmmb-dev_4.0.0+dfsg-2_arm64.deb 6884de15d465a480c319678c5dee6d2f53207219 27492676 libmmb4.0-dbgsym_4.0.0+dfsg-2_arm64.deb 240c623e8aaf3988c337dc2a94145bdd87d3abad 976140 libmmb4.0_4.0.0+dfsg-2_arm64.deb eae7f415841db2c131bd69ff05c29770dbd93b25 10262 macromoleculebuilder_4.0.0+dfsg-2_arm64.buildinfo c92ba73d62d4d3e5cdf841230fd6095b2960da20 1605336 mmb-dbgsym_4.0.0+dfsg-2_arm64.deb de2000aa0150b6e25d6790b717f5c8b44d706ce0 27240 mmb_4.0.0+dfsg-2_arm64.deb Checksums-Sha256: 2f8f11ee5ed8fe500c399e2dc3db63ec4d2cf81e6290656044dcbc7533296ab2 76384 libmmb-dev_4.0.0+dfsg-2_arm64.deb 03a82391c5bdd00ee873edf3b16bfcee9f4c861ba91e7ed454c39ef23a73cf17 27492676 libmmb4.0-dbgsym_4.0.0+dfsg-2_arm64.deb 04718622b3604d4d24825c96a15511d21adc84d7043434a0e109dd32aec42001 976140 libmmb4.0_4.0.0+dfsg-2_arm64.deb 85c667a10654c3ff10b16716e2ca33a4ef7f1a8fe0ccd5364757aedd431a9879 10262 macromoleculebuilder_4.0.0+dfsg-2_arm64.buildinfo 0c96137973e00bea5cb8d22a39b1318193bced2ab3fa77bccb9d720bbd5d7e61 1605336 mmb-dbgsym_4.0.0+dfsg-2_arm64.deb b78690671ed4604c0ef00ebd136ca2b5594e4062c12a00acaf34991320ec6507 27240 mmb_4.0.0+dfsg-2_arm64.deb Files: ac763dea766abb9dead4dfbfd9e7dbfb 76384 libdevel optional libmmb-dev_4.0.0+dfsg-2_arm64.deb 7fbeef774466d6abb6b84d92d6df6419 27492676 debug optional libmmb4.0-dbgsym_4.0.0+dfsg-2_arm64.deb b3a5762d6ae9f96d781c3f4f3510908f 976140 libs optional libmmb4.0_4.0.0+dfsg-2_arm64.deb 083f6def8b8fef1287b08417f4f3d1f1 10262 science optional macromoleculebuilder_4.0.0+dfsg-2_arm64.buildinfo 5e8770bf1367b500f4f3073aeb1ea6f8 1605336 debug optional mmb-dbgsym_4.0.0+dfsg-2_arm64.deb d6aa363b1c339e73df4fbb078d11678e 27240 science optional mmb_4.0.0+dfsg-2_arm64.deb /<>/macromoleculebuilder_4.0.0+dfsg-2_arm64.changes.new could not be renamed to /<>/macromoleculebuilder_4.0.0+dfsg-2_arm64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: macromoleculebuilder Binary: libmmb-dev libmmb4.0 libmmb4.0-dbgsym mmb mmb-dbgsym Architecture: arm64 Version: 4.0.0+dfsg-2 Checksums-Md5: ac763dea766abb9dead4dfbfd9e7dbfb 76384 libmmb-dev_4.0.0+dfsg-2_arm64.deb 7fbeef774466d6abb6b84d92d6df6419 27492676 libmmb4.0-dbgsym_4.0.0+dfsg-2_arm64.deb b3a5762d6ae9f96d781c3f4f3510908f 976140 libmmb4.0_4.0.0+dfsg-2_arm64.deb 5e8770bf1367b500f4f3073aeb1ea6f8 1605336 mmb-dbgsym_4.0.0+dfsg-2_arm64.deb d6aa363b1c339e73df4fbb078d11678e 27240 mmb_4.0.0+dfsg-2_arm64.deb Checksums-Sha1: 141a577b3d71ee2c5ac430146787de4b9be5804e 76384 libmmb-dev_4.0.0+dfsg-2_arm64.deb 6884de15d465a480c319678c5dee6d2f53207219 27492676 libmmb4.0-dbgsym_4.0.0+dfsg-2_arm64.deb 240c623e8aaf3988c337dc2a94145bdd87d3abad 976140 libmmb4.0_4.0.0+dfsg-2_arm64.deb c92ba73d62d4d3e5cdf841230fd6095b2960da20 1605336 mmb-dbgsym_4.0.0+dfsg-2_arm64.deb de2000aa0150b6e25d6790b717f5c8b44d706ce0 27240 mmb_4.0.0+dfsg-2_arm64.deb Checksums-Sha256: 2f8f11ee5ed8fe500c399e2dc3db63ec4d2cf81e6290656044dcbc7533296ab2 76384 libmmb-dev_4.0.0+dfsg-2_arm64.deb 03a82391c5bdd00ee873edf3b16bfcee9f4c861ba91e7ed454c39ef23a73cf17 27492676 libmmb4.0-dbgsym_4.0.0+dfsg-2_arm64.deb 04718622b3604d4d24825c96a15511d21adc84d7043434a0e109dd32aec42001 976140 libmmb4.0_4.0.0+dfsg-2_arm64.deb 0c96137973e00bea5cb8d22a39b1318193bced2ab3fa77bccb9d720bbd5d7e61 1605336 mmb-dbgsym_4.0.0+dfsg-2_arm64.deb b78690671ed4604c0ef00ebd136ca2b5594e4062c12a00acaf34991320ec6507 27240 mmb_4.0.0+dfsg-2_arm64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 12 Apr 2023 11:55:52 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs 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 (= 0.21-12), autotools-dev (= 20220109.1), base-files (= 12.4), base-passwd (= 3.6.1), bash (= 5.2.15-2+b1), binutils (= 2.40-2), binutils-common (= 2.40-2), binutils-x86-64-linux-gnu (= 2.40-2), bsdextrautils (= 2.38.1-5+b1), bsdutils (= 1:2.38.1-5+b1), build-essential (= 12.9), bzip2 (= 1.0.8-5+b1), cmake (= 3.25.1-1), cmake-data (= 3.25.1-1), coreutils (= 9.1-1), cpp (= 4:12.2.0-3), cpp-11 (= 11.3.0-12), cpp-12 (= 12.2.0-14), dash (= 0.5.12-2), debconf (= 1.5.82), debhelper (= 13.11.4), debianutils (= 5.7-0.4), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.8-4), docbook-xml (= 4.5-12), docbook-xsl (= 1.79.2+dfsg-2), dpkg (= 1.21.21), dpkg-dev (= 1.21.21), dwz (= 0.15-1), file (= 1:5.44-3), findutils (= 4.9.0-4), freeglut3-dev (= 3.4.0-1), g++ (= 4:12.2.0-3), g++-12 (= 12.2.0-14), gcc (= 4:12.2.0-3), gcc-11 (= 11.3.0-12), gcc-11-base (= 11.3.0-12), gcc-12 (= 12.2.0-14), gcc-12-base (= 12.2.0-14), gemmi-dev (= 0.5.7+ds-2+b1), gettext (= 0.21-12), gettext-base (= 0.21-12), grep (= 3.8-5), groff-base (= 1.22.4-10), gzip (= 1.12-1), hostname (= 3.23+nmu1), 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 (= 3.6.2-1), libasan6 (= 11.3.0-12), libasan8 (= 12.2.0-14), libatomic1 (= 12.2.0-14), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.0.9-1), libaudit1 (= 1:3.0.9-1), libbinutils (= 2.40-2), libblas-dev (= 3.11.0-2), libblas3 (= 3.11.0-2), libblkid1 (= 2.38.1-5+b1), libbrotli1 (= 1.0.9-2+b6), libbsd0 (= 0.11.7-4), libbz2-1.0 (= 1.0.8-5+b1), libc-bin (= 2.36-9), libc-dev-bin (= 2.36-9), libc6 (= 2.36-9), libc6-dev (= 2.36-9), libcap-ng0 (= 0.8.3-1+b3), libcap2 (= 1:2.66-3), libcc1-0 (= 12.2.0-14), libcom-err2 (= 1.47.0-2), libcrypt-dev (= 1:4.4.33-2), libcrypt1 (= 1:4.4.33-2), libctf-nobfd0 (= 2.40-2), libctf0 (= 2.40-2), libcurl4 (= 7.88.1-8), libdb5.3 (= 5.3.28+dfsg2-1), libdebconfclient0 (= 0.268), libdebhelper-perl (= 13.11.4), libdpkg-perl (= 1.21.21), libdrm-amdgpu1 (= 2.4.114-1+b1), libdrm-common (= 2.4.114-1), libdrm-nouveau2 (= 2.4.114-1+b1), libdrm-radeon1 (= 2.4.114-1+b1), libdrm2 (= 2.4.114-1+b1), libedit2 (= 3.1-20221030-2), libegl-dev (= 1.6.0-1), libegl-mesa0 (= 22.3.6-1+deb12u1), libegl1 (= 1.6.0-1), libelf1 (= 0.188-2.1), libexpat1 (= 2.5.0-1), libffi8 (= 3.4.4-1), libfile-find-rule-perl (= 0.34-3), libfile-stripnondeterminism-perl (= 1.13.1-1), libgbm1 (= 22.3.6-1+deb12u1), libgcc-11-dev (= 11.3.0-12), libgcc-12-dev (= 12.2.0-14), libgcc-s1 (= 12.2.0-14), libgcrypt20 (= 1.10.1-3), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgfortran5 (= 12.2.0-14), libgl-dev (= 1.6.0-1), libgl1 (= 1.6.0-1), libgl1-mesa-dev (= 22.3.6-1+deb12u1), libgl1-mesa-dri (= 22.3.6-1+deb12u1), libglapi-mesa (= 22.3.6-1+deb12u1), 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 (= 22.3.6-1+deb12u1), libglx0 (= 1.6.0-1), libgmp10 (= 2:6.2.1+dfsg1-1.1), libgnutls30 (= 3.7.9-1), libgomp1 (= 12.2.0-14), libgpg-error0 (= 1.46-1), libgprofng0 (= 2.40-2), libgssapi-krb5-2 (= 1.20.1-1+b1), libhogweed6 (= 3.8.1-2), libice-dev (= 2:1.0.10-1), libice6 (= 2:1.0.10-1), libicu72 (= 72.1-3), libidn2-0 (= 2.3.3-1+b1), libisl23 (= 0.25-1), libitm1 (= 12.2.0-14), libjansson4 (= 2.14-2), libjsoncpp25 (= 1.9.5-4), libk5crypto3 (= 1.20.1-1+b1), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-1+b1), libkrb5support0 (= 1.20.1-1+b1), liblapack-dev (= 3.11.0-2), liblapack3 (= 3.11.0-2), libldap-2.5-0 (= 2.5.13+dfsg-5), libllvm15 (= 1:15.0.7-4), liblsan0 (= 12.2.0-14), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.1-0.2), libmagic-mgc (= 1:5.44-3), libmagic1 (= 1:5.44-3), libmd0 (= 1.0.4-2), libmount1 (= 2.38.1-5+b1), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.0-1), libncursesw6 (= 6.4-2), libnettle8 (= 3.8.1-2), libnghttp2-14 (= 1.52.0-1), libnsl-dev (= 1.3.0-2), libnsl2 (= 1.3.0-2), libnumber-compare-perl (= 0.03-3), libopengl-dev (= 1.6.0-1), libopengl0 (= 1.6.0-1), libopenmm-dev (= 7.7.0+dfsg-9+b1), libopenmm7.7 (= 7.7.0+dfsg-9+b1), libp11-kit0 (= 0.24.1-2), libpam-modules (= 1.5.2-6), libpam-modules-bin (= 1.5.2-6), libpam-runtime (= 1.5.2-6), libpam0g (= 1.5.2-6), libpcre2-8-0 (= 10.42-1), libperl5.36 (= 5.36.0-7), libpipeline1 (= 1.5.7-1), libproc2-0 (= 2:4.0.3-1), libpsl5 (= 0.21.2-1), libpthread-stubs0-dev (= 0.4-1), libpython3-stdlib (= 3.11.2-1+b1), libpython3.11-minimal (= 3.11.2-6), libpython3.11-stdlib (= 3.11.2-6), libquadmath0 (= 12.2.0-14), libreadline8 (= 8.2-1.3), librhash0 (= 1.4.3-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2), libsasl2-2 (= 2.1.28+dfsg-11), libsasl2-modules-db (= 2.1.28+dfsg-11), libseccomp2 (= 2.5.4-1+b3), libselinux1 (= 3.4-1+b5), libsensors-config (= 1:3.6.0-7.1), libsensors5 (= 1:3.6.0-7.1), libseqan2-dev (= 2.4.0+dfsg-15), libsimbody-dev (= 3.7+dfsg-3), libsimbody3.7 (= 3.7+dfsg-3), libsimtkmolmodel-dev (= 3.1.0-2), libsimtkmolmodel-plugins (= 3.1.0-2), libsimtkmolmodel3.1 (= 3.1.0-2), libsm-dev (= 2:1.2.3-1), libsm6 (= 2:1.2.3-1), libsmartcols1 (= 2.38.1-5+b1), libsqlite3-0 (= 3.40.1-2), libssh2-1 (= 1.10.0-3+b1), libssl3 (= 3.0.8-1), libstb-dev (= 0.0~git20220908.8b5f1f3+ds-1), libstb0 (= 0.0~git20220908.8b5f1f3+ds-1), libstdc++-12-dev (= 12.2.0-14), libstdc++6 (= 12.2.0-14), libsub-override-perl (= 0.09-4), libsystemd0 (= 252.6-1), libtasn1-6 (= 4.19.0-2), libtext-glob-perl (= 0.11-3), 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), libtsan0 (= 11.3.0-12), libtsan2 (= 12.2.0-14), libubsan1 (= 12.2.0-14), libuchardet0 (= 0.0.7-1), libudev1 (= 252.6-1), libunistring2 (= 1.0-2), libuuid1 (= 2.38.1-5+b1), libuv1 (= 1.44.2-1), libwayland-client0 (= 1.21.0-1), libwayland-server0 (= 1.21.0-1), libx11-6 (= 2:1.8.4-2), libx11-data (= 2:1.8.4-2), libx11-dev (= 2:1.8.4-2), libx11-xcb1 (= 2:1.8.4-2), libxau-dev (= 1:1.0.9-1), libxau6 (= 1:1.0.9-1), libxcb-dri2-0 (= 1.15-1), libxcb-dri3-0 (= 1.15-1), libxcb-glx0 (= 1.15-1), libxcb-present0 (= 1.15-1), libxcb-randr0 (= 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 (= 1:1.1.2-3), libxdmcp6 (= 1:1.1.2-3), libxext-dev (= 2:1.3.4-1+b1), libxext6 (= 2:1.3.4-1+b1), libxfixes-dev (= 1:6.0.0-2), libxfixes3 (= 1:6.0.0-2), libxi-dev (= 2:1.8-1+b1), libxi6 (= 2:1.8-1+b1), libxml2 (= 2.9.14+dfsg-1.1+b3), libxml2-utils (= 2.9.14+dfsg-1.1+b3), libxmu-dev (= 2:1.1.3-3), libxmu-headers (= 2:1.1.3-3), libxmu6 (= 2:1.1.3-3), libxshmfence1 (= 1.3-1), libxslt1.1 (= 1.1.35-1), libxt-dev (= 1:1.2.1-1.1), libxt6 (= 1:1.2.1-1.1), libxxf86vm1 (= 1:1.1.4-1+b2), libz3-4 (= 4.8.12-3.1), libzstd1 (= 1.5.4+dfsg2-5), linux-libc-dev (= 6.1.20-2), login (= 1:4.13+dfsg1-1+b1), m4 (= 1.4.19-3), make (= 4.3-4.1), man-db (= 2.11.2-2), mawk (= 1.3.4.20200120-3.1), media-types (= 10.0.0), ncurses-base (= 6.4-2), ncurses-bin (= 6.4-2), patch (= 2.7.6-7), 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 (= 2:4.0.3-1), python3 (= 3.11.2-1+b1), python3-minimal (= 3.11.2-1+b1), python3.11 (= 3.11.2-6), python3.11-minimal (= 3.11.2-6), readline-common (= 8.2-1.3), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-1), sensible-utils (= 0.0.17+nmu1), sgml-base (= 1.31), sgml-data (= 2.0.11+nmu1), sysvinit-utils (= 3.06-4), tao-pegtl-dev (= 3.2.7-1), tar (= 1.34+dfsg-1.2), usrmerge (= 35), util-linux (= 2.38.1-5+b1), util-linux-extra (= 2.38.1-5+b1), x11-common (= 1:7.7+23), 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 (= 5.4.1-0.2), zlib1g (= 1:1.2.13.dfsg-1), zlib1g-dev (= 1:1.2.13.dfsg-1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1670835856" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libmmb-dev_4.0.0+dfsg-2_arm64.deb --------------------------------- new Debian package, version 2.0. size 76384 bytes: control archive=2900 bytes. 774 bytes, 20 lines control 5113 bytes, 72 lines md5sums Package: libmmb-dev Source: macromoleculebuilder Version: 4.0.0+dfsg-2 Architecture: arm64 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/aarch64-linux-gnu/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/lib/aarch64-linux-gnu/cmake/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/lib/aarch64-linux-gnu/cmake/mmb/ -rw-r--r-- root/root 2872 2022-12-12 09:04 ./usr/lib/aarch64-linux-gnu/cmake/mmb/MmbConfigVersion.cmake -rw-r--r-- root/root 820 2022-12-12 09:04 ./usr/lib/aarch64-linux-gnu/cmake/mmb/MmbTargets-release.cmake -rw-r--r-- root/root 4454 2022-12-12 09:04 ./usr/lib/aarch64-linux-gnu/cmake/mmb/MmbTargets.cmake lrwxrwxrwx root/root 0 2022-12-12 09:04 ./usr/lib/aarch64-linux-gnu/libMMB.so -> libMMB.so.4.0 drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/lib/aarch64-linux-gnu/pkgconfig/ -rw-r--r-- root/root 195 2022-12-12 09:04 ./usr/lib/aarch64-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/ -rw-r--r-- root/root 1136 2022-12-12 09:04 ./usr/share/doc/libmmb-dev/changelog.Debian.gz -rw-r--r-- root/root 1550 2022-12-12 09:04 ./usr/share/doc/libmmb-dev/copyright libmmb4.0-dbgsym_4.0.0+dfsg-2_arm64.deb --------------------------------------- new Debian package, version 2.0. size 27492676 bytes: control archive=564 bytes. 400 bytes, 13 lines control 106 bytes, 1 lines md5sums Package: libmmb4.0-dbgsym Source: macromoleculebuilder Version: 4.0.0+dfsg-2 Auto-Built-Package: debug-symbols Architecture: arm64 Maintainer: Debichem Team Installed-Size: 28753 Depends: libmmb4.0 (= 4.0.0+dfsg-2) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libmmb4.0 Build-Ids: 0aceb255c03873a2b31d0c4d39cbe96fb3801fe6 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/debug/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/lib/debug/.build-id/0a/ -rw-r--r-- root/root 29432504 2022-12-12 09:04 ./usr/lib/debug/.build-id/0a/ceb255c03873a2b31d0c4d39cbe96fb3801fe6.debug 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/ lrwxrwxrwx root/root 0 2022-12-12 09:04 ./usr/share/doc/libmmb4.0-dbgsym -> libmmb4.0 libmmb4.0_4.0.0+dfsg-2_arm64.deb -------------------------------- new Debian package, version 2.0. size 976140 bytes: control archive=1012 bytes. 837 bytes, 18 lines control 220 bytes, 3 lines md5sums 37 bytes, 1 lines shlibs 68 bytes, 2 lines triggers Package: libmmb4.0 Source: macromoleculebuilder Version: 4.0.0+dfsg-2 Architecture: arm64 Maintainer: Debichem Team Installed-Size: 4250 Depends: libc6 (>= 2.33), libgcc-s1 (>= 3.0), 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/aarch64-linux-gnu/ -rw-r--r-- root/root 4337112 2022-12-12 09:04 ./usr/lib/aarch64-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 1136 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-dbgsym_4.0.0+dfsg-2_arm64.deb --------------------------------- new Debian package, version 2.0. size 1605336 bytes: control archive=544 bytes. 364 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: mmb-dbgsym Source: macromoleculebuilder Version: 4.0.0+dfsg-2 Auto-Built-Package: debug-symbols Architecture: arm64 Maintainer: Debichem Team Installed-Size: 1623 Depends: mmb (= 4.0.0+dfsg-2) Section: debug Priority: optional Description: debug symbols for mmb Build-Ids: 92fc44dc3b358a826da1ede8954dfbb770f6c364 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/debug/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2022-12-12 09:04 ./usr/lib/debug/.build-id/92/ -rw-r--r-- root/root 1650720 2022-12-12 09:04 ./usr/lib/debug/.build-id/92/fc44dc3b358a826da1ede8954dfbb770f6c364.debug 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/ lrwxrwxrwx root/root 0 2022-12-12 09:04 ./usr/share/doc/mmb-dbgsym -> mmb mmb_4.0.0+dfsg-2_arm64.deb -------------------------- new Debian package, version 2.0. size 27240 bytes: control archive=884 bytes. 769 bytes, 15 lines control 242 bytes, 4 lines md5sums Package: mmb Source: macromoleculebuilder Version: 4.0.0+dfsg-2 Architecture: arm64 Maintainer: Debichem Team Installed-Size: 146 Depends: mmb-common, libc6 (>= 2.34), libgcc-s1 (>= 3.0), 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 134200 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/ -rw-r--r-- root/root 1136 2022-12-12 09:04 ./usr/share/doc/mmb/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 lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [633 B] Get:5 copy:/<>/apt_archive ./ Packages [720 B] Fetched 2316 B in 0s (0 B/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libregexp-ipv6-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip t1utils unzip Suggested packages: isoquery libxml-parser-perl libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl zip Recommended packages: gnupg libcgi-fast-perl libhtml-format-perl liblist-someutils-xs-perl libfreezethaw-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl libxstring-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl The following NEW packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libregexp-ipv6-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip sbuild-build-depends-lintian-dummy:arm64 t1utils unzip 0 upgraded, 124 newly installed, 0 to remove and 0 not upgraded. Need to get 12.6 MB of archives. After this operation, 49.0 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://localhost:3142/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:3 http://localhost:3142/debian sid/main amd64 openssl amd64 3.0.8-1 [1407 kB] Get:4 http://localhost:3142/debian sid/main amd64 ca-certificates all 20230311 [153 kB] Get:5 http://localhost:3142/debian sid/main amd64 diffstat amd64 1.65-1 [33.3 kB] Get:6 http://localhost:3142/debian sid/main amd64 libassuan0 amd64 2.5.5-5 [48.5 kB] Get:7 http://localhost:3142/debian sid/main amd64 gpgconf amd64 2.2.40-1.1 [564 kB] Get:8 http://localhost:3142/debian sid/main amd64 gpg amd64 2.2.40-1.1 [949 kB] Get:9 http://localhost:3142/debian sid/main amd64 iso-codes all 4.13.0-1 [2899 kB] Get:10 http://localhost:3142/debian sid/main amd64 libaliased-perl all 0.34-3 [13.5 kB] Get:11 http://localhost:3142/debian sid/main amd64 libapt-pkg-perl amd64 0.1.40+b2 [69.2 kB] Get:12 http://localhost:3142/debian sid/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB] Get:13 http://localhost:3142/debian sid/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get:14 http://localhost:3142/debian sid/main amd64 libdevel-callchecker-perl amd64 0.008-2 [15.8 kB] Get:15 http://localhost:3142/debian sid/main amd64 libparams-classify-perl amd64 0.015-2+b1 [23.1 kB] Get:16 http://localhost:3142/debian sid/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:17 http://localhost:3142/debian sid/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:18 http://localhost:3142/debian sid/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:19 http://localhost:3142/debian sid/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:20 http://localhost:3142/debian sid/main amd64 libvariable-magic-perl amd64 0.63-1+b1 [44.0 kB] Get:21 http://localhost:3142/debian sid/main amd64 libb-hooks-endofscope-perl all 0.26-1 [19.6 kB] Get:22 http://localhost:3142/debian sid/main amd64 libberkeleydb-perl amd64 0.64-2+b1 [123 kB] Get:23 http://localhost:3142/debian sid/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:24 http://localhost:3142/debian sid/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get:25 http://localhost:3142/debian sid/main amd64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get:26 http://localhost:3142/debian sid/main amd64 liburi-perl all 5.17-1 [90.4 kB] Get:27 http://localhost:3142/debian sid/main amd64 libhtml-parser-perl amd64 3.81-1 [101 kB] Get:28 http://localhost:3142/debian sid/main amd64 libcgi-pm-perl all 4.55-1 [220 kB] Get:29 http://localhost:3142/debian sid/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:30 http://localhost:3142/debian sid/main amd64 libclass-method-modifiers-perl all 2.14-1 [18.1 kB] Get:31 http://localhost:3142/debian sid/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b1 [36.4 kB] Get:32 http://localhost:3142/debian sid/main amd64 libclone-perl amd64 0.46-1 [13.7 kB] Get:33 http://localhost:3142/debian sid/main amd64 libconfig-tiny-perl all 2.28-2 [16.4 kB] Get:34 http://localhost:3142/debian sid/main amd64 libparams-util-perl amd64 1.102-2+b1 [24.8 kB] Get:35 http://localhost:3142/debian sid/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get:36 http://localhost:3142/debian sid/main amd64 libdata-optlist-perl all 0.113-1 [10.6 kB] Get:37 http://localhost:3142/debian sid/main amd64 libsub-exporter-perl all 0.989-1 [50.5 kB] Get:38 http://localhost:3142/debian sid/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get:39 http://localhost:3142/debian sid/main amd64 libcpanel-json-xs-perl amd64 4.35-1 [131 kB] Get:40 http://localhost:3142/debian sid/main amd64 libdevel-stacktrace-perl all 2.0400-2 [26.8 kB] Get:41 http://localhost:3142/debian sid/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:42 http://localhost:3142/debian sid/main amd64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:43 http://localhost:3142/debian sid/main amd64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:44 http://localhost:3142/debian sid/main amd64 libdata-dpath-perl all 0.58-2 [43.6 kB] Get:45 http://localhost:3142/debian sid/main amd64 libdata-messagepack-perl amd64 1.02-1+b1 [35.2 kB] Get:46 http://localhost:3142/debian sid/main amd64 libnet-domain-tld-perl all 1.75-3 [31.9 kB] Get:47 http://localhost:3142/debian sid/main amd64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:48 http://localhost:3142/debian sid/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:49 http://localhost:3142/debian sid/main amd64 libnet-netmask-perl all 2.0002-2 [28.6 kB] Get:50 http://localhost:3142/debian sid/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-2+b1 [99.5 kB] Get:51 http://localhost:3142/debian sid/main amd64 libdata-validate-ip-perl all 0.31-1 [20.6 kB] Get:52 http://localhost:3142/debian sid/main amd64 libdata-validate-uri-perl all 0.07-2 [11.2 kB] Get:53 http://localhost:3142/debian sid/main amd64 libdevel-size-perl amd64 0.83-2+b1 [24.3 kB] Get:54 http://localhost:3142/debian sid/main amd64 libemail-address-xs-perl amd64 1.05-1+b1 [29.4 kB] Get:55 http://localhost:3142/debian sid/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:56 http://localhost:3142/debian sid/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:57 http://localhost:3142/debian sid/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:58 http://localhost:3142/debian sid/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:59 http://localhost:3142/debian sid/main amd64 libhttp-date-perl all 6.05-2 [10.5 kB] Get:60 http://localhost:3142/debian sid/main amd64 libfile-listing-perl all 6.15-1 [12.6 kB] Get:61 http://localhost:3142/debian sid/main amd64 libfont-ttf-perl all 1.06-2 [318 kB] Get:62 http://localhost:3142/debian sid/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:63 http://localhost:3142/debian sid/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:64 http://localhost:3142/debian sid/main amd64 libhttp-message-perl all 6.44-1 [81.7 kB] Get:65 http://localhost:3142/debian sid/main amd64 libhtml-form-perl all 6.11-1 [33.1 kB] Get:66 http://localhost:3142/debian sid/main amd64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:67 http://localhost:3142/debian sid/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:68 http://localhost:3142/debian sid/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get:69 http://localhost:3142/debian sid/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:70 http://localhost:3142/debian sid/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get:71 http://localhost:3142/debian sid/main amd64 libnet-ssleay-perl amd64 1.92-2+b1 [317 kB] Get:72 http://localhost:3142/debian sid/main amd64 libio-socket-ssl-perl all 2.081-2 [219 kB] Get:73 http://localhost:3142/debian sid/main amd64 libnet-http-perl all 6.22-1 [25.3 kB] Get:74 http://localhost:3142/debian sid/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get:75 http://localhost:3142/debian sid/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:76 http://localhost:3142/debian sid/main amd64 libwww-perl all 6.68-1 [186 kB] Get:77 http://localhost:3142/debian sid/main amd64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:78 http://localhost:3142/debian sid/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:79 http://localhost:3142/debian sid/main amd64 libio-interactive-perl all 1.023-2 [11.0 kB] Get:80 http://localhost:3142/debian sid/main amd64 libipc-run3-perl all 0.048-3 [33.2 kB] Get:81 http://localhost:3142/debian sid/main amd64 libjson-maybexs-perl all 1.004004-1 [13.3 kB] Get:82 http://localhost:3142/debian sid/main amd64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:83 http://localhost:3142/debian sid/main amd64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:84 http://localhost:3142/debian sid/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:85 http://localhost:3142/debian sid/main amd64 liblz1 amd64 1.13-5 [37.7 kB] Get:86 http://localhost:3142/debian sid/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB] Get:87 http://localhost:3142/debian sid/main amd64 libmarkdown2 amd64 2.2.7-2 [37.0 kB] Get:88 http://localhost:3142/debian sid/main amd64 libmldbm-perl all 2.05-4 [16.8 kB] Get:89 http://localhost:3142/debian sid/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:90 http://localhost:3142/debian sid/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get:91 http://localhost:3142/debian sid/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get:92 http://localhost:3142/debian sid/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:93 http://localhost:3142/debian sid/main amd64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:94 http://localhost:3142/debian sid/main amd64 libmouse-perl amd64 2.5.10-1+b3 [170 kB] Get:95 http://localhost:3142/debian sid/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:96 http://localhost:3142/debian sid/main amd64 libsub-identify-perl amd64 0.14-3 [10.9 kB] Get:97 http://localhost:3142/debian sid/main amd64 libsub-name-perl amd64 0.26-2+b1 [12.6 kB] Get:98 http://localhost:3142/debian sid/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:99 http://localhost:3142/debian sid/main amd64 libpath-tiny-perl all 0.144-1 [56.4 kB] Get:100 http://localhost:3142/debian sid/main amd64 libperlio-gzip-perl amd64 0.20-1+b1 [17.3 kB] Get:101 http://localhost:3142/debian sid/main amd64 libperlio-utf8-strict-perl amd64 0.010-1 [11.4 kB] Get:102 http://localhost:3142/debian sid/main amd64 libproc-processtable-perl amd64 0.634-1+b2 [43.1 kB] Get:103 http://localhost:3142/debian sid/main amd64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:104 http://localhost:3142/debian sid/main amd64 libsereal-decoder-perl amd64 5.003+ds-1 [99.5 kB] Get:105 http://localhost:3142/debian sid/main amd64 libsereal-encoder-perl amd64 5.003+ds-1 [102 kB] Get:106 http://localhost:3142/debian sid/main amd64 libsort-versions-perl all 1.62-3 [8928 B] Get:107 http://localhost:3142/debian sid/main amd64 libxs-parse-keyword-perl amd64 0.33-1 [58.4 kB] Get:108 http://localhost:3142/debian sid/main amd64 libsyntax-keyword-try-perl amd64 0.28-1 [28.6 kB] Get:109 http://localhost:3142/debian sid/main amd64 libterm-readkey-perl amd64 2.38-2+b1 [24.5 kB] Get:110 http://localhost:3142/debian sid/main amd64 libtext-levenshteinxs-perl amd64 0.03-5+b1 [8404 B] Get:111 http://localhost:3142/debian sid/main amd64 libtext-markdown-discount-perl amd64 0.16-1 [13.0 kB] Get:112 http://localhost:3142/debian sid/main amd64 libtext-xslate-perl amd64 3.5.9-1+b2 [198 kB] Get:113 http://localhost:3142/debian sid/main amd64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:114 http://localhost:3142/debian sid/main amd64 libtime-moment-perl amd64 0.44-2+b1 [73.0 kB] Get:115 http://localhost:3142/debian sid/main amd64 libunicode-utf8-perl amd64 0.62-2 [20.2 kB] Get:116 http://localhost:3142/debian sid/main amd64 libwww-mechanize-perl all 2.16-1 [116 kB] Get:117 http://localhost:3142/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:118 http://localhost:3142/debian sid/main amd64 libyaml-libyaml-perl amd64 0.86+ds-1 [34.4 kB] Get:119 http://localhost:3142/debian sid/main amd64 plzip amd64 1.10-5 [61.9 kB] Get:120 http://localhost:3142/debian sid/main amd64 lzop amd64 1.04-2 [84.2 kB] Get:121 http://localhost:3142/debian sid/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get:122 http://localhost:3142/debian sid/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:123 http://localhost:3142/debian sid/main amd64 unzip amd64 6.0-28 [166 kB] Get:124 http://localhost:3142/debian sid/main amd64 lintian all 2.116.3 [1130 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.6 MB in 0s (101 MB/s) Selecting previously unselected package netbase. (Reading database ... 30682 files and directories currently installed.) Preparing to unpack .../000-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package openssl. Preparing to unpack .../001-openssl_3.0.8-1_amd64.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../002-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package diffstat. Preparing to unpack .../003-diffstat_1.65-1_amd64.deb ... Unpacking diffstat (1.65-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../004-libassuan0_2.5.5-5_amd64.deb ... Unpacking libassuan0:amd64 (2.5.5-5) ... Selecting previously unselected package gpgconf. Preparing to unpack .../005-gpgconf_2.2.40-1.1_amd64.deb ... Unpacking gpgconf (2.2.40-1.1) ... Selecting previously unselected package gpg. Preparing to unpack .../006-gpg_2.2.40-1.1_amd64.deb ... Unpacking gpg (2.2.40-1.1) ... Selecting previously unselected package iso-codes. Preparing to unpack .../007-iso-codes_4.13.0-1_all.deb ... Unpacking iso-codes (4.13.0-1) ... Selecting previously unselected package libaliased-perl. Preparing to unpack .../008-libaliased-perl_0.34-3_all.deb ... Unpacking libaliased-perl (0.34-3) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../009-libapt-pkg-perl_0.1.40+b2_amd64.deb ... Unpacking libapt-pkg-perl (0.1.40+b2) ... Selecting previously unselected package libb-hooks-op-check-perl:amd64. Preparing to unpack .../010-libb-hooks-op-check-perl_0.22-2+b1_amd64.deb ... Unpacking libb-hooks-op-check-perl:amd64 (0.22-2+b1) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../011-libdynaloader-functions-perl_0.003-3_all.deb ... Unpacking libdynaloader-functions-perl (0.003-3) ... Selecting previously unselected package libdevel-callchecker-perl:amd64. Preparing to unpack .../012-libdevel-callchecker-perl_0.008-2_amd64.deb ... Unpacking libdevel-callchecker-perl:amd64 (0.008-2) ... Selecting previously unselected package libparams-classify-perl:amd64. Preparing to unpack .../013-libparams-classify-perl_0.015-2+b1_amd64.deb ... Unpacking libparams-classify-perl:amd64 (0.015-2+b1) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../014-libmodule-runtime-perl_0.016-2_all.deb ... Unpacking libmodule-runtime-perl (0.016-2) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../015-libtry-tiny-perl_0.31-2_all.deb ... Unpacking libtry-tiny-perl (0.31-2) ... Selecting previously unselected package libmodule-implementation-perl. Preparing to unpack .../016-libmodule-implementation-perl_0.09-2_all.deb ... Unpacking libmodule-implementation-perl (0.09-2) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../017-libsub-exporter-progressive-perl_0.001013-3_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001013-3) ... Selecting previously unselected package libvariable-magic-perl. Preparing to unpack .../018-libvariable-magic-perl_0.63-1+b1_amd64.deb ... Unpacking libvariable-magic-perl (0.63-1+b1) ... Selecting previously unselected package libb-hooks-endofscope-perl. Preparing to unpack .../019-libb-hooks-endofscope-perl_0.26-1_all.deb ... Unpacking libb-hooks-endofscope-perl (0.26-1) ... Selecting previously unselected package libberkeleydb-perl:amd64. Preparing to unpack .../020-libberkeleydb-perl_0.64-2+b1_amd64.deb ... Unpacking libberkeleydb-perl:amd64 (0.64-2+b1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../021-libcapture-tiny-perl_0.48-2_all.deb ... Unpacking libcapture-tiny-perl (0.48-2) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../022-libhtml-tagset-perl_3.20-6_all.deb ... Unpacking libhtml-tagset-perl (3.20-6) ... Selecting previously unselected package libregexp-ipv6-perl. Preparing to unpack .../023-libregexp-ipv6-perl_0.03-3_all.deb ... Unpacking libregexp-ipv6-perl (0.03-3) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../024-liburi-perl_5.17-1_all.deb ... Unpacking liburi-perl (5.17-1) ... Selecting previously unselected package libhtml-parser-perl:amd64. Preparing to unpack .../025-libhtml-parser-perl_3.81-1_amd64.deb ... Unpacking libhtml-parser-perl:amd64 (3.81-1) ... Selecting previously unselected package libcgi-pm-perl. Preparing to unpack .../026-libcgi-pm-perl_4.55-1_all.deb ... Unpacking libcgi-pm-perl (4.55-1) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../027-libclass-data-inheritable-perl_0.08-3_all.deb ... Unpacking libclass-data-inheritable-perl (0.08-3) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../028-libclass-method-modifiers-perl_2.14-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.14-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../029-libclass-xsaccessor-perl_1.19-4+b1_amd64.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b1) ... Selecting previously unselected package libclone-perl:amd64. Preparing to unpack .../030-libclone-perl_0.46-1_amd64.deb ... Unpacking libclone-perl:amd64 (0.46-1) ... Selecting previously unselected package libconfig-tiny-perl. Preparing to unpack .../031-libconfig-tiny-perl_2.28-2_all.deb ... Unpacking libconfig-tiny-perl (2.28-2) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../032-libparams-util-perl_1.102-2+b1_amd64.deb ... Unpacking libparams-util-perl (1.102-2+b1) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../033-libsub-install-perl_0.929-1_all.deb ... Unpacking libsub-install-perl (0.929-1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../034-libdata-optlist-perl_0.113-1_all.deb ... Unpacking libdata-optlist-perl (0.113-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../035-libsub-exporter-perl_0.989-1_all.deb ... Unpacking libsub-exporter-perl (0.989-1) ... Selecting previously unselected package libconst-fast-perl. Preparing to unpack .../036-libconst-fast-perl_0.014-2_all.deb ... Unpacking libconst-fast-perl (0.014-2) ... Selecting previously unselected package libcpanel-json-xs-perl:amd64. Preparing to unpack .../037-libcpanel-json-xs-perl_4.35-1_amd64.deb ... Unpacking libcpanel-json-xs-perl:amd64 (4.35-1) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../038-libdevel-stacktrace-perl_2.0400-2_all.deb ... Unpacking libdevel-stacktrace-perl (2.0400-2) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../039-libexception-class-perl_1.45-1_all.deb ... Unpacking libexception-class-perl (1.45-1) ... Selecting previously unselected package libiterator-perl. Preparing to unpack .../040-libiterator-perl_0.03+ds1-2_all.deb ... Unpacking libiterator-perl (0.03+ds1-2) ... Selecting previously unselected package libiterator-util-perl. Preparing to unpack .../041-libiterator-util-perl_0.02+ds1-2_all.deb ... Unpacking libiterator-util-perl (0.02+ds1-2) ... Selecting previously unselected package libdata-dpath-perl. Preparing to unpack .../042-libdata-dpath-perl_0.58-2_all.deb ... Unpacking libdata-dpath-perl (0.58-2) ... Selecting previously unselected package libdata-messagepack-perl. Preparing to unpack .../043-libdata-messagepack-perl_1.02-1+b1_amd64.deb ... Unpacking libdata-messagepack-perl (1.02-1+b1) ... Selecting previously unselected package libnet-domain-tld-perl. Preparing to unpack .../044-libnet-domain-tld-perl_1.75-3_all.deb ... Unpacking libnet-domain-tld-perl (1.75-3) ... Selecting previously unselected package libdata-validate-domain-perl. Preparing to unpack .../045-libdata-validate-domain-perl_0.10-1.1_all.deb ... Unpacking libdata-validate-domain-perl (0.10-1.1) ... Selecting previously unselected package libnet-ipv6addr-perl. Preparing to unpack .../046-libnet-ipv6addr-perl_1.02-1_all.deb ... Unpacking libnet-ipv6addr-perl (1.02-1) ... Selecting previously unselected package libnet-netmask-perl. Preparing to unpack .../047-libnet-netmask-perl_2.0002-2_all.deb ... Unpacking libnet-netmask-perl (2.0002-2) ... Selecting previously unselected package libnetaddr-ip-perl. Preparing to unpack .../048-libnetaddr-ip-perl_4.079+dfsg-2+b1_amd64.deb ... Unpacking libnetaddr-ip-perl (4.079+dfsg-2+b1) ... Selecting previously unselected package libdata-validate-ip-perl. Preparing to unpack .../049-libdata-validate-ip-perl_0.31-1_all.deb ... Unpacking libdata-validate-ip-perl (0.31-1) ... Selecting previously unselected package libdata-validate-uri-perl. Preparing to unpack .../050-libdata-validate-uri-perl_0.07-2_all.deb ... Unpacking libdata-validate-uri-perl (0.07-2) ... Selecting previously unselected package libdevel-size-perl. Preparing to unpack .../051-libdevel-size-perl_0.83-2+b1_amd64.deb ... Unpacking libdevel-size-perl (0.83-2+b1) ... Selecting previously unselected package libemail-address-xs-perl. Preparing to unpack .../052-libemail-address-xs-perl_1.05-1+b1_amd64.deb ... Unpacking libemail-address-xs-perl (1.05-1+b1) ... Selecting previously unselected package libencode-locale-perl. Preparing to unpack .../053-libencode-locale-perl_1.05-3_all.deb ... Unpacking libencode-locale-perl (1.05-3) ... Selecting previously unselected package libipc-system-simple-perl. Preparing to unpack .../054-libipc-system-simple-perl_1.30-2_all.deb ... Unpacking libipc-system-simple-perl (1.30-2) ... Selecting previously unselected package libfile-basedir-perl. Preparing to unpack .../055-libfile-basedir-perl_0.09-2_all.deb ... Unpacking libfile-basedir-perl (0.09-2) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../056-libtimedate-perl_2.3300-2_all.deb ... Unpacking libtimedate-perl (2.3300-2) ... Selecting previously unselected package libhttp-date-perl. Preparing to unpack .../057-libhttp-date-perl_6.05-2_all.deb ... Unpacking libhttp-date-perl (6.05-2) ... Selecting previously unselected package libfile-listing-perl. Preparing to unpack .../058-libfile-listing-perl_6.15-1_all.deb ... Unpacking libfile-listing-perl (6.15-1) ... Selecting previously unselected package libfont-ttf-perl. Preparing to unpack .../059-libfont-ttf-perl_1.06-2_all.deb ... Unpacking libfont-ttf-perl (1.06-2) ... Selecting previously unselected package libio-html-perl. Preparing to unpack .../060-libio-html-perl_1.004-3_all.deb ... Unpacking libio-html-perl (1.004-3) ... Selecting previously unselected package liblwp-mediatypes-perl. Preparing to unpack .../061-liblwp-mediatypes-perl_6.04-2_all.deb ... Unpacking liblwp-mediatypes-perl (6.04-2) ... Selecting previously unselected package libhttp-message-perl. Preparing to unpack .../062-libhttp-message-perl_6.44-1_all.deb ... Unpacking libhttp-message-perl (6.44-1) ... Selecting previously unselected package libhtml-form-perl. Preparing to unpack .../063-libhtml-form-perl_6.11-1_all.deb ... Unpacking libhtml-form-perl (6.11-1) ... Selecting previously unselected package libhtml-html5-entities-perl. Preparing to unpack .../064-libhtml-html5-entities-perl_0.004-3_all.deb ... Unpacking libhtml-html5-entities-perl (0.004-3) ... Selecting previously unselected package libhtml-tree-perl. Preparing to unpack .../065-libhtml-tree-perl_5.07-3_all.deb ... Unpacking libhtml-tree-perl (5.07-3) ... Selecting previously unselected package libhttp-cookies-perl. Preparing to unpack .../066-libhttp-cookies-perl_6.10-1_all.deb ... Unpacking libhttp-cookies-perl (6.10-1) ... Selecting previously unselected package libhttp-negotiate-perl. Preparing to unpack .../067-libhttp-negotiate-perl_6.01-2_all.deb ... Unpacking libhttp-negotiate-perl (6.01-2) ... Selecting previously unselected package perl-openssl-defaults:amd64. Preparing to unpack .../068-perl-openssl-defaults_7+b1_amd64.deb ... Unpacking perl-openssl-defaults:amd64 (7+b1) ... Selecting previously unselected package libnet-ssleay-perl:amd64. Preparing to unpack .../069-libnet-ssleay-perl_1.92-2+b1_amd64.deb ... Unpacking libnet-ssleay-perl:amd64 (1.92-2+b1) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../070-libio-socket-ssl-perl_2.081-2_all.deb ... Unpacking libio-socket-ssl-perl (2.081-2) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../071-libnet-http-perl_6.22-1_all.deb ... Unpacking libnet-http-perl (6.22-1) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../072-liblwp-protocol-https-perl_6.10-1_all.deb ... Unpacking liblwp-protocol-https-perl (6.10-1) ... Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../073-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../074-libwww-perl_6.68-1_all.deb ... Unpacking libwww-perl (6.68-1) ... Selecting previously unselected package libhtml-tokeparser-simple-perl. Preparing to unpack .../075-libhtml-tokeparser-simple-perl_3.16-4_all.deb ... Unpacking libhtml-tokeparser-simple-perl (3.16-4) ... Selecting previously unselected package libimport-into-perl. Preparing to unpack .../076-libimport-into-perl_1.002005-2_all.deb ... Unpacking libimport-into-perl (1.002005-2) ... Selecting previously unselected package libio-interactive-perl. Preparing to unpack .../077-libio-interactive-perl_1.023-2_all.deb ... Unpacking libio-interactive-perl (1.023-2) ... Selecting previously unselected package libipc-run3-perl. Preparing to unpack .../078-libipc-run3-perl_0.048-3_all.deb ... Unpacking libipc-run3-perl (0.048-3) ... Selecting previously unselected package libjson-maybexs-perl. Preparing to unpack .../079-libjson-maybexs-perl_1.004004-1_all.deb ... Unpacking libjson-maybexs-perl (1.004004-1) ... Selecting previously unselected package liblist-compare-perl. Preparing to unpack .../080-liblist-compare-perl_0.55-2_all.deb ... Unpacking liblist-compare-perl (0.55-2) ... Selecting previously unselected package liblist-someutils-perl. Preparing to unpack .../081-liblist-someutils-perl_0.59-1_all.deb ... Unpacking liblist-someutils-perl (0.59-1) ... Selecting previously unselected package liblist-utilsby-perl. Preparing to unpack .../082-liblist-utilsby-perl_0.12-2_all.deb ... Unpacking liblist-utilsby-perl (0.12-2) ... Selecting previously unselected package liblz1:amd64. Preparing to unpack .../083-liblz1_1.13-5_amd64.deb ... Unpacking liblz1:amd64 (1.13-5) ... Selecting previously unselected package liblzo2-2:amd64. Preparing to unpack .../084-liblzo2-2_2.10-2_amd64.deb ... Unpacking liblzo2-2:amd64 (2.10-2) ... Selecting previously unselected package libmarkdown2:amd64. Preparing to unpack .../085-libmarkdown2_2.2.7-2_amd64.deb ... Unpacking libmarkdown2:amd64 (2.2.7-2) ... Selecting previously unselected package libmldbm-perl. Preparing to unpack .../086-libmldbm-perl_2.05-4_all.deb ... Unpacking libmldbm-perl (2.05-4) ... Selecting previously unselected package librole-tiny-perl. Preparing to unpack .../087-librole-tiny-perl_2.002004-1_all.deb ... Unpacking librole-tiny-perl (2.002004-1) ... Selecting previously unselected package libsub-quote-perl. Preparing to unpack .../088-libsub-quote-perl_2.006008-1_all.deb ... Unpacking libsub-quote-perl (2.006008-1) ... Selecting previously unselected package libmoo-perl. Preparing to unpack .../089-libmoo-perl_2.005005-1_all.deb ... Unpacking libmoo-perl (2.005005-1) ... Selecting previously unselected package libstrictures-perl. Preparing to unpack .../090-libstrictures-perl_2.000006-1_all.deb ... Unpacking libstrictures-perl (2.000006-1) ... Selecting previously unselected package libmoox-aliases-perl. Preparing to unpack .../091-libmoox-aliases-perl_0.001006-2_all.deb ... Unpacking libmoox-aliases-perl (0.001006-2) ... Selecting previously unselected package libmouse-perl. Preparing to unpack .../092-libmouse-perl_2.5.10-1+b3_amd64.deb ... Unpacking libmouse-perl (2.5.10-1+b3) ... Selecting previously unselected package libpackage-stash-perl. Preparing to unpack .../093-libpackage-stash-perl_0.40-1_all.deb ... Unpacking libpackage-stash-perl (0.40-1) ... Selecting previously unselected package libsub-identify-perl. Preparing to unpack .../094-libsub-identify-perl_0.14-3_amd64.deb ... Unpacking libsub-identify-perl (0.14-3) ... Selecting previously unselected package libsub-name-perl:amd64. Preparing to unpack .../095-libsub-name-perl_0.26-2+b1_amd64.deb ... Unpacking libsub-name-perl:amd64 (0.26-2+b1) ... Selecting previously unselected package libnamespace-clean-perl. Preparing to unpack .../096-libnamespace-clean-perl_0.27-2_all.deb ... Unpacking libnamespace-clean-perl (0.27-2) ... Selecting previously unselected package libpath-tiny-perl. Preparing to unpack .../097-libpath-tiny-perl_0.144-1_all.deb ... Unpacking libpath-tiny-perl (0.144-1) ... Selecting previously unselected package libperlio-gzip-perl. Preparing to unpack .../098-libperlio-gzip-perl_0.20-1+b1_amd64.deb ... Unpacking libperlio-gzip-perl (0.20-1+b1) ... Selecting previously unselected package libperlio-utf8-strict-perl. Preparing to unpack .../099-libperlio-utf8-strict-perl_0.010-1_amd64.deb ... Unpacking libperlio-utf8-strict-perl (0.010-1) ... Selecting previously unselected package libproc-processtable-perl:amd64. Preparing to unpack .../100-libproc-processtable-perl_0.634-1+b2_amd64.deb ... Unpacking libproc-processtable-perl:amd64 (0.634-1+b2) ... Selecting previously unselected package libregexp-wildcards-perl. Preparing to unpack .../101-libregexp-wildcards-perl_1.05-3_all.deb ... Unpacking libregexp-wildcards-perl (1.05-3) ... Selecting previously unselected package libsereal-decoder-perl. Preparing to unpack .../102-libsereal-decoder-perl_5.003+ds-1_amd64.deb ... Unpacking libsereal-decoder-perl (5.003+ds-1) ... Selecting previously unselected package libsereal-encoder-perl. Preparing to unpack .../103-libsereal-encoder-perl_5.003+ds-1_amd64.deb ... Unpacking libsereal-encoder-perl (5.003+ds-1) ... Selecting previously unselected package libsort-versions-perl. Preparing to unpack .../104-libsort-versions-perl_1.62-3_all.deb ... Unpacking libsort-versions-perl (1.62-3) ... Selecting previously unselected package libxs-parse-keyword-perl. Preparing to unpack .../105-libxs-parse-keyword-perl_0.33-1_amd64.deb ... Unpacking libxs-parse-keyword-perl (0.33-1) ... Selecting previously unselected package libsyntax-keyword-try-perl. Preparing to unpack .../106-libsyntax-keyword-try-perl_0.28-1_amd64.deb ... Unpacking libsyntax-keyword-try-perl (0.28-1) ... Selecting previously unselected package libterm-readkey-perl. Preparing to unpack .../107-libterm-readkey-perl_2.38-2+b1_amd64.deb ... Unpacking libterm-readkey-perl (2.38-2+b1) ... Selecting previously unselected package libtext-levenshteinxs-perl. Preparing to unpack .../108-libtext-levenshteinxs-perl_0.03-5+b1_amd64.deb ... Unpacking libtext-levenshteinxs-perl (0.03-5+b1) ... Selecting previously unselected package libtext-markdown-discount-perl. Preparing to unpack .../109-libtext-markdown-discount-perl_0.16-1_amd64.deb ... Unpacking libtext-markdown-discount-perl (0.16-1) ... Selecting previously unselected package libtext-xslate-perl:amd64. Preparing to unpack .../110-libtext-xslate-perl_3.5.9-1+b2_amd64.deb ... Unpacking libtext-xslate-perl:amd64 (3.5.9-1+b2) ... Selecting previously unselected package libtime-duration-perl. Preparing to unpack .../111-libtime-duration-perl_1.21-2_all.deb ... Unpacking libtime-duration-perl (1.21-2) ... Selecting previously unselected package libtime-moment-perl. Preparing to unpack .../112-libtime-moment-perl_0.44-2+b1_amd64.deb ... Unpacking libtime-moment-perl (0.44-2+b1) ... Selecting previously unselected package libunicode-utf8-perl. Preparing to unpack .../113-libunicode-utf8-perl_0.62-2_amd64.deb ... Unpacking libunicode-utf8-perl (0.62-2) ... Selecting previously unselected package libwww-mechanize-perl. Preparing to unpack .../114-libwww-mechanize-perl_2.16-1_all.deb ... Unpacking libwww-mechanize-perl (2.16-1) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../115-libyaml-0-2_0.2.5-1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1) ... Selecting previously unselected package libyaml-libyaml-perl. Preparing to unpack .../116-libyaml-libyaml-perl_0.86+ds-1_amd64.deb ... Unpacking libyaml-libyaml-perl (0.86+ds-1) ... Selecting previously unselected package plzip. Preparing to unpack .../117-plzip_1.10-5_amd64.deb ... Unpacking plzip (1.10-5) ... Selecting previously unselected package lzop. Preparing to unpack .../118-lzop_1.04-2_amd64.deb ... Unpacking lzop (1.04-2) ... Selecting previously unselected package patchutils. Preparing to unpack .../119-patchutils_0.4.2-1_amd64.deb ... Unpacking patchutils (0.4.2-1) ... Selecting previously unselected package t1utils. Preparing to unpack .../120-t1utils_1.41-4_amd64.deb ... Unpacking t1utils (1.41-4) ... Selecting previously unselected package unzip. Preparing to unpack .../121-unzip_6.0-28_amd64.deb ... Unpacking unzip (6.0-28) ... Selecting previously unselected package lintian. Preparing to unpack .../122-lintian_2.116.3_all.deb ... Unpacking lintian (2.116.3) ... Selecting previously unselected package sbuild-build-depends-lintian-dummy:arm64. Preparing to unpack .../123-sbuild-build-depends-lintian-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-lintian-dummy:arm64 (0.invalid.0) ... Setting up libapt-pkg-perl (0.1.40+b2) ... Setting up liblz1:amd64 (1.13-5) ... Setting up libberkeleydb-perl:amd64 (0.64-2+b1) ... Setting up plzip (1.10-5) ... update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode Setting up libunicode-utf8-perl (0.62-2) ... Setting up libmouse-perl (2.5.10-1+b3) ... Setting up libdata-messagepack-perl (1.02-1+b1) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libclass-method-modifiers-perl (2.14-1) ... Setting up liblist-compare-perl (0.55-2) ... Setting up libclone-perl:amd64 (0.46-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up libsub-identify-perl (0.14-3) ... Setting up libcpanel-json-xs-perl:amd64 (4.35-1) ... Setting up libhtml-tagset-perl (3.20-6) ... Setting up libdevel-size-perl (0.83-2+b1) ... Setting up unzip (6.0-28) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libyaml-libyaml-perl (0.86+ds-1) ... Setting up libio-interactive-perl (1.023-2) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up perl-openssl-defaults:amd64 (7+b1) ... Setting up libmldbm-perl (2.05-4) ... Setting up liblzo2-2:amd64 (2.10-2) ... Setting up libtime-moment-perl (0.44-2+b1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libassuan0:amd64 (2.5.5-5) ... Setting up libconfig-tiny-perl (2.28-2) ... Setting up libsereal-encoder-perl (5.003+ds-1) ... Setting up liblist-utilsby-perl (0.12-2) ... Setting up libnet-netmask-perl (2.0002-2) ... Setting up libsub-install-perl (0.929-1) ... Setting up patchutils (0.4.2-1) ... Setting up libjson-maybexs-perl (1.004004-1) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2+b1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libxs-parse-keyword-perl (0.33-1) ... Setting up libipc-system-simple-perl (1.30-2) ... Setting up libnet-domain-tld-perl (1.75-3) ... Setting up libperlio-utf8-strict-perl (0.010-1) ... Setting up t1utils (1.41-4) ... Setting up diffstat (1.65-1) ... Setting up libvariable-magic-perl (0.63-1+b1) ... Setting up libio-html-perl (1.004-3) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-2+b1) ... Setting up libparams-util-perl (1.102-2+b1) ... Setting up libtime-duration-perl (1.21-2) ... Setting up libtext-xslate-perl:amd64 (3.5.9-1+b2) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libregexp-ipv6-perl (0.03-3) ... Setting up libsub-name-perl:amd64 (0.26-2+b1) ... Setting up libsyntax-keyword-try-perl (0.28-1) ... Setting up libdata-validate-domain-perl (0.10-1.1) ... Setting up libproc-processtable-perl:amd64 (0.634-1+b2) ... Setting up libpath-tiny-perl (0.144-1) ... Setting up lzop (1.04-2) ... Setting up gpgconf (2.2.40-1.1) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.048-3) ... Setting up libregexp-wildcards-perl (1.05-3) ... Setting up libaliased-perl (0.34-3) ... Setting up netbase (6.4) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libdevel-stacktrace-perl (2.0400-2) ... Setting up libclass-xsaccessor-perl (1.19-4+b1) ... Setting up libsort-versions-perl (1.62-3) ... Setting up libterm-readkey-perl (2.38-2+b1) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.0.8-1) ... Setting up libtext-levenshteinxs-perl (0.03-5+b1) ... Setting up libperlio-gzip-perl (0.20-1+b1) ... Setting up libhtml-html5-entities-perl (0.004-3) ... Setting up libsereal-decoder-perl (5.003+ds-1) ... Setting up libmarkdown2:amd64 (2.2.7-2) ... Setting up liburi-perl (5.17-1) ... Setting up iso-codes (4.13.0-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up gpg (2.2.40-1.1) ... Setting up libdata-validate-ip-perl (0.31-1) ... Setting up libemail-address-xs-perl (1.05-1+b1) ... Setting up libnet-ssleay-perl:amd64 (1.92-2+b1) ... Setting up libhttp-date-perl (6.05-2) ... Setting up libfile-basedir-perl (0.09-2) ... Setting up libfile-listing-perl (6.15-1) ... Setting up libnet-http-perl (6.22-1) ... Setting up libtext-markdown-discount-perl (0.16-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libdata-validate-uri-perl (0.07-2) ... Setting up libdata-optlist-perl (0.113-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl:amd64 (3.81-1) ... Setting up libio-socket-ssl-perl (2.081-2) ... Setting up libsub-exporter-perl (0.989-1) ... Setting up libhttp-message-perl (6.44-1) ... Setting up libhtml-form-perl (6.11-1) ... Setting up libiterator-perl (0.03+ds1-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libiterator-util-perl (0.02+ds1-2) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:amd64 (0.015-2+b1) ... Setting up libcgi-pm-perl (4.55-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.58-2) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblist-someutils-perl (0.59-1) ... Setting up libmoox-aliases-perl (0.001006-2) ... Setting up libb-hooks-endofscope-perl (0.26-1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-perl (6.68-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.16-1) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for sgml-base (1.31) ... Setting up lintian (2.116.3) ... Setting up sbuild-build-depends-lintian-dummy:arm64 (0.invalid.0) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Running lintian... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 703196 Build-Time: 546 Distribution: unstable Foreign Architectures: arm64 Host Architecture: arm64 Install-Time: 22 Job: macromoleculebuilder_4.0.0+dfsg-2 Lintian: pass Machine Architecture: amd64 Package: macromoleculebuilder Package-Time: 579 Source-Version: 4.0.0+dfsg-2 Space: 703196 Status: successful Version: 4.0.0+dfsg-2 -------------------------------------------------------------------------------- Finished at 2023-04-12T11:55:52Z Build needed 00:09:39, 703196k disk space