sbuild (Debian sbuild) 0.89.3+deb13u4 (28 December 2025) on mjolnir.einval.org +==============================================================================+ | macromoleculebuilder 4.2+dfsg-2 (amd64) Sun, 22 Feb 2026 10:13:22 +0000 | +==============================================================================+ Package: macromoleculebuilder Version: 4.2+dfsg-2 Source Version: 4.2+dfsg-2 Distribution: unstable Machine Architecture: arm64 Host Architecture: amd64 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any I: Unpacking /home/helmut/.cache/sbuild/unstable-arm64-sbuild.tar.zst to /tmp/tmp.sbuild.CoRmcPqMiH... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sun, 22 Feb 2026 10:13:39 +0000 | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian unstable InRelease [187 kB] Get:2 http://mirror.einval.org/debian unstable/main Sources [11.3 MB] Get:3 http://mirror.einval.org/debian unstable/main amd64 Packages [10.2 MB] Get:4 http://mirror.einval.org/debian unstable/main arm64 Packages [10.1 MB] Fetched 31.7 MB in 7s (4319 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 Sun, 22 Feb 2026 10:13:55 +0000 | +------------------------------------------------------------------------------+ 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 2090 kB of source archives. Get:1 http://mirror.einval.org/debian unstable/main macromoleculebuilder 4.2+dfsg-2 (dsc) [2485 B] Get:2 http://mirror.einval.org/debian unstable/main macromoleculebuilder 4.2+dfsg-2 (tar) [2080 kB] Get:3 http://mirror.einval.org/debian unstable/main macromoleculebuilder 4.2+dfsg-2 (diff) [7420 B] Fetched 2090 kB in 0s (7486 kB/s) Download complete and in download only mode +------------------------------------------------------------------------------+ | Install package build dependencies Sun, 22 Feb 2026 10:13:57 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: architecture-is-64-bit, asciidoc-base, cmake, debhelper-compat (= 13), docbook-xml, dpkg-dev (>= 1.22.5), libgemmi-dev (>= 0.6.2+ds-2), libopenmm-dev, libseqan2-dev (>= 2.5.0), libsimbody-dev, libsimtkmolmodel-dev (>= 3.1.0), libsimtkmolmodel-plugins, libstb-dev, tao-pegtl-dev, zlib1g-dev, libc-dev, libstdc++-dev, build-essential:arm64, crossbuild-essential-amd64:arm64, apt-utils:arm64, libc-dev:amd64, libstdc++-dev:amd64 Filtered Build-Depends: architecture-is-64-bit, asciidoc-base, cmake, debhelper-compat (= 13), docbook-xml, dpkg-dev (>= 1.22.5), libgemmi-dev (>= 0.6.2+ds-2), libopenmm-dev, libseqan2-dev (>= 2.5.0), libsimbody-dev, libsimtkmolmodel-dev (>= 3.1.0), libsimtkmolmodel-plugins, libstb-dev, tao-pegtl-dev, zlib1g-dev, libc-dev, libstdc++-dev, build-essential:arm64, crossbuild-essential-amd64:arm64, apt-utils:arm64, libc-dev:amd64, libstdc++-dev:amd64 dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-2NJ4tQ/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/reproducible-path/resolver-2NJ4tQ/apt_archive ./ InRelease Get:2 copy:/build/reproducible-path/resolver-2NJ4tQ/apt_archive ./ Release [612 B] Ign:3 copy:/build/reproducible-path/resolver-2NJ4tQ/apt_archive ./ Release.gpg Get:4 copy:/build/reproducible-path/resolver-2NJ4tQ/apt_archive ./ Sources [981 B] Get:5 copy:/build/reproducible-path/resolver-2NJ4tQ/apt_archive ./ Packages [1025 B] Fetched 2618 B in 0s (121 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: architecture-properties:amd64 asciidoc-base asciidoc-common autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cmake cmake-data cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism docbook-xml docbook-xsl dwz file freeglut3-dev:amd64 g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-15-base:amd64 gcc-15-cross-base gcc-15-x86-64-linux-gnu gcc-15-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13t64 libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libblas-dev:amd64 libblas3:amd64 libbrotli1 libbsd0:amd64 libc-gconv-modules-extra:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcom-err2 libcurl4t64 libdebhelper-perl libdrm-amdgpu1:amd64 libdrm-common libdrm-intel1:amd64 libdrm2:amd64 libedit2:amd64 libelf1t64 libelf1t64:amd64 libexpat1 libexpat1:amd64 libffi8 libffi8:amd64 libfile-stripnondeterminism-perl libgbm1:amd64 libgcc-15-dev:amd64 libgcc-15-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgcrypt20 libgemmi-dev:amd64 libgfortran5:amd64 libgl-dev:amd64 libgl1:amd64 libgl1-mesa-dri:amd64 libglu1-mesa:amd64 libglu1-mesa-dev:amd64 libglut-dev:amd64 libglut3.12:amd64 libglvnd0:amd64 libglx-dev:amd64 libglx-mesa0:amd64 libglx0:amd64 libgnutls30t64 libgomp1:amd64 libgomp1-amd64-cross libgpg-error0 libgssapi-krb5-2 libhwasan0:amd64 libhwasan0-amd64-cross libice-dev:amd64 libice6:amd64 libidn2-0 libitm1:amd64 libitm1-amd64-cross libjsoncpp26 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev:amd64 liblapack3:amd64 libldap2 libllvm21:amd64 liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc libmagic1t64 libmd0:amd64 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-ossl0 libopengl-dev:amd64 libopengl0:amd64 libopenmm-dev:amd64 libopenmm8.1:amd64 libp11-kit0 libpciaccess0:amd64 libpipeline1 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libquadmath0:amd64 libquadmath0-amd64-cross libreadline8t64 librhash1 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5:amd64 libseqan2-dev libsimbody-dev:amd64 libsimbody3.7:amd64 libsimtkmolmodel-dev:amd64 libsimtkmolmodel-plugins:amd64 libsimtkmolmodel3.1t64:amd64 libsm-dev:amd64 libsm6:amd64 libsqlite3-0 libssh2-1t64 libstb-dev:amd64 libstb0t64:amd64 libstdc++-15-dev:amd64 libstdc++-15-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libtasn1-6 libtinfo6:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunistring5 libuuid1:amd64 libuv1t64 libvulkan1:amd64 libx11-6 libx11-6:amd64 libx11-data libx11-dev libx11-dev:amd64 libx11-xcb1:amd64 libxau-dev libxau-dev:amd64 libxau6 libxau6:amd64 libxcb-dri3-0:amd64 libxcb-glx0:amd64 libxcb-present0:amd64 libxcb-randr0:amd64 libxcb-shm0:amd64 libxcb-sync1:amd64 libxcb-xfixes0:amd64 libxcb1 libxcb1:amd64 libxcb1-dev libxcb1-dev:amd64 libxdmcp-dev libxdmcp-dev:amd64 libxdmcp6 libxdmcp6:amd64 libxext-dev:amd64 libxext6:amd64 libxfixes-dev:amd64 libxfixes3:amd64 libxi-dev:amd64 libxi6:amd64 libxml2-16 libxml2-16:amd64 libxml2-utils libxmu-dev:amd64 libxmu-headers libxmu6:amd64 libxshmfence1:amd64 libxslt1.1 libxt-dev:amd64 libxt6t64:amd64 libxxf86vm1:amd64 libz3-4:amd64 libzstd1:amd64 linux-libc-dev-amd64-cross m4 man-db media-types mesa-libgallium:amd64 netbase po-debconf procps python3 python3-minimal python3.13 python3.13-minimal readline-common sensible-utils sgml-base sgml-data tao-pegtl-dev tzdata uuid-dev:amd64 x11-common x11proto-dev xml-core xorg-sgml-doctools xsltproc xtrans-dev zlib1g:amd64 zlib1g-dev:amd64 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-15-locales cpp-15-doc cpp-doc dh-make docbook docbook-defguide docbook-dsssl 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 gcc-15-doc manpages-dev flex bison gdb-x86-64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff lrzip liblapack-doc:amd64 glibc-doc:amd64 libc-l10n:amd64 locales:amd64 libnss-nis:amd64 libnss-nisplus:amd64 manpages-dev:amd64 rng-tools gnutls-bin krb5-doc krb5-user libice-doc:amd64 pciutils:amd64 lm-sensors lm-sensors:amd64 libsm-doc:amd64 libstdc++-15-doc:amd64 libtool-doc gfortran | fortran95-compiler uuid-runtime:amd64 libx11-doc libx11-doc:amd64 libxcb-doc libxcb-doc:amd64 libxext-doc:amd64 libxt-doc:amd64 m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.13-venv python3.13-doc binfmt-support readline-doc sgml-base-doc perlsgml w3-recs opensp Recommended packages: xmlto curl | wget | lynx libidn2-0:amd64 ca-certificates libarchive-cpio-perl libgpg-error-l10n krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules libltdl-dev mesa-vulkan-drivers:amd64 | vulkan-icd:amd64 libmail-sendmail-perl psmisc linux-sysctl-defaults The following NEW packages will be installed: architecture-properties:amd64 asciidoc-base asciidoc-common autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cmake cmake-data cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism docbook-xml docbook-xsl dwz file freeglut3-dev:amd64 g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-15-base:amd64 gcc-15-cross-base gcc-15-x86-64-linux-gnu gcc-15-x86-64-linux-gnu-base gcc-x86-64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13t64 libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libblas-dev:amd64 libblas3:amd64 libbrotli1 libbsd0:amd64 libc-gconv-modules-extra:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libcom-err2 libcurl4t64 libdebhelper-perl libdrm-amdgpu1:amd64 libdrm-common libdrm-intel1:amd64 libdrm2:amd64 libedit2:amd64 libelf1t64 libelf1t64:amd64 libexpat1 libexpat1:amd64 libffi8 libffi8:amd64 libfile-stripnondeterminism-perl libgbm1:amd64 libgcc-15-dev:amd64 libgcc-15-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgcrypt20 libgemmi-dev:amd64 libgfortran5:amd64 libgl-dev:amd64 libgl1:amd64 libgl1-mesa-dri:amd64 libglu1-mesa:amd64 libglu1-mesa-dev:amd64 libglut-dev:amd64 libglut3.12:amd64 libglvnd0:amd64 libglx-dev:amd64 libglx-mesa0:amd64 libglx0:amd64 libgnutls30t64 libgomp1:amd64 libgomp1-amd64-cross libgpg-error0 libgssapi-krb5-2 libhwasan0:amd64 libhwasan0-amd64-cross libice-dev:amd64 libice6:amd64 libidn2-0 libitm1:amd64 libitm1-amd64-cross libjsoncpp26 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev:amd64 liblapack3:amd64 libldap2 libllvm21:amd64 liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc libmagic1t64 libmd0:amd64 libncursesw6 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-ossl0 libopengl-dev:amd64 libopengl0:amd64 libopenmm-dev:amd64 libopenmm8.1:amd64 libp11-kit0 libpciaccess0:amd64 libpipeline1 libproc2-0 libpsl5t64 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libquadmath0:amd64 libquadmath0-amd64-cross libreadline8t64 librhash1 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5:amd64 libseqan2-dev libsimbody-dev:amd64 libsimbody3.7:amd64 libsimtkmolmodel-dev:amd64 libsimtkmolmodel-plugins:amd64 libsimtkmolmodel3.1t64:amd64 libsm-dev:amd64 libsm6:amd64 libsqlite3-0 libssh2-1t64 libstb-dev:amd64 libstb0t64:amd64 libstdc++-15-dev:amd64 libstdc++-15-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libtasn1-6 libtinfo6:amd64 libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunistring5 libuuid1:amd64 libuv1t64 libvulkan1:amd64 libx11-6 libx11-6:amd64 libx11-data libx11-dev libx11-dev:amd64 libx11-xcb1:amd64 libxau-dev libxau-dev:amd64 libxau6 libxau6:amd64 libxcb-dri3-0:amd64 libxcb-glx0:amd64 libxcb-present0:amd64 libxcb-randr0:amd64 libxcb-shm0:amd64 libxcb-sync1:amd64 libxcb-xfixes0:amd64 libxcb1 libxcb1:amd64 libxcb1-dev libxcb1-dev:amd64 libxdmcp-dev libxdmcp-dev:amd64 libxdmcp6 libxdmcp6:amd64 libxext-dev:amd64 libxext6:amd64 libxfixes-dev:amd64 libxfixes3:amd64 libxi-dev:amd64 libxi6:amd64 libxml2-16 libxml2-16:amd64 libxml2-utils libxmu-dev:amd64 libxmu-headers libxmu6:amd64 libxshmfence1:amd64 libxslt1.1 libxt-dev:amd64 libxt6t64:amd64 libxxf86vm1:amd64 libz3-4:amd64 libzstd1:amd64 linux-libc-dev-amd64-cross m4 man-db media-types mesa-libgallium:amd64 netbase po-debconf procps python3 python3-minimal python3.13 python3.13-minimal readline-common sbuild-build-depends-main-dummy:amd64 sensible-utils sgml-base sgml-data tao-pegtl-dev tzdata uuid-dev:amd64 x11-common x11proto-dev xml-core xorg-sgml-doctools xsltproc xtrans-dev zlib1g:amd64 zlib1g-dev:amd64 0 upgraded, 234 newly installed, 0 to remove and 0 not upgraded. Need to get 224 MB of archives. After this operation, 996 MB of additional disk space will be used. Get:1 copy:/build/reproducible-path/resolver-2NJ4tQ/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1032 B] Get:2 http://mirror.einval.org/debian unstable/main amd64 gcc-15-base amd64 15.2.0-13 [54.8 kB] Get:3 http://mirror.einval.org/debian unstable/main amd64 libgcc-s1 amd64 15.2.0-13 [71.5 kB] Get:4 http://mirror.einval.org/debian unstable/main amd64 libc-gconv-modules-extra amd64 2.42-13 [1123 kB] Get:5 http://mirror.einval.org/debian unstable/main amd64 libc6 amd64 2.42-13 [1814 kB] Get:6 http://mirror.einval.org/debian unstable/main amd64 libexpat1 amd64 2.7.4-1 [116 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 libexpat1 arm64 2.7.4-1 [101 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.12-1 [860 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.12-1 [2070 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 python3-minimal arm64 3.13.9-3 [27.6 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 media-types all 14.0.0 [30.8 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 tzdata all 2025c-3 [263 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 libffi8 arm64 3.5.2-3+b1 [23.3 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 libncursesw6 arm64 6.6+20251231-1 [125 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 readline-common all 8.3-4 [74.8 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 libreadline8t64 arm64 8.3-4 [168 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 libsqlite3-0 arm64 3.46.1-9 [854 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.12-1 [1908 kB] Get:20 http://mirror.einval.org/debian unstable/main arm64 python3.13 arm64 3.13.12-1 [776 kB] Get:21 http://mirror.einval.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.9-3 [10.5 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 python3 arm64 3.13.9-3 [27.6 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-9+b1 [62.4 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 procps arm64 2:4.0.4-9+b1 [871 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5+b1 [338 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5+b1 [103 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 file arm64 1:5.46-5+b1 [44.0 kB] Get:29 http://mirror.einval.org/debian unstable/main arm64 gettext-base arm64 0.23.2-1 [242 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2+b1 [69.1 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 groff-base arm64 1.23.0-10+b1 [1133 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 bsdextrautils arm64 2.41.3-4 [98.1 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-2 [40.3 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 man-db arm64 2.13.1-1+b1 [1455 kB] Get:35 http://mirror.einval.org/debian unstable/main amd64 architecture-properties amd64 0.2.6+b1 [2652 B] Get:36 http://mirror.einval.org/debian unstable/main arm64 asciidoc-common all 10.2.1-1 [104 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 sgml-base all 1.31+nmu1 [10.9 kB] Get:38 http://mirror.einval.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get:39 http://mirror.einval.org/debian unstable/main arm64 docbook-xsl all 1.79.2+dfsg-8 [1214 kB] Get:40 http://mirror.einval.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-2+b1 [591 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 libxml2-utils arm64 2.15.1+dfsg-2+b1 [122 kB] Get:42 http://mirror.einval.org/debian unstable/main arm64 libgpg-error0 arm64 1.58-2 [84.6 kB] Get:43 http://mirror.einval.org/debian unstable/main arm64 libgcrypt20 arm64 1.11.2-3+b1 [763 kB] Get:44 http://mirror.einval.org/debian unstable/main arm64 libxslt1.1 arm64 1.1.43-0.3 [146 kB] Get:45 http://mirror.einval.org/debian unstable/main arm64 xsltproc arm64 1.1.43-0.3 [43.6 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 asciidoc-base all 10.2.1-1 [84.9 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 m4 arm64 1.4.21-1 [323 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 automake all 1:1.18.1-3 [878 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 autopoint all 0.23.2-1 [772 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 cmake-data all 4.2.3-2 [2556 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 libarchive13t64 arm64 3.8.5-1 [329 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 libnghttp3-9 arm64 1.12.0-1 [63.6 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libngtcp2-16 arm64 1.16.0-1 [123 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 libbrotli1 arm64 1.2.0-3 [295 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 libkrb5support0 arm64 1.22.1-2 [32.2 kB] Get:58 http://mirror.einval.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-3+b8 [24.9 kB] Get:59 http://mirror.einval.org/debian unstable/main arm64 libk5crypto3 arm64 1.22.1-2 [77.1 kB] Get:60 http://mirror.einval.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6+b1 [9852 B] Get:61 http://mirror.einval.org/debian unstable/main arm64 libkrb5-3 arm64 1.22.1-2 [315 kB] Get:62 http://mirror.einval.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.22.1-2 [127 kB] Get:63 http://mirror.einval.org/debian unstable/main arm64 libunistring5 arm64 1.3-2+b1 [459 kB] Get:64 http://mirror.einval.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-4+b1 [108 kB] Get:65 http://mirror.einval.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-10 [19.8 kB] Get:66 http://mirror.einval.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-10 [55.0 kB] Get:67 http://mirror.einval.org/debian unstable/main arm64 libldap2 arm64 2.6.10+dfsg-1+b1 [179 kB] Get:68 http://mirror.einval.org/debian unstable/main arm64 libnghttp2-14 arm64 1.68.0-1 [74.6 kB] Get:69 http://mirror.einval.org/debian unstable/main arm64 libngtcp2-crypto-ossl0 arm64 1.16.0-1 [25.7 kB] Get:70 http://mirror.einval.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b2 [59.6 kB] Get:71 http://mirror.einval.org/debian unstable/main arm64 libp11-kit0 arm64 0.26.2-2 [436 kB] Get:72 http://mirror.einval.org/debian unstable/main arm64 libtasn1-6 arm64 4.21.0-2 [48.0 kB] Get:73 http://mirror.einval.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.12-3 [1409 kB] Get:74 http://mirror.einval.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3+b1 [57.7 kB] Get:75 http://mirror.einval.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1+b1 [235 kB] Get:76 http://mirror.einval.org/debian unstable/main arm64 libcurl4t64 arm64 8.19.0~rc2-1 [374 kB] Get:77 http://mirror.einval.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-5 [72.4 kB] Get:78 http://mirror.einval.org/debian unstable/main arm64 librhash1 arm64 1.4.6-1.1 [128 kB] Get:79 http://mirror.einval.org/debian unstable/main arm64 libuv1t64 arm64 1.51.0-2+b1 [149 kB] Get:80 http://mirror.einval.org/debian unstable/main arm64 cmake arm64 4.2.3-2 [10.7 MB] Get:81 http://mirror.einval.org/debian unstable/main arm64 gcc-15-x86-64-linux-gnu-base arm64 15.2.0-13cross1 [55.0 kB] Get:82 http://mirror.einval.org/debian unstable/main arm64 cpp-15-x86-64-linux-gnu arm64 15.2.0-13cross1 [11.3 MB] Get:83 http://mirror.einval.org/debian unstable/main arm64 cpp-x86-64-linux-gnu arm64 4:15.2.0-5 [5324 B] Get:84 http://mirror.einval.org/debian unstable/main arm64 binutils-x86-64-linux-gnu arm64 2.46-2 [1534 kB] Get:85 http://mirror.einval.org/debian unstable/main arm64 gcc-15-cross-base all 15.2.0-13cross1 [50.4 kB] Get:86 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1-amd64-cross all 15.2.0-13cross1 [71.6 kB] Get:87 http://mirror.einval.org/debian unstable/main arm64 libgomp1-amd64-cross all 15.2.0-13cross1 [132 kB] Get:88 http://mirror.einval.org/debian unstable/main arm64 libitm1-amd64-cross all 15.2.0-13cross1 [25.9 kB] Get:89 http://mirror.einval.org/debian unstable/main arm64 libatomic1-amd64-cross all 15.2.0-13cross1 [9244 B] Get:90 http://mirror.einval.org/debian unstable/main arm64 libasan8-amd64-cross all 15.2.0-13cross1 [2770 kB] Get:91 http://mirror.einval.org/debian unstable/main arm64 liblsan0-amd64-cross all 15.2.0-13cross1 [1248 kB] Get:92 http://mirror.einval.org/debian unstable/main arm64 libtsan2-amd64-cross all 15.2.0-13cross1 [2480 kB] Get:93 http://mirror.einval.org/debian unstable/main arm64 libc6-amd64-cross all 2.42-12cross1 [1577 kB] Get:94 http://mirror.einval.org/debian unstable/main arm64 libstdc++6-amd64-cross all 15.2.0-13cross1 [689 kB] Get:95 http://mirror.einval.org/debian unstable/main arm64 libubsan1-amd64-cross all 15.2.0-13cross1 [1107 kB] Get:96 http://mirror.einval.org/debian unstable/main arm64 libhwasan0-amd64-cross all 15.2.0-13cross1 [1533 kB] Get:97 http://mirror.einval.org/debian unstable/main arm64 libquadmath0-amd64-cross all 15.2.0-13cross1 [145 kB] Get:98 http://mirror.einval.org/debian unstable/main arm64 libgcc-15-dev-amd64-cross all 15.2.0-13cross1 [2706 kB] Get:99 http://mirror.einval.org/debian unstable/main arm64 gcc-15-x86-64-linux-gnu arm64 15.2.0-13cross1 [21.8 MB] Get:100 http://mirror.einval.org/debian unstable/main arm64 gcc-x86-64-linux-gnu arm64 4:15.2.0-5 [1448 B] Get:101 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev-amd64-cross all 6.18.12-1 [12.2 kB] Get:102 http://mirror.einval.org/debian unstable/main arm64 libc6-dev-amd64-cross all 2.42-12cross1 [2010 kB] Get:103 http://mirror.einval.org/debian unstable/main arm64 libstdc++-15-dev-amd64-cross all 15.2.0-13cross1 [2426 kB] Get:104 http://mirror.einval.org/debian unstable/main arm64 g++-15-x86-64-linux-gnu arm64 15.2.0-13cross1 [12.2 MB] Get:105 http://mirror.einval.org/debian unstable/main arm64 g++-x86-64-linux-gnu arm64 4:15.2.0-5 [1204 B] Get:106 http://mirror.einval.org/debian unstable/main arm64 crossbuild-essential-amd64 all 12.12 [3552 B] Get:107 http://mirror.einval.org/debian unstable/main arm64 libdebhelper-perl all 13.30 [92.7 kB] Get:108 http://mirror.einval.org/debian unstable/main arm64 libtool all 2.5.4-9 [540 kB] Get:109 http://mirror.einval.org/debian unstable/main arm64 dh-autoreconf all 21+nmu1 [11.7 kB] Get:110 http://mirror.einval.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:111 http://mirror.einval.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get:112 http://mirror.einval.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get:113 http://mirror.einval.org/debian unstable/main arm64 libelf1t64 arm64 0.194-1 [184 kB] Get:114 http://mirror.einval.org/debian unstable/main arm64 dwz arm64 0.16-2+b1 [100 kB] Get:115 http://mirror.einval.org/debian unstable/main arm64 gettext arm64 0.23.2-1 [1613 kB] Get:116 http://mirror.einval.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:117 http://mirror.einval.org/debian unstable/main arm64 po-debconf all 1.0.22 [216 kB] Get:118 http://mirror.einval.org/debian unstable/main arm64 debhelper all 13.30 [942 kB] Get:119 http://mirror.einval.org/debian unstable/main arm64 sgml-data all 2.0.11+nmu1 [179 kB] Get:120 http://mirror.einval.org/debian unstable/main arm64 docbook-xml all 4.5-13 [77.4 kB] Get:121 http://mirror.einval.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-3 [51.1 kB] Get:122 http://mirror.einval.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1+b1 [20.8 kB] Get:123 http://mirror.einval.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-2 [27.9 kB] Get:124 http://mirror.einval.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b2 [144 kB] Get:125 http://mirror.einval.org/debian unstable/main arm64 libx11-data all 2:1.8.12-1 [343 kB] Get:126 http://mirror.einval.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1+b1 [824 kB] Get:127 http://mirror.einval.org/debian unstable/main arm64 libdrm-common all 2.4.131-1 [9168 B] Get:128 http://mirror.einval.org/debian unstable/main amd64 libdrm2 amd64 2.4.131-1 [39.9 kB] Get:129 http://mirror.einval.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.131-1 [24.5 kB] Get:130 http://mirror.einval.org/debian unstable/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-3 [89.0 kB] Get:131 http://mirror.einval.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b4 [52.1 kB] Get:132 http://mirror.einval.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.131-1 [65.6 kB] Get:133 http://mirror.einval.org/debian unstable/main amd64 libzstd1 amd64 1.5.7+dfsg-3+b1 [308 kB] Get:134 http://mirror.einval.org/debian unstable/main amd64 libelf1t64 amd64 0.194-1 [185 kB] Get:135 http://mirror.einval.org/debian unstable/main amd64 libmd0 amd64 1.1.0-2+b2 [36.2 kB] Get:136 http://mirror.einval.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-2+b1 [132 kB] Get:137 http://mirror.einval.org/debian unstable/main amd64 libtinfo6 amd64 6.6+20251231-1 [354 kB] Get:138 http://mirror.einval.org/debian unstable/main amd64 libedit2 amd64 3.1-20251016-1 [93.6 kB] Get:139 http://mirror.einval.org/debian unstable/main amd64 libffi8 amd64 3.5.2-3+b1 [26.4 kB] Get:140 http://mirror.einval.org/debian unstable/main amd64 libstdc++6 amd64 15.2.0-13 [737 kB] Get:141 http://mirror.einval.org/debian unstable/main amd64 libxml2-16 amd64 2.15.1+dfsg-2+b1 [641 kB] Get:142 http://mirror.einval.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1+b1 [8646 kB] Get:143 http://mirror.einval.org/debian unstable/main amd64 libllvm21 amd64 1:21.1.8-3+b1 [28.3 MB] Get:144 http://mirror.einval.org/debian unstable/main arm64 libsensors-config all 1:3.6.2-2 [16.2 kB] Get:145 http://mirror.einval.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.2-2+b1 [37.7 kB] Get:146 http://mirror.einval.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.12-1+b1 [247 kB] Get:147 http://mirror.einval.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b2 [107 kB] Get:148 http://mirror.einval.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2+b2 [106 kB] Get:149 http://mirror.einval.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2+b2 [117 kB] Get:150 http://mirror.einval.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2+b2 [109 kB] Get:151 http://mirror.einval.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b2 [109 kB] Get:152 http://mirror.einval.org/debian unstable/main amd64 libxshmfence1 amd64 1.3.3-1+b1 [11.2 kB] Get:153 http://mirror.einval.org/debian unstable/main amd64 mesa-libgallium amd64 26.0.0-1 [10.4 MB] Get:154 http://mirror.einval.org/debian unstable/main amd64 libgbm1 amd64 26.0.0-1 [60.6 kB] Get:155 http://mirror.einval.org/debian unstable/main amd64 libvulkan1 amd64 1.4.341.0-1 [141 kB] Get:156 http://mirror.einval.org/debian unstable/main amd64 libgl1-mesa-dri amd64 26.0.0-1 [49.4 kB] Get:157 http://mirror.einval.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2+b2 [122 kB] Get:158 http://mirror.einval.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b2 [105 kB] Get:159 http://mirror.einval.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b4 [50.7 kB] Get:160 http://mirror.einval.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-2 [19.9 kB] Get:161 http://mirror.einval.org/debian unstable/main amd64 libglx-mesa0 amd64 26.0.0-1 [130 kB] Get:162 http://mirror.einval.org/debian unstable/main amd64 libglx0 amd64 1.7.0-3 [36.1 kB] Get:163 http://mirror.einval.org/debian unstable/main amd64 libgl1 amd64 1.7.0-3 [88.0 kB] Get:164 http://mirror.einval.org/debian unstable/main amd64 libxi6 amd64 2:1.8.2-2 [79.8 kB] Get:165 http://mirror.einval.org/debian unstable/main amd64 libglut3.12 amd64 3.4.0-6+b1 [142 kB] Get:166 http://mirror.einval.org/debian unstable/main amd64 libopengl0 amd64 1.7.0-3 [31.2 kB] Get:167 http://mirror.einval.org/debian unstable/main amd64 libglu1-mesa amd64 9.0.2-1.1+b4 [191 kB] Get:168 http://mirror.einval.org/debian unstable/main arm64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get:169 http://mirror.einval.org/debian unstable/main arm64 x11proto-dev all 2025.1-1 [605 kB] Get:170 http://mirror.einval.org/debian unstable/main amd64 libxau-dev amd64 1:1.0.11-1+b1 [23.9 kB] Get:171 http://mirror.einval.org/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.5-2 [43.7 kB] Get:172 http://mirror.einval.org/debian unstable/main arm64 xtrans-dev all 1.6.0-1 [93.5 kB] Get:173 http://mirror.einval.org/debian unstable/main amd64 libxcb1-dev amd64 1.17.0-2+b2 [181 kB] Get:174 http://mirror.einval.org/debian unstable/main amd64 libx11-dev amd64 2:1.8.12-1+b1 [901 kB] Get:175 http://mirror.einval.org/debian unstable/main amd64 libglx-dev amd64 1.7.0-3 [15.8 kB] Get:176 http://mirror.einval.org/debian unstable/main amd64 libgl-dev amd64 1.7.0-3 [101 kB] Get:177 http://mirror.einval.org/debian unstable/main amd64 libopengl-dev amd64 1.7.0-3 [5360 B] Get:178 http://mirror.einval.org/debian unstable/main amd64 libglu1-mesa-dev amd64 9.0.2-1.1+b4 [229 kB] Get:179 http://mirror.einval.org/debian unstable/main amd64 libxext-dev amd64 2:1.3.4-1+b4 [105 kB] Get:180 http://mirror.einval.org/debian unstable/main arm64 x11-common all 1:7.7+26 [217 kB] Get:181 http://mirror.einval.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1+b1 [66.8 kB] Get:182 http://mirror.einval.org/debian unstable/main amd64 libuuid1 amd64 2.41.3-4 [39.1 kB] Get:183 http://mirror.einval.org/debian unstable/main amd64 libsm6 amd64 2:1.2.6-1+b1 [37.9 kB] Get:184 http://mirror.einval.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.3+b1 [191 kB] Get:185 http://mirror.einval.org/debian unstable/main amd64 libice-dev amd64 2:1.1.1-1+b1 [75.3 kB] Get:186 http://mirror.einval.org/debian unstable/main amd64 libc6-dev amd64 2.42-13 [2016 kB] Get:187 http://mirror.einval.org/debian unstable/main amd64 uuid-dev amd64 2.41.3-4 [50.5 kB] Get:188 http://mirror.einval.org/debian unstable/main amd64 libsm-dev amd64 2:1.2.6-1+b1 [40.3 kB] Get:189 http://mirror.einval.org/debian unstable/main amd64 libxt-dev amd64 1:1.2.1-1.3+b1 [410 kB] Get:190 http://mirror.einval.org/debian unstable/main amd64 libglut-dev amd64 3.4.0-6+b1 [166 kB] Get:191 http://mirror.einval.org/debian unstable/main amd64 freeglut3-dev amd64 3.4.0-6+b1 [53.9 kB] Get:192 http://mirror.einval.org/debian unstable/main amd64 libasan8 amd64 15.2.0-13 [2779 kB] Get:193 http://mirror.einval.org/debian unstable/main amd64 libatomic1 amd64 15.2.0-13 [9492 B] Get:194 http://mirror.einval.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7+b1 [209 kB] Get:195 http://mirror.einval.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-7+b1 [222 kB] Get:196 http://mirror.einval.org/debian unstable/main amd64 libgomp1 amd64 15.2.0-13 [141 kB] Get:197 http://mirror.einval.org/debian unstable/main amd64 libitm1 amd64 15.2.0-13 [26.5 kB] Get:198 http://mirror.einval.org/debian unstable/main amd64 liblsan0 amd64 15.2.0-13 [1249 kB] Get:199 http://mirror.einval.org/debian unstable/main amd64 libtsan2 amd64 15.2.0-13 [2491 kB] Get:200 http://mirror.einval.org/debian unstable/main amd64 libubsan1 amd64 15.2.0-13 [1108 kB] Get:201 http://mirror.einval.org/debian unstable/main amd64 libhwasan0 amd64 15.2.0-13 [1538 kB] Get:202 http://mirror.einval.org/debian unstable/main amd64 libquadmath0 amd64 15.2.0-13 [145 kB] Get:203 http://mirror.einval.org/debian unstable/main amd64 libgcc-15-dev amd64 15.2.0-13 [2719 kB] Get:204 http://mirror.einval.org/debian unstable/main arm64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] Get:205 http://mirror.einval.org/debian unstable/main amd64 libgemmi-dev amd64 0.7.4+ds-1 [15.5 MB] Get:206 http://mirror.einval.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-13 [862 kB] Get:207 http://mirror.einval.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7+b1 [2550 kB] Get:208 http://mirror.einval.org/debian unstable/main amd64 liblapack-dev amd64 3.12.1-7+b1 [5228 kB] Get:209 http://mirror.einval.org/debian unstable/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-12+b1 [1053 kB] Get:210 http://mirror.einval.org/debian unstable/main amd64 libopenmm-dev amd64 8.1.2+dfsg-12+b1 [345 kB] Get:211 http://mirror.einval.org/debian unstable/main arm64 libseqan2-dev all 2.5.2-1 [1224 kB] Get:212 http://mirror.einval.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b5 [20.3 kB] Get:213 http://mirror.einval.org/debian unstable/main amd64 libxfixes-dev amd64 1:6.0.0-2+b5 [22.4 kB] Get:214 http://mirror.einval.org/debian unstable/main amd64 libxi-dev amd64 2:1.8.2-2 [243 kB] Get:215 http://mirror.einval.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-4 [59.4 kB] Get:216 http://mirror.einval.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1+b1 [20.8 kB] Get:217 http://mirror.einval.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-2 [27.9 kB] Get:218 http://mirror.einval.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b2 [142 kB] Get:219 http://mirror.einval.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.12-1+b1 [794 kB] Get:220 http://mirror.einval.org/debian unstable/main arm64 libxau-dev arm64 1:1.0.11-1+b1 [24.1 kB] Get:221 http://mirror.einval.org/debian unstable/main arm64 libxdmcp-dev arm64 1:1.1.5-2 [43.5 kB] Get:222 http://mirror.einval.org/debian unstable/main arm64 libxcb1-dev arm64 1.17.0-2+b2 [182 kB] Get:223 http://mirror.einval.org/debian unstable/main arm64 libx11-dev arm64 2:1.8.12-1+b1 [877 kB] Get:224 http://mirror.einval.org/debian unstable/main arm64 libxmu-headers all 2:1.1.3-4 [66.1 kB] Get:225 http://mirror.einval.org/debian unstable/main amd64 libxmu-dev amd64 2:1.1.3-4 [65.7 kB] Get:226 http://mirror.einval.org/debian unstable/main amd64 libsimbody3.7 amd64 3.7+dfsg-5 [3393 kB] Get:227 http://mirror.einval.org/debian unstable/main amd64 libsimbody-dev amd64 3.7+dfsg-5 [2727 kB] Get:228 http://mirror.einval.org/debian unstable/main amd64 libsimtkmolmodel3.1t64 amd64 3.1.0-5 [583 kB] Get:229 http://mirror.einval.org/debian unstable/main amd64 libsimtkmolmodel-dev amd64 3.1.0-5 [1863 kB] Get:230 http://mirror.einval.org/debian unstable/main amd64 libsimtkmolmodel-plugins amd64 3.1.0-5 [19.4 kB] Get:231 http://mirror.einval.org/debian unstable/main amd64 libstb0t64 amd64 0.0~git20250907.fede005+ds-1+b1 [225 kB] Get:232 http://mirror.einval.org/debian unstable/main amd64 libstb-dev amd64 0.0~git20250907.fede005+ds-1+b1 [662 kB] Get:233 http://mirror.einval.org/debian unstable/main amd64 libstdc++-15-dev amd64 15.2.0-13 [2446 kB] Get:234 http://mirror.einval.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-3 [919 kB] Preconfiguring packages ... 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Unpacking libxmu-dev:amd64 (2:1.1.3-4) ... Selecting previously unselected package libsimbody3.7:amd64. Preparing to unpack .../204-libsimbody3.7_3.7+dfsg-5_amd64.deb ... Unpacking libsimbody3.7:amd64 (3.7+dfsg-5) ... Selecting previously unselected package libsimbody-dev:amd64. Preparing to unpack .../205-libsimbody-dev_3.7+dfsg-5_amd64.deb ... Unpacking libsimbody-dev:amd64 (3.7+dfsg-5) ... Selecting previously unselected package libsimtkmolmodel3.1t64:amd64. Preparing to unpack .../206-libsimtkmolmodel3.1t64_3.1.0-5_amd64.deb ... Unpacking libsimtkmolmodel3.1t64:amd64 (3.1.0-5) ... Selecting previously unselected package libsimtkmolmodel-dev:amd64. Preparing to unpack .../207-libsimtkmolmodel-dev_3.1.0-5_amd64.deb ... Unpacking libsimtkmolmodel-dev:amd64 (3.1.0-5) ... Selecting previously unselected package libsimtkmolmodel-plugins:amd64. Preparing to unpack .../208-libsimtkmolmodel-plugins_3.1.0-5_amd64.deb ... Unpacking libsimtkmolmodel-plugins:amd64 (3.1.0-5) ... 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Unpacking sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ... Setting up media-types (14.0.0) ... Setting up libpipeline1:arm64 (1.5.8-2) ... Setting up libzstd1:amd64 (1.5.7+dfsg-3+b1) ... Setting up libxau6:amd64 (1:1.0.11-1+b1) ... Setting up libxau6:arm64 (1:1.0.11-1+b1) ... Setting up libxdmcp6:amd64 (1:1.1.5-2) ... Setting up libxdmcp6:arm64 (1:1.1.5-2) ... Setting up libkeyutils1:arm64 (1.6.3-6+b1) ... Setting up libxcb1:amd64 (1.17.0-2+b2) ... Setting up libxcb1:arm64 (1.17.0-2+b2) ... Setting up libxcb-xfixes0:amd64 (1.17.0-2+b2) ... Setting up linux-libc-dev-amd64-cross (6.18.12-1) ... Setting up bsdextrautils (2.41.3-4) ... Setting up libgpg-error0:arm64 (1.58-2) ... Setting up libmagic-mgc (1:5.46-5+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up architecture-properties:amd64 (0.2.6+b1) ... Setting up libglvnd0:amd64 (1.7.0-3) ... Setting up libxml2-16:arm64 (2.15.1+dfsg-2+b1) ... Setting up libxcb-glx0:amd64 (1.17.0-2+b2) ... Setting up libdebhelper-perl (13.30) ... Setting up libbrotli1:arm64 (1.2.0-3) ... Setting up libsqlite3-0:arm64 (3.46.1-9) ... Setting up libuv1t64:arm64 (1.51.0-2+b1) ... Setting up libmagic1t64:arm64 (1:5.46-5+b1) ... Setting up x11-common (1:7.7+26) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: WARNING: No init system and policy-rc.d missing! Defaulting to block. Setting up libsensors-config (1:3.6.2-2) ... Setting up libnghttp2-14:arm64 (1.68.0-1) ... Setting up gettext-base (0.23.2-1) ... Setting up m4 (1.4.21-1) ... Setting up libgcrypt20:arm64 (1.11.2-3+b1) ... Setting up gcc-15-x86-64-linux-gnu-base:arm64 (15.2.0-13cross1) ... Setting up zlib1g:amd64 (1:1.3.dfsg+really1.3.1-3) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b2) ... Setting up libcom-err2:arm64 (1.47.2-3+b8) ... Setting up file (1:5.46-5+b1) ... Setting up cpp-15-x86-64-linux-gnu (15.2.0-13cross1) ... Setting up libgomp1:amd64 (15.2.0-13) ... Setting up libopengl0:amd64 (1.7.0-3) ... Setting up libelf1t64:amd64 (0.194-1) ... Setting up libelf1t64:arm64 (0.194-1) ... Setting up libkrb5support0:arm64 (1.22.1-2) ... Setting up libseqan2-dev (2.5.2-1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-10) ... Setting up tzdata (2025c-3) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Feb 22 10:15:16 UTC 2026. Universal Time is now: Sun Feb 22 10:15:16 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b2) ... Setting up xtrans-dev (1.6.0-1) ... Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-7+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libx11-data (2:1.8.12-1) ... Setting up libxcb-sync1:amd64 (1.17.0-2+b2) ... Setting up libjsoncpp26:arm64 (1.9.6-5) ... Setting up libquadmath0:amd64 (15.2.0-13) ... 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Setting up libasan8:amd64 (15.2.0-13) ... Setting up libuchardet0:arm64 (0.0.8-2+b1) ... Setting up procps (2:4.0.4-9+b1) ... Setting up libxslt1.1:arm64 (1.1.43-0.3) ... Setting up libtasn1-6:arm64 (4.21.0-2) ... Setting up libc6-dev:amd64 (2.42-13) ... Setting up libx11-6:amd64 (2:1.8.12-1+b1) ... Setting up libx11-6:arm64 (2:1.8.12-1+b1) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up netbase (6.5) ... Setting up libngtcp2-16:arm64 (1.16.0-1) ... Setting up sgml-base (1.31+nmu1) ... Setting up cmake-data (4.2.3-2) ... Setting up librhash1:arm64 (1.4.6-1.1) ... Setting up libkrb5-3:arm64 (1.22.1-2) ... Setting up libssh2-1t64:arm64 (1.11.1-1+b1) ... Setting up libtsan2:amd64 (15.2.0-13) ... Setting up libopengl-dev:amd64 (1.7.0-3) ... Setting up gcc-15-cross-base (15.2.0-13cross1) ... Setting up libgcc-s1-amd64-cross (15.2.0-13cross1) ... Setting up libstb0t64:amd64 (0.0~git20250907.fede005+ds-1+b1) ... Setting up libbsd0:amd64 (0.12.2-2+b1) ... Setting up libdrm-common (2.4.131-1) ... Setting up libarchive13t64:arm64 (3.8.5-1) ... Setting up readline-common (8.3-4) ... Setting up libldap2:arm64 (2.6.10+dfsg-1+b1) ... Setting up libstdc++6:amd64 (15.2.0-13) ... Setting up liblsan0:amd64 (15.2.0-13) ... Setting up libblas-dev:amd64 (3.12.1-7+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up tao-pegtl-dev (3.2.7-1) ... Setting up libitm1:amd64 (15.2.0-13) ... Setting up libtinfo6:amd64 (6.6+20251231-1) ... Setting up binutils-x86-64-linux-gnu (2.46-2) ... Setting up libstdc++6-amd64-cross (15.2.0-13cross1) ... Setting up cpp-x86-64-linux-gnu (4:15.2.0-5) ... Setting up automake (1:1.18.1-3) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2025.1-1) ... Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2+b2) ... Setting up libgemmi-dev:amd64 (0.7.4+ds-1) ... Setting up libx11-xcb1:amd64 (2:1.8.12-1+b1) ... Setting up libice6:amd64 (2:1.1.1-1+b1) ... Setting up libpciaccess0:amd64 (0.17-3+b4) ... Setting up liblapack3:amd64 (3.12.1-7+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.23.2-1) ... Setting up libxau-dev:amd64 (1:1.0.11-1+b1) ... Setting up libxau-dev:arm64 (1:1.0.11-1+b1) ... Setting up libice-dev:amd64 (2:1.1.1-1+b1) ... Setting up libtool (2.5.4-9) ... Setting up libasan8-amd64-cross (15.2.0-13cross1) ... Setting up libxml2-16:amd64 (2.15.1+dfsg-2+b1) ... Setting up liblsan0-amd64-cross (15.2.0-13cross1) ... Setting up libc6-dev-amd64-cross (2.42-12cross1) ... Setting up libedit2:amd64 (3.1-20251016-1) ... Setting up xsltproc (1.1.43-0.3) ... Setting up libxext6:amd64 (2:1.3.4-1+b4) ... Setting up libtsan2-amd64-cross (15.2.0-13cross1) ... Setting up libidn2-0:arm64 (2.3.8-4+b1) ... Setting up libgomp1-amd64-cross (15.2.0-13cross1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21+nmu1) ... Setting up libitm1-amd64-cross (15.2.0-13cross1) ... Setting up libxdmcp-dev:amd64 (1:1.1.5-2) ... Setting up libxdmcp-dev:arm64 (1:1.1.5-2) ... Setting up libz3-4:amd64 (4.13.3-1+b1) ... Setting up libatomic1-amd64-cross (15.2.0-13cross1) ... Setting up libhwasan0-amd64-cross (15.2.0-13cross1) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b5) ... Setting up uuid-dev:amd64 (2.41.3-4) ... Setting up libllvm21:amd64 (1:21.1.8-3+b1) ... Setting up libp11-kit0:arm64 (0.26.2-2) ... Setting up liblapack-dev:amd64 (3.12.1-7+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libquadmath0-amd64-cross (15.2.0-13cross1) ... Setting up libgssapi-krb5-2:arm64 (1.22.1-2) ... Setting up libubsan1-amd64-cross (15.2.0-13cross1) ... Setting up libngtcp2-crypto-ossl0:arm64 (1.16.0-1) ... Setting up libreadline8t64:arm64 (8.3-4) ... Setting up libubsan1:amd64 (15.2.0-13) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-3) ... Setting up libdrm2:amd64 (2.4.131-1) ... Setting up libstb-dev:amd64 (0.0~git20250907.fede005+ds-1+b1) ... Setting up groff-base (1.23.0-10+b1) ... Setting up xml-core (0.19) ... Setting up libglu1-mesa:amd64 (9.0.2-1.1+b4) ... Setting up libxml2-utils (2.15.1+dfsg-2+b1) ... Setting up libopenmm8.1:amd64 (8.1.2+dfsg-12+b1) ... Setting up libsm6:amd64 (2:1.2.6-1+b1) ... Setting up libpython3.13-stdlib:arm64 (3.13.12-1) ... Setting up libpython3-stdlib:arm64 (3.13.9-3) ... Setting up libdrm-amdgpu1:amd64 (2.4.131-1) ... Setting up libgnutls30t64:arm64 (3.8.12-3) ... Setting up libgcc-15-dev:amd64 (15.2.0-13) ... Setting up libxcb1-dev:amd64 (1.17.0-2+b2) ... Setting up libxcb1-dev:arm64 (1.17.0-2+b2) ... Setting up libxi6:amd64 (2:1.8.2-2) ... Setting up python3.13 (3.13.12-1) ... Setting up libsm-dev:amd64 (2:1.2.6-1+b1) ... Setting up po-debconf (1.0.22) ... Setting up libdrm-intel1:amd64 (2.4.131-1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b2) ... Setting up libx11-dev:amd64 (2:1.8.12-1+b1) ... Setting up libx11-dev:arm64 (2:1.8.12-1+b1) ... Setting up python3 (3.13.9-3) ... Setting up man-db (2.13.1-1+b1) ... Not building database; man-db/auto-update is not 'true'. Setting up libopenmm-dev:amd64 (8.1.2+dfsg-12+b1) ... Setting up libxfixes-dev:amd64 (1:6.0.0-2+b5) ... Setting up asciidoc-common (10.2.1-1) ... Setting up libstdc++-15-dev:amd64 (15.2.0-13) ... Setting up libgcc-15-dev-amd64-cross (15.2.0-13cross1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-3+b1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.3+b1) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b4) ... Setting up libxi-dev:amd64 (2:1.8.2-2) ... Setting up libstdc++-15-dev-amd64-cross (15.2.0-13cross1) ... Setting up mesa-libgallium:amd64 (26.0.0-1) ... Setting up libxmu-headers (2:1.1.3-4) ... Setting up libxmu6:amd64 (2:1.1.3-4) ... Setting up libcurl4t64:arm64 (8.19.0~rc2-1) ... Setting up libgbm1:amd64 (26.0.0-1) ... Setting up libgl1-mesa-dri:amd64 (26.0.0-1) ... Setting up debhelper (13.30) ... Setting up gcc-15-x86-64-linux-gnu (15.2.0-13cross1) ... Setting up libxt-dev:amd64 (1:1.2.1-1.3+b1) ... Setting up cmake (4.2.3-2) ... Setting up g++-15-x86-64-linux-gnu (15.2.0-13cross1) ... Setting up libglx-mesa0:amd64 (26.0.0-1) ... Setting up gcc-x86-64-linux-gnu (4:15.2.0-5) ... Setting up libglx0:amd64 (1.7.0-3) ... Setting up libxmu-dev:amd64 (2:1.1.3-4) ... Setting up libgl1:amd64 (1.7.0-3) ... Setting up libglut3.12:amd64 (3.4.0-6+b1) ... Setting up libsimbody3.7:amd64 (3.7+dfsg-5) ... Setting up g++-x86-64-linux-gnu (4:15.2.0-5) ... Setting up libglx-dev:amd64 (1.7.0-3) ... Setting up libgl-dev:amd64 (1.7.0-3) ... Setting up libsimtkmolmodel3.1t64:amd64 (3.1.0-5) ... Setting up crossbuild-essential-amd64 (12.12) ... Setting up libglu1-mesa-dev:amd64 (9.0.2-1.1+b4) ... Setting up libglut-dev:amd64 (3.4.0-6+b1) ... Setting up libsimtkmolmodel-plugins:amd64 (3.1.0-5) ... Setting up libsimtkmolmodel-dev:amd64 (3.1.0-5) ... Setting up freeglut3-dev:amd64 (3.4.0-6+b1) ... Setting up libsimbody-dev:amd64 (3.7+dfsg-5) ... Processing triggers for base-files (14) ... Processing triggers for libc-bin (2.42-13) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up docbook-xsl (1.79.2+dfsg-8) ... Setting up sgml-data (2.0.11+nmu1) ... Setting up asciidoc-base (10.2.1-1) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up docbook-xml (4.5-13) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures Sun, 22 Feb 2026 10:15:32 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment Sun, 22 Feb 2026 10:15:33 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.57+deb13-arm64 #1 SMP Debian 6.12.57-1 (2025-11-05) arm64 (aarch64) Toolchain package versions: binutils_2.46-2 dpkg-dev_1.23.5 g++-15_15.2.0-13 gcc-15_15.2.0-13 libc6-dev_2.42-13 libstdc++-15-dev_15.2.0-13 libstdc++-15-dev-amd64-cross_15.2.0-13cross1 libstdc++6_15.2.0-13 libstdc++6-amd64-cross_15.2.0-13cross1 linux-libc-dev_6.18.12-1 Package versions: apt_3.1.16 apt-utils_3.1.16 architecture-properties_0.2.6+b1 asciidoc-base_10.2.1-1 asciidoc-common_10.2.1-1 autoconf_2.72-3.1 automake_1:1.18.1-3 autopoint_0.23.2-1 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.8+b1 bash_5.3-2 binutils_2.46-2 binutils-aarch64-linux-gnu_2.46-2 binutils-common_2.46-2 binutils-x86-64-linux-gnu_2.46-2 bsdextrautils_2.41.3-4 build-essential_12.12 bzip2_1.0.8-6+b1 cmake_4.2.3-2 cmake-data_4.2.3-2 coreutils_9.7-3+b1 cpp_4:15.2.0-5 cpp-15_15.2.0-13 cpp-15-aarch64-linux-gnu_15.2.0-13 cpp-15-x86-64-linux-gnu_15.2.0-13cross1 cpp-aarch64-linux-gnu_4:15.2.0-5 cpp-x86-64-linux-gnu_4:15.2.0-5 crossbuild-essential-amd64_12.12 dash_0.5.12-12+b1 debconf_1.5.92 debhelper_13.30 debian-archive-keyring_2025.1 debianutils_5.23.2+b1 dh-autoreconf_21+nmu1 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1+b1 docbook-xml_4.5-13 docbook-xsl_1.79.2+dfsg-8 dpkg_1.23.5 dpkg-dev_1.23.5 dwz_0.16-2+b1 file_1:5.46-5+b1 findutils_4.10.0-3+b1 freeglut3-dev_3.4.0-6+b1 g++_4:15.2.0-5 g++-15_15.2.0-13 g++-15-aarch64-linux-gnu_15.2.0-13 g++-15-x86-64-linux-gnu_15.2.0-13cross1 g++-aarch64-linux-gnu_4:15.2.0-5 g++-x86-64-linux-gnu_4:15.2.0-5 gcc_4:15.2.0-5 gcc-15_15.2.0-13 gcc-15-aarch64-linux-gnu_15.2.0-13 gcc-15-base_15.2.0-13 gcc-15-cross-base_15.2.0-13cross1 gcc-15-x86-64-linux-gnu_15.2.0-13cross1 gcc-15-x86-64-linux-gnu-base_15.2.0-13cross1 gcc-aarch64-linux-gnu_4:15.2.0-5 gcc-x86-64-linux-gnu_4:15.2.0-5 gettext_0.23.2-1 gettext-base_0.23.2-1 grep_3.12-1+b1 groff-base_1.23.0-10+b1 gzip_1.13-1+b1 hostname_3.25+b1 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-3 libapt-pkg7.0_3.1.16 libarchive-zip-perl_1.68-1 libarchive13t64_3.8.5-1 libasan8_15.2.0-13 libasan8-amd64-cross_15.2.0-13cross1 libatomic1_15.2.0-13 libatomic1-amd64-cross_15.2.0-13cross1 libattr1_1:2.5.2-4 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46-2 libblas-dev_3.12.1-7+b1 libblas3_3.12.1-7+b1 libblkid1_2.41.3-4 libbrotli1_1.2.0-3 libbsd0_0.12.2-2+b1 libbz2-1.0_1.0.8-6+b1 libc-bin_2.42-13 libc-dev-bin_2.42-13 libc-gconv-modules-extra_2.42-13 libc6_2.42-13 libc6-amd64-cross_2.42-12cross1 libc6-dev_2.42-13 libc6-dev-amd64-cross_2.42-12cross1 libcap-ng0_0.9.1-1 libcap2_1:2.75-10+b5 libcc1-0_15.2.0-13 libcom-err2_1.47.2-3+b8 libcrypt1_1:4.5.1-1 libctf-nobfd0_2.46-2 libctf0_2.46-2 libcurl4t64_8.19.0~rc2-1 libdb5.3t64_5.3.28+dfsg2-11 libdebconfclient0_0.282+b2 libdebhelper-perl_13.30 libdpkg-perl_1.23.5 libdrm-amdgpu1_2.4.131-1 libdrm-common_2.4.131-1 libdrm-intel1_2.4.131-1 libdrm2_2.4.131-1 libedit2_3.1-20251016-1 libelf1t64_0.194-1 libexpat1_2.7.4-1 libffi8_3.5.2-3+b1 libfile-stripnondeterminism-perl_1.15.0-1 libgbm1_26.0.0-1 libgcc-15-dev_15.2.0-13 libgcc-15-dev-amd64-cross_15.2.0-13cross1 libgcc-s1_15.2.0-13 libgcc-s1-amd64-cross_15.2.0-13cross1 libgcrypt20_1.11.2-3+b1 libgdbm-compat4t64_1.26-1+b1 libgdbm6t64_1.26-1+b1 libgemmi-dev_0.7.4+ds-1 libgfortran5_15.2.0-13 libgl-dev_1.7.0-3 libgl1_1.7.0-3 libgl1-mesa-dri_26.0.0-1 libglu1-mesa_9.0.2-1.1+b4 libglu1-mesa-dev_9.0.2-1.1+b4 libglut-dev_3.4.0-6+b1 libglut3.12_3.4.0-6+b1 libglvnd0_1.7.0-3 libglx-dev_1.7.0-3 libglx-mesa0_26.0.0-1 libglx0_1.7.0-3 libgmp10_2:6.3.0+dfsg-5+b1 libgnutls30t64_3.8.12-3 libgomp1_15.2.0-13 libgomp1-amd64-cross_15.2.0-13cross1 libgpg-error0_1.58-2 libgprofng0_2.46-2 libgssapi-krb5-2_1.22.1-2 libhogweed6t64_3.10.2-1 libhwasan0_15.2.0-13 libhwasan0-amd64-cross_15.2.0-13cross1 libice-dev_2:1.1.1-1+b1 libice6_2:1.1.1-1+b1 libidn2-0_2.3.8-4+b1 libisl23_0.27-1+b1 libitm1_15.2.0-13 libitm1-amd64-cross_15.2.0-13cross1 libjansson4_2.14-2+b4 libjsoncpp26_1.9.6-5 libk5crypto3_1.22.1-2 libkeyutils1_1.6.3-6+b1 libkrb5-3_1.22.1-2 libkrb5support0_1.22.1-2 liblapack-dev_3.12.1-7+b1 liblapack3_3.12.1-7+b1 libldap2_2.6.10+dfsg-1+b1 libllvm21_1:21.1.8-3+b1 liblsan0_15.2.0-13 liblsan0-amd64-cross_15.2.0-13cross1 liblz4-1_1.10.0-6 liblzma5_5.8.2-2 libmagic-mgc_1:5.46-5+b1 libmagic1t64_1:5.46-5+b1 libmd0_1.1.0-2+b2 libmount1_2.41.3-4 libmpc3_1.3.1-2+b1 libmpfr6_4.2.2-2+b1 libncursesw6_6.6+20251231-1 libnettle8t64_3.10.2-1 libnghttp2-14_1.68.0-1 libnghttp3-9_1.12.0-1 libngtcp2-16_1.16.0-1 libngtcp2-crypto-ossl0_1.16.0-1 libopengl-dev_1.7.0-3 libopengl0_1.7.0-3 libopenmm-dev_8.1.2+dfsg-12+b1 libopenmm8.1_8.1.2+dfsg-12+b1 libp11-kit0_0.26.2-2 libpam-modules_1.7.0-5+b1 libpam-modules-bin_1.7.0-5+b1 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5+b1 libpciaccess0_0.17-3+b4 libpcre2-8-0_10.46-1+b1 libperl5.40_5.40.1-7 libpipeline1_1.5.8-2 libproc2-0_2:4.0.4-9+b1 libpsl5t64_0.21.2-1.1+b2 libpython3-stdlib_3.13.9-3 libpython3.13-minimal_3.13.12-1 libpython3.13-stdlib_3.13.12-1 libquadmath0_15.2.0-13 libquadmath0-amd64-cross_15.2.0-13cross1 libreadline8t64_8.3-4 librhash1_1.4.6-1.1 librtmp1_2.4+20151223.gitfa8646d.1-3+b1 libsasl2-2_2.1.28+dfsg1-10 libsasl2-modules-db_2.1.28+dfsg1-10 libseccomp2_2.6.0-2+b1 libselinux1_3.9-4+b1 libsensors-config_1:3.6.2-2 libsensors5_1:3.6.2-2+b1 libseqan2-dev_2.5.2-1 libsframe3_2.46-2 libsimbody-dev_3.7+dfsg-5 libsimbody3.7_3.7+dfsg-5 libsimtkmolmodel-dev_3.1.0-5 libsimtkmolmodel-plugins_3.1.0-5 libsimtkmolmodel3.1t64_3.1.0-5 libsm-dev_2:1.2.6-1+b1 libsm6_2:1.2.6-1+b1 libsmartcols1_2.41.3-4 libsqlite3-0_3.46.1-9 libssh2-1t64_1.11.1-1+b1 libssl3t64_3.5.5-1 libstb-dev_0.0~git20250907.fede005+ds-1+b1 libstb0t64_0.0~git20250907.fede005+ds-1+b1 libstdc++-15-dev_15.2.0-13 libstdc++-15-dev-amd64-cross_15.2.0-13cross1 libstdc++6_15.2.0-13 libstdc++6-amd64-cross_15.2.0-13cross1 libsystemd0_259.1-1 libtasn1-6_4.21.0-2 libtinfo6_6.6+20251231-1 libtool_2.5.4-9 libtsan2_15.2.0-13 libtsan2-amd64-cross_15.2.0-13cross1 libubsan1_15.2.0-13 libubsan1-amd64-cross_15.2.0-13cross1 libuchardet0_0.0.8-2+b1 libudev1_259.1-1 libunistring5_1.3-2+b1 libuuid1_2.41.3-4 libuv1t64_1.51.0-2+b1 libvulkan1_1.4.341.0-1 libx11-6_2:1.8.12-1+b1 libx11-data_2:1.8.12-1 libx11-dev_2:1.8.12-1+b1 libx11-xcb1_2:1.8.12-1+b1 libxau-dev_1:1.0.11-1+b1 libxau6_1:1.0.11-1+b1 libxcb-dri3-0_1.17.0-2+b2 libxcb-glx0_1.17.0-2+b2 libxcb-present0_1.17.0-2+b2 libxcb-randr0_1.17.0-2+b2 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perl-modules-5.40_5.40.1-7 po-debconf_1.0.22 procps_2:4.0.4-9+b1 python3_3.13.9-3 python3-minimal_3.13.9-3 python3.13_3.13.12-1 python3.13-minimal_3.13.12-1 readline-common_8.3-4 rpcsvc-proto_1.4.3-1+b2 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2+b2 sensible-utils_0.0.26 sgml-base_1.31+nmu1 sgml-data_2.0.11+nmu1 sqv_1.3.0-5 sysvinit-utils_3.15-6+b1 tao-pegtl-dev_3.2.7-1 tar_1.35+dfsg-4 tzdata_2025c-3 util-linux_2.41.3-4 uuid-dev_2.41.3-4 x11-common_1:7.7+26 x11proto-dev_2025.1-1 xml-core_0.19 xorg-sgml-doctools_1:1.11-1.1 xsltproc_1.1.43-0.3 xtrans-dev_1.6.0-1 xz-utils_5.8.2-2 zlib1g_1:1.3.dfsg+really1.3.1-3 zlib1g-dev_1:1.3.dfsg+really1.3.1-3 +------------------------------------------------------------------------------+ | Build Sun, 22 Feb 2026 10:15:33 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: macromoleculebuilder Binary: libmmb-dev, libmmb4.1, mmb, mmb-common Architecture: any all Version: 4.2+dfsg-2 Maintainer: Debichem Team Uploaders: Andrius Merkys , Homepage: https://simtk.org/projects/rnatoolbox Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/debichem-team/macromoleculebuilder Vcs-Git: https://salsa.debian.org/debichem-team/macromoleculebuilder.git Build-Depends: architecture-is-64-bit, asciidoc-base, cmake, debhelper-compat (= 13), docbook-xml, dpkg-dev (>= 1.22.5), libgemmi-dev (>= 0.6.2+ds-2), libopenmm-dev, libseqan2-dev (>= 2.5.0), 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 libmmb4.1 deb libs optional arch=any mmb deb science optional arch=any mmb-common deb science optional arch=all Checksums-Sha1: b4d715369a6ec4c6833c2513515476865c740904 2079836 macromoleculebuilder_4.2+dfsg.orig.tar.xz e3c05782ed87256306c97930883a38127c3b6aa4 7420 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/build/reproducible-path/macromoleculebuilder-4.2+dfsg dpkg-source: info: unpacking macromoleculebuilder_4.2+dfsg.orig.tar.xz dpkg-source: info: unpacking macromoleculebuilder_4.2+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying drop-CMAKE_CXX_STANDARD.patch dpkg-source: info: applying ignore-gemmi-check.patch dpkg-source: info: applying fix-gemmi-incompatibility.patch dpkg-source: info: applying fix-seqan-incompatibility.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.amd64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LC_ALL=C.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aamd64 -Pcross,nocheck -us -uc -B --jobs-try=1 dpkg-buildpackage: info: source package macromoleculebuilder dpkg-buildpackage: info: source version 4.2+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-architecture: warning: specified GNU system type x86_64-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 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 '/build/reproducible-path/macromoleculebuilder-4.2+dfsg' dh_auto_configure -- \ -DCMAKE_BUILD_TYPE=Release \ -DENABLE_LEPTON=OFF \ -DGEMMI_DIR=/usr \ -DOpenMM_INCLUDE_DIR=/usr/include \ -DSimTKmolmodel=/usr \ -DCMAKE_CXX_FLAGS="-D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0" cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/x86_64-linux-gnu-pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_SYSTEM_NAME=Linux -DCMAKE_SYSTEM_PROCESSOR=x86_64 -DCMAKE_C_COMPILER=x86_64-linux-gnu-gcc -DCMAKE_CXX_COMPILER=x86_64-linux-gnu-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/x86_64-linux-gnu-pkg-config -DQMAKE_EXECUTABLE=/usr/bin/x86_64-linux-gnu-qmake -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_TESTING:BOOL=OFF -DCMAKE_BUILD_TYPE=Release -DENABLE_LEPTON=OFF -DGEMMI_DIR=/usr -DOpenMM_INCLUDE_DIR=/usr/include -DSimTKmolmodel=/usr -DCMAKE_CXX_FLAGS="-D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0" .. -- The CXX compiler identification is GNU 15.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/x86_64-linux-gnu-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found OpenMM: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Found gemmi version 0.7.4 -- Looking for copy_file_range -- Looking for copy_file_range - found -- Looking for sendfile -- Looking for sendfile - found -- Configuring done (1.8s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: BUILD_TESTING 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: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg' dh_auto_build -a cd obj-x86_64-linux-gnu && make -j1 INSTALL="install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/macromoleculebuilder-4.2+dfsg -B/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/depend make[3]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/macromoleculebuilder-4.2+dfsg /build/reproducible-path/macromoleculebuilder-4.2+dfsg /build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MMB.dir/DependInfo.cmake "--color=" MMB make[3]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/build make[3]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu' [ 3%] Building CXX object CMakeFiles/MMB.dir/src/Utils.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/Utils.cpp.o -MF CMakeFiles/MMB.dir/src/Utils.cpp.o.d -o CMakeFiles/MMB.dir/src/Utils.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Utils.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Utils.cpp:12: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ [ 6%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o -MF CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o.d -o CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Mutation.h:4, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:14: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClass::renumberPdbResidues(ResidueID)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:551:9: warning: unused variable ‘myNewResidueNumberWithoutInsertionCode’ [-Wunused-variable] 551 | int myNewResidueNumberWithoutInsertionCode = firstResidueID.getResidueNumber() ; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::matchCoordinates(const SimTK::PdbStructure&, bool, bool, bool, bool, bool, bool, double, double)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:669:45: warning: variable ‘biopolymerAtomTargetsIterator’ set but not used [-Wunused-but-set-variable] 669 | Compound::AtomTargetLocations::iterator biopolymerAtomTargetsIterator = biopolymerAtomTargets.begin(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp: In member function ‘ResidueID BiopolymerClass::sum(ResidueID, int) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:2172:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2172 | if ((newResidueIndex < 0) || (newResidueIndex >= residueIDVector.size())) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:16: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:4680:61: required from here 4680 | myResidueStretchContainer.addIntraChainInterfaceResidues( radius, chain, *this ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:283:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 283 | for (int i = 0; i < chainAtomInfoVector.size() ; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:300:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 300 | for ( int j = 0 ; j < neighborList.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = MobilizerStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:2584:54: required from ‘void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch&, ResidueStretchContainer&) [with ResidueStretchType = MobilizerStretch]’ 2584 | residueStretchContainer.printResidueStretchVector(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:2588:181: required from here 2588 | template void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch &residueStretch, ResidueStretchContainer &residueStretchContainer); | ^ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 61 | for (int i = 0 ; i ::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:320:27: required from ‘void ResidueStretchContainer::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’ 320 | if (!(vectorHasResidueStretch(myResidueStretch1))) {addResidueStretchToVector(myResidueStretch1); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:4680:61: required from here 4680 | myResidueStretchContainer.addIntraChainInterfaceResidues( radius, chain, *this ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:104:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 104 | for (int i = 0 ; i ::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:4825:54: required from ‘void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer&, ResidueStretchContainer&) [with ResidueStretchType = DensityStretch]’ 4825 | residueStretchContainer.printResidueStretchVector(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:4828:213: required from here 4828 | template void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer &mobilizerContainer, ResidueStretchContainer &residueStretchContainer); | ^ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 61 | for (int i = 0 ; i & SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:875:14: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i&, double, double, const std::vector&, PdbStructureMapType&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:875:14: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i&, double, double, const std::vector&, PdbStructureMapType&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:875:14: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i&, double, double, const std::vector&, PdbStructureMapType&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:876:44: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i&, double, double, const std::vector&, PdbStructureMapType&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:876:44: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i&, double, double, const std::vector&, PdbStructureMapType&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72 875 | Rotation myRotation; | ^~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector&, double, double, const std::vector&, PdbStructureMapType&)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClass.cpp:876:44: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i&, double, double, const std::vector&, PdbStructureMapType&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/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/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o -MF CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o.d -o CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/UnitCellParameters.cpp [ 12%] Building CXX object CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o -MF CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:12: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp: In member function ‘double AtomSpringContainer::calcRmsd(SimTK::State&, BiopolymerClassContainer&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:65:12: warning: unused variable ‘myExtension’ [-Wunused-variable] 65 | double myExtension = 0.0; | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::deleteAtomSpring(int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:194:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 194 | if(id < 0 || id >= atomSpringVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateAtomSpring(int, const AtomSpring&, BiopolymerClassContainer&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:201:21: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 201 | if(id < 0 || id >= atomSpringVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::deleteThreading(int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:260:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 260 | if(id < 0 || id >= threadingStructVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateThreading(int, const ThreadingStruct&, BiopolymerClassContainer&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:268:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 268 | if(id < 0 || id >= threadingStructVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateThreading(int, SimTK::String, ResidueID, ResidueID, SimTK::String, ResidueID, ResidueID, double, bool, BiopolymerClassContainer&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:279:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 279 | if(id < 0 || id >= threadingStructVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::deleteGappedThreading(int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:446:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 446 | if(id < 0 || id >= gappedThreadingStructVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateGappedThreading(int, const ThreadingStruct&, BiopolymerClassContainer&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:454:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 454 | if(id < 0 || id >= gappedThreadingStructVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateGappedThreading(int, SimTK::String, SimTK::String, double, bool, BiopolymerClassContainer&, double, SimTK::String)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:463:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 463 | if(id < 0 || id >= gappedThreadingStructVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::createSpringsFromGappedThreading(BiopolymerClassContainer&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:493:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘seqan2::Size > >::Type’ {aka ‘long unsigned int’} [-Wsign-compare] 493 | while ((aIndex < length(thread.updThreadingPartner(0).sequence)) && | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/AtomSpringContainer.cpp:494:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘seqan2::Size > >::Type’ {aka ‘long unsigned int’} [-Wsign-compare] 494 | (bIndex < length(thread.updThreadingPartner(1).sequence))) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93, from /usr/include/simbody/SimTKcommon/Simmatrix.h:37, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:23: In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Mat<3, 3> [1]’ [-Warray-bounds=] 784 | { for(int i=0;i R(0.0); | ^ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Mat<3, 3> [1]’ [-Warray-bounds=] 784 | { for(int i=0;i R(0.0); | ^ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Mat<3, 3> [1]’ [-Warray-bounds=] 784 | { for(int i=0;i R(0.0); | ^ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:183:23: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Mat<3, 3> [1]’ [-Warray-bounds=] 784 | { for(int i=0;i U(0.0); // initialize 2-d array | ^ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:183:23: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Mat<3, 3> [1]’ [-Warray-bounds=] 784 | { for(int i=0;i U(0.0); // initialize 2-d array | ^ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:183:23: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Mat<3, 3> [1]’ [-Warray-bounds=] 784 | { for(int i=0;i U(0.0); // initialize 2-d array | ^ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:201:33: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i’ of size 72 201 | rotation = Rotation(); | ^ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:201:33: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i’ of size 72 201 | rotation = Rotation(); | ^ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:201:33: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i’ of size 72 201 | rotation = Rotation(); | ^ [ 15%] Building CXX object CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o -MF CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DisplacementContainer.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Mutation.h:4, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DisplacementContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DisplacementContainer.cpp:12: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 18%] Building CXX object CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o -MF CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MobilizerContainer.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MobilizerContainer.cpp:11: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MobilizerContainer.cpp:12: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MobilizerContainer.cpp: In member function ‘void MobilizerContainer::addMobilizerDomainsInterfacesToVector(const std::vector&, BiopolymerClassContainer&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MobilizerContainer.cpp:190:37: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 190 | if( (dist <= it->range) && | ~~~~~~~~~~~~~~~~~~~~^~ 191 | (it->domain1.contains(chain1, res1) && it->domain2.contains(chain2, res2)) || | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 21%] Building CXX object CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o -MF CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MoleculeContainer.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ConstraintContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/MoleculeContainer.h:8, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MoleculeContainer.cpp:3: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MoleculeContainer.cpp: In constructor ‘CustomMolecule::CustomMolecule(std::vector >, SimTK::DuMMForceFieldSubsystem&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MoleculeContainer.cpp:324:15: warning: unused variable ‘myAngle1’ [-Wunused-variable] 324 | Angle myAngle1 = 180*Deg2Rad; // this is a bond angle | ^~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 25%] Building CXX object CMakeFiles/MMB.dir/src/DensityContainer.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DensityContainer.cpp.o -MF CMakeFiles/MMB.dir/src/DensityContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityContainer.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Mutation.h:4, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:4, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityContainer.cpp:11: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityContainer.cpp: In member function ‘void DensityContainer::updateDensityStretch(int, const DensityStretch&, BiopolymerClassContainer&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityContainer.cpp:18:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 18 | if(id < 0 || id >= residueStretchVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 28%] Building CXX object CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o -MF CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BasePairContainer.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Mutation.h:4, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BasePairContainer.h:17, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BasePairContainer.cpp:11: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BasePairContainer.cpp: In member function ‘void BasePairContainer::updateBasePair(int, SimTK::String, int, SimTK::String, SimTK::String, int, SimTK::String, SimTK::String, BiopolymerClassContainer&, const LeontisWesthofClass&, bool)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BasePairContainer.cpp:44:28: warning: ignoring return value of ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::at(size_type) [with _Tp = BaseInteraction; _Alloc = std::allocator; reference = BaseInteraction&; size_type = long unsigned int]’, declared with attribute ‘nodiscard’ [-Wunused-result] 44 | myBasePairVector.at(index); | ~~~~~~~~~~~~~~~~~~~^~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/15/vector:68, from /usr/include/simbody/SimTKcommon/internal/Array.h:39, from /usr/include/simbody/SimTKcommon/basics.h:53, from /usr/include/simbody/SimTKcommon.h:32, from /usr/include/simbody/Simbody.h:38, from /usr/include/molmodel/SimTKmolmodel.h:47, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BasePairContainer.h:16: /usr/x86_64-linux-gnu/include/c++/15/bits/stl_vector.h:1313:7: note: declared here 1313 | at(size_type __n) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 31%] Building CXX object CMakeFiles/MMB.dir/src/ContactContainer.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ContactContainer.cpp.o -MF CMakeFiles/MMB.dir/src/ContactContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/ContactContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:11: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:12: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp: In member function ‘void ContactContainer::validateContact(ContactStretch, BiopolymerClassContainer&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:26:10: warning: variable ‘myEndCapsOn’ set but not used [-Wunused-but-set-variable] 26 | bool myEndCapsOn; | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp: In member function ‘void ContactContainer::deleteContactWithin(int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:70:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 70 | if(id < 0 || id >= contactWithinVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp: In member function ‘void ContactContainer::updateContactWithin(int, SimTK::String, int, double, SimTK::String, BiopolymerClassContainer&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:77:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 77 | if(id < 0 || id >= contactWithinVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp: In member function ‘void ContactContainer::deleteContact(int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:275:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 275 | if(id < 0 || id >= residueStretchVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp: In member function ‘void ContactContainer::updateContact(int, std::string, int, int, std::string, BiopolymerClassContainer&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:283:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 283 | if(id < 0 || id >= residueStretchVector.size()){ | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp: In member function ‘bool ContactContainer::hasSharedContact(SimTK::String, ResidueID, ResidueID, SimTK::String)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ContactContainer.cpp:313:71: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 313 | ((tempContactStretch.getStartResidue() <= endResidueID) && (tempContactStretch.getEndResidue() >= endResidueID) || // the supplied end residue is in the range of this ContactStretch (with index $i). | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 34%] Building CXX object CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o -MF CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ConstraintContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp:10: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp:11: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp: In member function ‘void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp:129:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 129 | if(index < 0 || index >= constraintClassVector.size()) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp: In member function ‘void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ConstraintContainer.cpp:146:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 146 | if(index < 0 || index >= constraintClassVector.size()) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 37%] Building CXX object CMakeFiles/MMB.dir/src/Repel.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/Repel.cpp.o -MF CMakeFiles/MMB.dir/src/Repel.cpp.o.d -o CMakeFiles/MMB.dir/src/Repel.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/PeriodicScrubber.h:16, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Repel.h:24, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:12: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp: In member function ‘void ConstrainedDynamics::constraintsAndRestraints(ParameterReader&, BiopolymerClassContainer&, SimTK::GeneralForceSubsystem&, SimTK::SimbodyMatterSubsystem&, SimTK::State&, SimTK::CompoundSystem&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:172:31: warning: variable ‘myResidueID’ set but not used [-Wunused-but-set-variable] 172 | ResidueID myResidueID = myConstraintClass.getResidueID1(); | ^~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Repel.h: In constructor ‘ConstrainedDynamics::ConstrainedDynamics(ParameterReader*)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Repel.h:269:29: warning: ‘ConstrainedDynamics::_parameterReader’ will be initialized after [-Wreorder] 269 | ParameterReader * _parameterReader; | ^~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Repel.h:259:29: warning: ‘SimTK::SimbodyMatterSubsystem ConstrainedDynamics::_matter’ [-Wreorder] 259 | SimbodyMatterSubsystem _matter; | ^~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:342:1: warning: when initialized here [-Wreorder] 342 | ConstrainedDynamics::ConstrainedDynamics(ParameterReader * myParameterReader) : _parameterReader(myParameterReader), | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp: In member function ‘void ConstrainedDynamics::initializeBiopolymer(SimTK::String, SimTK::String)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:405:10: warning: variable ‘readFromFile’ set but not used [-Wunused-but-set-variable] 405 | bool readFromFile = false; | ^~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp: In member function ‘void ConstrainedDynamics::runAllSteps()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:1040:22: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 1040 | for(; _nextFrame <= _parameterReader->numReportingIntervals; _nextFrame++){ | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:470:84: required from here 470 | _parameterReader->mobilizerContainer.addStretchesToVectorFromInterfaceContainer(_parameterReader->myBiopolymerClassContainer); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:208:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 208 | for (int i = 0; i < interfaceContainer.numInterfaces(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:573:84: required from here 573 | _parameterReader-> physicsContainer.addStretchesToVectorFromInterfaceContainer(_parameterReader->myBiopolymerClassContainer); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:208:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 208 | for (int i = 0; i < interfaceContainer.numInterfaces(); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::addAllMutualChainResidues(double, std::vector, std::vector, BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:210:4: required from ‘void ResidueStretchContainer::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]’ 210 | addAllMutualChainResidues(tempInterface.Depth, tempInterface.Chains, tempInterface.PartnerChains, myBiopolymerClassContainer); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:470:84: required from here 470 | _parameterReader->mobilizerContainer.addStretchesToVectorFromInterfaceContainer(_parameterReader->myBiopolymerClassContainer); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:232:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 232 | for (int i = 0; i < concatenatedAtomInfoVector.size() ; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:244:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 244 | for ( int j = 0 ; j < neighborList.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::addAllMutualChainResidues(double, std::vector, std::vector, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:210:4: required from ‘void ResidueStretchContainer::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’ 210 | addAllMutualChainResidues(tempInterface.Depth, tempInterface.Chains, tempInterface.PartnerChains, myBiopolymerClassContainer); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:573:84: required from here 573 | _parameterReader-> physicsContainer.addStretchesToVectorFromInterfaceContainer(_parameterReader->myBiopolymerClassContainer); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:232:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 232 | for (int i = 0; i < concatenatedAtomInfoVector.size() ; i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:244:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 244 | for ( int j = 0 ; j < neighborList.size(); j++) { | ~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘bool ResidueStretchContainer::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = MobilizerStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:264:27: required from ‘void ResidueStretchContainer::addAllMutualChainResidues(double, std::vector, std::vector, BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]’ 264 | if (!(vectorHasResidueStretch(myResidueStretch1))) {addStretch(myResidueStretch1); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:210:4: required from ‘void ResidueStretchContainer::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]’ 210 | addAllMutualChainResidues(tempInterface.Depth, tempInterface.Chains, tempInterface.PartnerChains, myBiopolymerClassContainer); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:470:84: required from here 470 | _parameterReader->mobilizerContainer.addStretchesToVectorFromInterfaceContainer(_parameterReader->myBiopolymerClassContainer); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:104:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 104 | for (int i = 0 ; i ::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:264:27: required from ‘void ResidueStretchContainer::addAllMutualChainResidues(double, std::vector, std::vector, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’ 264 | if (!(vectorHasResidueStretch(myResidueStretch1))) {addStretch(myResidueStretch1); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:210:4: required from ‘void ResidueStretchContainer::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’ 210 | addAllMutualChainResidues(tempInterface.Depth, tempInterface.Chains, tempInterface.PartnerChains, myBiopolymerClassContainer); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Repel.cpp:573:84: required from here 573 | _parameterReader-> physicsContainer.addStretchesToVectorFromInterfaceContainer(_parameterReader->myBiopolymerClassContainer); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:104:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 104 | for (int i = 0 ; i &, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 43%] Building CXX object CMakeFiles/MMB.dir/src/Spiral.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/Spiral.cpp.o -MF CMakeFiles/MMB.dir/src/Spiral.cpp.o.d -o CMakeFiles/MMB.dir/src/Spiral.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Spiral.h:16, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp:11: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp: In member function ‘void Spiral::clear()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp:92:12: warning: unused variable ‘helixAdvancePerBasePair’ [-Wunused-variable] 92 | double helixAdvancePerBasePair = -11111. ; // in nm // should be user specified. | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp: In member function ‘double Spiral::harmonicThetaAdjustment(double)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp:124:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 124 | for (int i =0; i < frequencyPhaseAmplitudeVector.size(); i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp: In member function ‘void Spiral::writeCylindricalSpiralCommandFile(MonoAtomsContainer&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp:140:10: warning: variable ‘deltaZ’ set but not used [-Wunused-but-set-variable] 140 | Vec3 deltaZ = Vec3(0,0,1) * sin(cylindricalSpiralSlopeAngle(pitch,radius))*helixAdvancePerBasePair ; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp: In member function ‘void Spiral::writeSphericalSpiralCommandFile(MonoAtomsContainer&)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp:238:16: warning: unused variable ‘currentPhi’ [-Wunused-variable] 238 | double currentPhi = priorPhi + deltaPhi ; // phiFromTheta(currentTheta, pitch, radius, phiOffset); | ^~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/Spiral.cpp:221:12: warning: unused variable ‘phiOffsetFromStartingTheta’ [-Wunused-variable] 221 | double phiOffsetFromStartingTheta = phiFromTheta(startTheta, pitch, radius, 0.0, spiralIsRightHanded); // use offset = 0 to retreive the original, non-offset phi | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 46%] Building CXX object CMakeFiles/MMB.dir/src/ParameterReader.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ParameterReader.cpp.o -MF CMakeFiles/MMB.dir/src/ParameterReader.cpp.o.d -o CMakeFiles/MMB.dir/src/ParameterReader.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:17: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp: In member function ‘void ParameterReader::removeNonPriorityBasePairs(int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:727:9: warning: unused variable ‘oldDutyCyclePriority’ [-Wunused-variable] 727 | int oldDutyCyclePriority=0; | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp: In member function ‘void ParameterReader::updateAllResiduesWithin(int, SimTK::String, int, double)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:776:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 776 | if(index < 0 || index >= includeAllResiduesWithinVector.size()){ | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp: In member function ‘void ParameterReader::deleteAllResiduesWithin(int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:785:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 785 | if(index < 0 || index >= includeAllResiduesWithinVector.size()){ | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:1578:17: warning: unused variable ‘myForceConstant’ [-Wunused-variable] 1578 | double myForceConstant = 1000000000.0; // set to super high value just to make sure it's being reset later. | ^~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2084:16: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 2084 | if ((parameterStringClass.getString(0).compare("constraint") == 0) || (parameterStringClass.getString(0).compare("restraint") == 0)) | ^ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2673:27: warning: variable ‘residueID1’ set but not used [-Wunused-but-set-variable] 2673 | ResidueID residueID1 = ResidueID(-11111,'X'); | ^~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2674:27: warning: variable ‘residueID2’ set but not used [-Wunused-but-set-variable] 2674 | ResidueID residueID2 = ResidueID(-11111,'X'); | ^~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2750:16: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 2750 | if ((parameterStringClass.getString(0).compare("constraint") == 0) || (parameterStringClass.getString(0).compare("restraint") == 0)) | ^ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::deleteResidueStretch(int) [with ResidueStretchType = SingleResidue]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:814:42: required from here 814 | physicsContainer.deleteResidueStretch(index); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93, from /usr/include/simbody/SimTKcommon/Simmatrix.h:37, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/SimTKsimbody.h:43, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:23: In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘Displacement::Displacement()’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:536:8, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2238:19: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘Displacement [1]’ [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘Displacement::Displacement()’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:536:8, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2238:19: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘Displacement [1]’ [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘Displacement::Displacement()’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:536:8, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2238:19: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘Displacement [1]’ [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2239:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2239:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2239:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2240:52: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2240:52: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2240:52: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘Displacement::Displacement()’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:536:8, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2222:30: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘Displacement [1]’ [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘Displacement::Displacement()’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:536:8, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2222:30: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘Displacement [1]’ [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘Displacement::Displacement()’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:536:8, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2222:30: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘Displacement [1]’ [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2224:26: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2224:26: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2224:26: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2225:56: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2225:56: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ParameterReader.cpp:2225:56: /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&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 53%] Building CXX object CMakeFiles/MMB.dir/src/TetherForce.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/TetherForce.cpp.o -MF CMakeFiles/MMB.dir/src/TetherForce.cpp.o.d -o CMakeFiles/MMB.dir/src/TetherForce.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/TetherForce.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/TetherForce.h:19, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/TetherForce.cpp:11: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 56%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o -MF CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o.d -o CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClassTwoTransformForces.h:17, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:10: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:279:16: warning: variable ‘dutyCycle’ set but not used [-Wunused-but-set-variable] 279 | double dutyCycle; //must be between 0 and 1. at 1, force is applied all the time. at 0, basically never applied. | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:280:16: warning: variable ‘scrubberPeriod’ set but not used [-Wunused-but-set-variable] 280 | double scrubberPeriod; | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93, from /usr/include/simbody/SimTKcommon/Simmatrix.h:37, from /usr/include/simbody/SimTKcommon.h:35, from /usr/include/simbody/Simbody.h:38, from /usr/include/molmodel/SimTKmolmodel.h:47, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClassTwoTransformForces.h:16: In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72 116 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72 116 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72 116 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:117:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72 116 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:117:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72 116 | Rotation rotation2; | ^~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_ > >&, SimTK::Vector_ >&, SimTK::Vector&) const’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:117:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i > >&, SimTK::Vector_ >&, SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72 116 | Rotation rotation2; | ^~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:254:29: warning: ‘myFrcScalar’ may be used uninitialized [-Wmaybe-uninitialized] 254 | myFrcScalar *= myParameterReader.twoTransformForceMultiplier; | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:167:20: note: ‘myFrcScalar’ was declared here 167 | double myFrcScalar; | ^~~~~~~~~~~ In member function ‘SimTK::Vec& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:319:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:319:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Vec& SimTK::Vec::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70, inlined from ‘SimTK::Mat::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56, inlined from ‘SimTK::Mat::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9, inlined from ‘SimTK::Rotation_

::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23, inlined from ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:319:22: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:320:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:320:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i& SimTK::Vec::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’, inlined from ‘SimTK::Mat& SimTK::Mat::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24, inlined from ‘SimTK::Mat& SimTK::Mat::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70, inlined from ‘SimTK::Rotation_

& SimTK::Rotation_

::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20, inlined from ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’ at /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/BiopolymerClassTwoTransformForces.cpp:320:50: /usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_ [1]’} [-Warray-bounds=] 784 | { for(int i=0;i&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/WaterDroplet.h:17: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 62%] Building CXX object CMakeFiles/MMB.dir/src/DensityMap.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DensityMap.cpp.o -MF CMakeFiles/MMB.dir/src/DensityMap.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityMap.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:11: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp: In member function ‘void DensityMap::resizeVectorOfAmplitudeAndRandomPhases()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:177:62: warning: comparison of integer expressions of different signedness: ‘std::vector > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 177 | if (vectorOfAmplitudeFrequencyAndRandomPhases.size() != (unitCellParameters.calcMaxFrequencyDoublingsZ()+1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:181:78: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 181 | if (vectorOfAmplitudeFrequencyAndRandomPhases[zIndex].size() != (unitCellParameters.calcMaxFrequencyDoublingsY()+1) ) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:185:90: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 185 | if (vectorOfAmplitudeFrequencyAndRandomPhases[zIndex][yIndex].size() != (unitCellParameters.calcMaxFrequencyDoublingsX()+1 )) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp: In member function ‘void DensityMap::densityAutocorrelation(bool, bool) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:209:12: warning: unused variable ‘ySquared’ [-Wunused-variable] 209 | double ySquared = 0.; | ^~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:210:12: warning: unused variable ‘zSquared’ [-Wunused-variable] 210 | double zSquared = 0.; | ^~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp: In member function ‘void DensityMap::populateNoiseMap()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:307:12: warning: unused variable ‘groundFrequencyX’ [-Wunused-variable] 307 | double groundFrequencyX = 1/unitCellParameters.getNa()/unitCellParameters.geta()/2; | ^~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:308:12: warning: unused variable ‘groundFrequencyY’ [-Wunused-variable] 308 | double groundFrequencyY = 1/unitCellParameters.getNb()/unitCellParameters.getb()/2; | ^~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:309:12: warning: unused variable ‘groundFrequencyZ’ [-Wunused-variable] 309 | double groundFrequencyZ = 1/unitCellParameters.getNc()/unitCellParameters.getc()/2; | ^~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:311:12: warning: unused variable ‘maxFrequencyX’ [-Wunused-variable] 311 | double maxFrequencyX = 1/unitCellParameters.geta()/2; | ^~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:312:12: warning: unused variable ‘maxFrequencyY’ [-Wunused-variable] 312 | double maxFrequencyY = 1/unitCellParameters.getb()/2; | ^~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:313:12: warning: unused variable ‘maxFrequencyZ’ [-Wunused-variable] 313 | double maxFrequencyZ = 1/unitCellParameters.getc()/2; | ^~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:318:12: warning: variable ‘signalToNoiseRatio’ set but not used [-Wunused-but-set-variable] 318 | double signalToNoiseRatio = 0.; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:319:12: warning: unused variable ‘inverseNoiseTemperatureToPower4’ [-Wunused-variable] 319 | double inverseNoiseTemperatureToPower4 = 1/pow(noiseTemperature,4); //Stefan–Boltzmann law says total radiance goes like T^4. So we normalize by this number to keep noise sort of constant with temperatuere. Of course our oven has a maximum wavenumber, so this won't be perfect. | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp: In member function ‘void DensityMap::writeDensityMapXplor(SimTK::String, bool, bool)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityMap.cpp:689:13: warning: unused variable ‘densitiesPerLine’ [-Wunused-variable] 689 | int densitiesPerLine = 6; | ^~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 65%] Building CXX object CMakeFiles/MMB.dir/src/DensityForce.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DensityForce.cpp.o -MF CMakeFiles/MMB.dir/src/DensityForce.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityForce.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityForce.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityForce.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/DensityForce.cpp:11: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 68%] Building CXX object CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o -MF CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o.d -o CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ElectrostaticPotentialGridForce.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ElectrostaticPotentialGridForce.h:19, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ElectrostaticPotentialGridForce.cpp:11: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 71%] Building CXX object CMakeFiles/MMB.dir/src/MMBLogger.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/MMBLogger.cpp.o -MF CMakeFiles/MMB.dir/src/MMBLogger.cpp.o.d -o CMakeFiles/MMB.dir/src/MMBLogger.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/MMBLogger.cpp [ 75%] Building CXX object CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -MF CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o.d -o CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/PeriodicPdbAndEnergyWriter.h:13, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:18: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp: In member function ‘virtual void SimTK::PeriodicPdbAndEnergyWriter::handleEvent(SimTK::State&, SimTK::Real, bool&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:201:30: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 201 | if(myEnergies.size() > myParameterReader.convergenceTimeout) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:202:20: warning: unused variable ‘lastEnergy’ [-Wunused-variable] 202 | double lastEnergy = myEnergies.back(); | ^~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:49:9: warning: unused variable ‘compoundNumber’ [-Wunused-variable] 49 | int compoundNumber = 1; | ^~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:50:9: warning: unused variable ‘requiredPrecision’ [-Wunused-variable] 50 | int requiredPrecision = 12; | ^~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 78%] Building CXX object CMakeFiles/MMB.dir/src/CifOutput.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/CifOutput.cpp.o -MF CMakeFiles/MMB.dir/src/CifOutput.cpp.o.d -o CMakeFiles/MMB.dir/src/CifOutput.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/CifOutput.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Mutation.h:4, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/CifOutput.h:5, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/CifOutput.cpp:1: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/PeriodicPdbAndEnergyWriter.h:13, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/CifOutput.h:12: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 81%] Building CXX object CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o -MF CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o.d -o CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/ProgressWriter.cpp [ 84%] Building CXX object CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o -MF CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o.d -o CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NTC_PARAMETER_READER.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/NtC_Class_Container.h:14, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NTC_PARAMETER_READER.cpp:16: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/NTC_FORCE_CLASS.h:4, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NTC_PARAMETER_READER.cpp:17: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 87%] Building CXX object CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o -MF CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NtCClassContainer.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Mutation.h:4, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NtCClassContainer.cpp:13: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | const char* spaces = " \t"; | ^~~~~~ [ 90%] Building CXX object CMakeFiles/MMB.dir/src/NtCForces.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NtCForces.cpp.o -MF CMakeFiles/MMB.dir/src/NtCForces.cpp.o.d -o CMakeFiles/MMB.dir/src/NtCForces.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NtCForces.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/NtCForces.h:13, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/NtCForces.cpp:11: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | 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/x86_64-linux-gnu-g++ -fPIC -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -shared -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/MMB.dir/link.d -Wl,-soname,libMMB.so.4.1 -o libMMB.so.4.1 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 -L/build/reproducible-path/macromoleculebuilder-4.2+dfsg/SYSTEM -Wl,-rpath,/build/reproducible-path/macromoleculebuilder-4.2+dfsg/SYSTEM: /usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 /usr/lib/x86_64-linux-gnu/libOpenMM.so /usr/lib/x86_64-linux-gnu/libz.so -lgemmi_cpp /usr/lib/x86_64-linux-gnu/libSimTKsimbody.so.3.7 /usr/lib/x86_64-linux-gnu/libSimTKmath.so.3.7 /usr/lib/x86_64-linux-gnu/libSimTKcommon.so.3.7 /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lpthread -lrt -ldl -lm /usr/bin/cmake -E cmake_symlink_library libMMB.so.4.1 libMMB.so.4.1 libMMB.so make[3]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu' [ 93%] Built target MMB make -f CMakeFiles/MMB_EXEC.dir/build.make CMakeFiles/MMB_EXEC.dir/depend make[3]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu' cd /build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/macromoleculebuilder-4.2+dfsg /build/reproducible-path/macromoleculebuilder-4.2+dfsg /build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MMB_EXEC.dir/DependInfo.cmake "--color=" MMB_EXEC make[3]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/MMB_EXEC.dir/build.make CMakeFiles/MMB_EXEC.dir/build make[3]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu' [ 96%] Building CXX object CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o /usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg -I/build/reproducible-path/macromoleculebuilder-4.2+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/RNABuilder.cpp In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:14, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:20, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/src/RNABuilder.cpp:22: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_&, const SimTK::Vector&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:282:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 282 | if (derivComponents.size() == 1) | ^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:284:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 284 | return 0; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:378:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 378 | if ((myStringStream.str()).length() != (totalWidth - 1)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:2, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:15: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); }; | ~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:95:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 95 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Threading.h:102:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 102 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){ | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/AtomSpringContainer.h:76:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 76 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}} | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ContactContainer.h:15, from /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ParameterReader.h:21: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:22:59: required from here 22 | void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector() | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 61 | for (int i = 0 ; i ::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/DensityContainer.h:25:59: required from here 25 | void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id) | ~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 144 | if(id >= 0 && id < residueStretchVector.size()) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h: At global scope: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:262:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable] 262 | const char* digits = "0123456789"; | ^~~~~~ /build/reproducible-path/macromoleculebuilder-4.2+dfsg/include/Utils.h:261:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable] 261 | 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/x86_64-linux-gnu-g++ -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/MMB_EXEC.dir/link.d CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o -o MMB -L/build/reproducible-path/macromoleculebuilder-4.2+dfsg/SYSTEM -Wl,-rpath,/build/reproducible-path/macromoleculebuilder-4.2+dfsg/SYSTEM:/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu: libMMB.so.4.1 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 /usr/lib/x86_64-linux-gnu/libSimTKsimbody.so.3.7 /usr/lib/x86_64-linux-gnu/libSimTKmath.so.3.7 /usr/lib/x86_64-linux-gnu/libSimTKcommon.so.3.7 /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lpthread -lrt -ldl -lm make[3]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu' [100%] Built target MMB_EXEC make[2]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-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-x86_64-linux-gnu && make -j1 install DESTDIR=/build/reproducible-path/macromoleculebuilder-4.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/macromoleculebuilder-4.2+dfsg -B/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/AddBackboneOxygenForces.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/AddNASTForces.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/AtomSpringContainer.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/BaseInteractionParameterReader.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/BasePairContainer.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/BiopolymerClass.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/BiopolymerClassTwoTransformForces.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/CalcTransformCorrection.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/CenterOfMass.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/CifOutput.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/Constexpr.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/ConstraintContainer.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/ContactContainer.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/DensityContainer.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/DensityForce.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/DensityMap.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/DisplacementContainer.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/ElectrostaticPotentialGridForce.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/ExportMacros.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/ExtraMath.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/GeometricCenter.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/HarmonicVelocityRescalingThermostat.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/Impossible.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/KBBackboneTorsionForce.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/Lepton.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/LigandDroplet.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/Ligands.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/Ligands.sam.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/MMBLogger.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/MobilizerContainer.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/MoleculeContainer.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/MonoAtoms.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/Mutation.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/NTC_FORCE_CLASS.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/NTC_PARAMETER_READER.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/NtCBackboneTorsionForce.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/NtCForces.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/NtCInteractionParameterReader.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/NtC_Class_Container.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/ParameterReader.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/ParameterReader_wrapper.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/PeriodicParameterReaderUpdater.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/PeriodicPdbAndCOMWriter.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/PeriodicPdbAndEnergySingleFrameWriter.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/PeriodicPdbAndEnergyWriter.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/PeriodicPdbSingleFrameWriter.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/PeriodicScrubber.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/ProgressWriter.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/RandomizeRNACoordinates.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/Repel.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/ResidueStretchContainer.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/RigidifyFormedHelices.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/SetChiMobility.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/SetSingleBondMobility.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/Spiral.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/StackingForceSubsystem.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/Sterics.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/TetherForce.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/Threading.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/UnitCellParameters.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/Utils.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/WadleyKeatingDuartePyleTorsionForce.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/Water.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/WaterDroplet.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/superimposer.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/include/MMB/MMB_config.h -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libMMB.so.4.1 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libMMB.so.4.1" to "" -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libMMB.so -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/share/MMB/parameters.csv -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/bin/MMB -- Set non-toolchain portion of runtime path of "/build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/bin/MMB" to "" -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/mmb/MmbConfigVersion.cmake -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/mmb/MmbTargets.cmake -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/mmb/MmbTargets-release.cmake -- Installing: /build/reproducible-path/macromoleculebuilder-4.2+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/mmb.pc make[1]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg/obj-x86_64-linux-gnu' dh_install -a dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg' a2x -d manpage -f manpage -D debian/tmp debian/MMB.1.asciidoc dh_installman make[1]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.2+dfsg' 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 dpkg-shlibdeps: warning: symbol gzseek used by debian/libmmb4.1/usr/lib/x86_64-linux-gnu/libMMB.so.4.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzungetc used by debian/libmmb4.1/usr/lib/x86_64-linux-gnu/libMMB.so.4.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gztell used by debian/libmmb4.1/usr/lib/x86_64-linux-gnu/libMMB.so.4.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzeof used by debian/libmmb4.1/usr/lib/x86_64-linux-gnu/libMMB.so.4.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzerror used by debian/libmmb4.1/usr/lib/x86_64-linux-gnu/libMMB.so.4.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzbuffer used by debian/libmmb4.1/usr/lib/x86_64-linux-gnu/libMMB.so.4.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzread used by debian/libmmb4.1/usr/lib/x86_64-linux-gnu/libMMB.so.4.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzgetc used by debian/libmmb4.1/usr/lib/x86_64-linux-gnu/libMMB.so.4.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzopen used by debian/libmmb4.1/usr/lib/x86_64-linux-gnu/libMMB.so.4.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzclose_r used by debian/libmmb4.1/usr/lib/x86_64-linux-gnu/libMMB.so.4.1 found in none of the libraries dpkg-shlibdeps: warning: 1 similar warning has been skipped (use -v to see it) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mmb/usr/bin/MMB was not linked against libz.so.1 (it uses none of the library's symbols) dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'libmmb-dev' in '../libmmb-dev_4.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'libmmb4.1' in '../libmmb4.1_4.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'libmmb4.1-dbgsym' in '../libmmb4.1-dbgsym_4.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'mmb' in '../mmb_4.2+dfsg-2_amd64.deb'. dpkg-deb: building package 'mmb-dbgsym' in '../mmb-dbgsym_4.2+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=any -O../macromoleculebuilder_4.2+dfsg-2_amd64.buildinfo dpkg-genchanges --build=any -O../macromoleculebuilder_4.2+dfsg-2_amd64.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 2026-02-22T10:50:00Z +------------------------------------------------------------------------------+ | Finished Timed Build Commands Sun, 22 Feb 2026 10:50:00 +0000 | +------------------------------------------------------------------------------+ rm -Rf /build/reproducible-path/macromoleculebuilder-4.2+dfsg/ -------------------------------------------------------------- I: Finished running 'rm -Rf /build/reproducible-path/macromoleculebuilder-4.2+dfsg/'. Finished processing commands. -------------------------------------------------------------------------------- Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Sun, 22 Feb 2026 10:50:01 +0000 | +------------------------------------------------------------------------------+ macromoleculebuilder_4.2+dfsg-2_amd64.changes: ---------------------------------------------- Format: 1.8 Date: Thu, 15 Jan 2026 05:05:05 -0500 Source: macromoleculebuilder Binary: libmmb-dev libmmb4.1 libmmb4.1-dbgsym mmb mmb-dbgsym Built-For-Profiles: cross nocheck Architecture: amd64 Version: 4.2+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Andrius Merkys Description: libmmb-dev - development files of MacroMoleculeBuilder libmmb4.1 - shared library of MacroMoleculeBuilder mmb - model the structure and dynamics of macromolecules Closes: 1123836 Changes: macromoleculebuilder (4.2+dfsg-2) unstable; urgency=medium . * Rename build dependency gemmi-dev -> libgemmi-dev (Closes: 1123836) * Fix incompatibility with seqan2 >= 2.5.0. 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b288badd18c6186f8ee3578df54875c0b89ee43749decf101deb5c778501f87d 1608640 mmb-dbgsym_4.2+dfsg-2_amd64.deb 55010111cc01b4818894debf8feaa9b0e3a4690c7da4c8f556918365ec5b3769 30936 mmb_4.2+dfsg-2_amd64.deb Files: 62d6409682970769a9a7867309618202 77088 libdevel optional libmmb-dev_4.2+dfsg-2_amd64.deb 05bc52660fad03cddeb24bd4ffdac0ac 29116412 debug optional libmmb4.1-dbgsym_4.2+dfsg-2_amd64.deb c0da2380cedbf01d3325a88911ac9a1e 1282740 libs optional libmmb4.1_4.2+dfsg-2_amd64.deb 6716ed509b4017f6bada52d8fd9bf1de 10082 science optional macromoleculebuilder_4.2+dfsg-2_amd64.buildinfo 4209ca9e0ac9328948006e6b6791f944 1608640 debug optional mmb-dbgsym_4.2+dfsg-2_amd64.deb 866e0ce42581446c5da9904ca9f9c37c 30936 science optional mmb_4.2+dfsg-2_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Sun, 22 Feb 2026 10:50:03 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: macromoleculebuilder 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libmmb-dev_4.2+dfsg-2_amd64.deb 184d6c796a04a30e159800dfaa53b84c0df3aec13552d58e61dc53accc05f9bb 29116412 libmmb4.1-dbgsym_4.2+dfsg-2_amd64.deb 5b4501a93bcb677bf1f0af38b7500cbaea4382f68fd39bb6d34f84597c882fe1 1282740 libmmb4.1_4.2+dfsg-2_amd64.deb b288badd18c6186f8ee3578df54875c0b89ee43749decf101deb5c778501f87d 1608640 mmb-dbgsym_4.2+dfsg-2_amd64.deb 55010111cc01b4818894debf8feaa9b0e3a4690c7da4c8f556918365ec5b3769 30936 mmb_4.2+dfsg-2_amd64.deb Build-Origin: Debian Build-Architecture: arm64 Build-Date: Sun, 22 Feb 2026 10:49:58 +0000 Build-Path: /build/reproducible-path/macromoleculebuilder-4.2+dfsg Installed-Build-Depends: architecture-properties (= 0.2.6+b1), asciidoc-base (= 10.2.1-1), asciidoc-common (= 10.2.1-1), autoconf (= 2.72-3.1), automake (= 1:1.18.1-3), autopoint (= 0.23.2-1), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.8+b1), bash (= 5.3-2), binutils (= 2.46-2), binutils-aarch64-linux-gnu (= 2.46-2), binutils-common (= 2.46-2), bsdextrautils (= 2.41.3-4), build-essential (= 12.12), bzip2 (= 1.0.8-6+b1), cmake (= 4.2.3-2), cmake-data (= 4.2.3-2), coreutils (= 9.7-3+b1), cpp (= 4:15.2.0-5), cpp-15 (= 15.2.0-13), cpp-15-aarch64-linux-gnu (= 15.2.0-13), cpp-aarch64-linux-gnu (= 4:15.2.0-5), dash (= 0.5.12-12+b1), debconf (= 1.5.92), debhelper (= 13.30), debianutils (= 5.23.2+b1), dh-autoreconf (= 21+nmu1), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.12-1+b1), docbook-xml (= 4.5-13), docbook-xsl (= 1.79.2+dfsg-8), dpkg (= 1.23.5), dpkg-dev (= 1.23.5), dwz (= 0.16-2+b1), file (= 1:5.46-5+b1), findutils (= 4.10.0-3+b1), freeglut3-dev (= 3.4.0-6+b1), g++ (= 4:15.2.0-5), g++-15 (= 15.2.0-13), g++-15-aarch64-linux-gnu (= 15.2.0-13), g++-aarch64-linux-gnu (= 4:15.2.0-5), gcc (= 4:15.2.0-5), gcc-15 (= 15.2.0-13), gcc-15-aarch64-linux-gnu (= 15.2.0-13), gcc-15-base (= 15.2.0-13), gcc-aarch64-linux-gnu (= 4:15.2.0-5), gettext (= 0.23.2-1), gettext-base (= 0.23.2-1), grep (= 3.12-1+b1), groff-base (= 1.23.0-10+b1), gzip (= 1.13-1+b1), hostname (= 3.25+b1), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-3), libarchive-zip-perl (= 1.68-1), libarchive13t64 (= 3.8.5-1), libasan8 (= 15.2.0-13), libatomic1 (= 15.2.0-13), libattr1 (= 1:2.5.2-4), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46-2), libblas-dev (= 3.12.1-7+b1), libblas3 (= 3.12.1-7+b1), libblkid1 (= 2.41.3-4), libbrotli1 (= 1.2.0-3), libbsd0 (= 0.12.2-2+b1), libbz2-1.0 (= 1.0.8-6+b1), libc-bin (= 2.42-13), libc-dev-bin (= 2.42-13), libc-gconv-modules-extra (= 2.42-13), libc6 (= 2.42-13), libc6-dev (= 2.42-13), libcap-ng0 (= 0.9.1-1), libcap2 (= 1:2.75-10+b5), libcc1-0 (= 15.2.0-13), libcom-err2 (= 1.47.2-3+b8), libcrypt1 (= 1:4.5.1-1), libctf-nobfd0 (= 2.46-2), libctf0 (= 2.46-2), libcurl4t64 (= 8.19.0~rc2-1), libdb5.3t64 (= 5.3.28+dfsg2-11), libdebconfclient0 (= 0.282+b2), libdebhelper-perl (= 13.30), libdpkg-perl (= 1.23.5), libdrm-amdgpu1 (= 2.4.131-1), libdrm-common (= 2.4.131-1), libdrm-intel1 (= 2.4.131-1), libdrm2 (= 2.4.131-1), libedit2 (= 3.1-20251016-1), libelf1t64 (= 0.194-1), libexpat1 (= 2.7.4-1), libffi8 (= 3.5.2-3+b1), libfile-stripnondeterminism-perl (= 1.15.0-1), libgbm1 (= 26.0.0-1), libgcc-15-dev (= 15.2.0-13), libgcc-s1 (= 15.2.0-13), libgcrypt20 (= 1.11.2-3+b1), libgdbm-compat4t64 (= 1.26-1+b1), libgdbm6t64 (= 1.26-1+b1), libgemmi-dev (= 0.7.4+ds-1), libgfortran5 (= 15.2.0-13), libgl-dev (= 1.7.0-3), libgl1 (= 1.7.0-3), libgl1-mesa-dri (= 26.0.0-1), libglu1-mesa (= 9.0.2-1.1+b4), libglu1-mesa-dev (= 9.0.2-1.1+b4), libglut-dev (= 3.4.0-6+b1), libglut3.12 (= 3.4.0-6+b1), libglvnd0 (= 1.7.0-3), libglx-dev (= 1.7.0-3), libglx-mesa0 (= 26.0.0-1), libglx0 (= 1.7.0-3), libgmp10 (= 2:6.3.0+dfsg-5+b1), libgnutls30t64 (= 3.8.12-3), libgomp1 (= 15.2.0-13), libgpg-error0 (= 1.58-2), libgprofng0 (= 2.46-2), libgssapi-krb5-2 (= 1.22.1-2), libhogweed6t64 (= 3.10.2-1), libhwasan0 (= 15.2.0-13), libice-dev (= 2:1.1.1-1+b1), libice6 (= 2:1.1.1-1+b1), libidn2-0 (= 2.3.8-4+b1), libisl23 (= 0.27-1+b1), libitm1 (= 15.2.0-13), libjansson4 (= 2.14-2+b4), libjsoncpp26 (= 1.9.6-5), libk5crypto3 (= 1.22.1-2), libkeyutils1 (= 1.6.3-6+b1), libkrb5-3 (= 1.22.1-2), libkrb5support0 (= 1.22.1-2), liblapack-dev (= 3.12.1-7+b1), liblapack3 (= 3.12.1-7+b1), libldap2 (= 2.6.10+dfsg-1+b1), libllvm21 (= 1:21.1.8-3+b1), liblsan0 (= 15.2.0-13), liblz4-1 (= 1.10.0-6), liblzma5 (= 5.8.2-2), libmagic-mgc (= 1:5.46-5+b1), libmagic1t64 (= 1:5.46-5+b1), libmd0 (= 1.1.0-2+b2), libmount1 (= 2.41.3-4), libmpc3 (= 1.3.1-2+b1), libmpfr6 (= 4.2.2-2+b1), libncursesw6 (= 6.6+20251231-1), libnettle8t64 (= 3.10.2-1), libnghttp2-14 (= 1.68.0-1), libnghttp3-9 (= 1.12.0-1), libngtcp2-16 (= 1.16.0-1), libngtcp2-crypto-ossl0 (= 1.16.0-1), libopengl-dev (= 1.7.0-3), libopengl0 (= 1.7.0-3), libopenmm-dev (= 8.1.2+dfsg-12+b1), libopenmm8.1 (= 8.1.2+dfsg-12+b1), libp11-kit0 (= 0.26.2-2), libpam-modules (= 1.7.0-5+b1), libpam-modules-bin (= 1.7.0-5+b1), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5+b1), libpciaccess0 (= 0.17-3+b4), libpcre2-8-0 (= 10.46-1+b1), libperl5.40 (= 5.40.1-7), libpipeline1 (= 1.5.8-2), libproc2-0 (= 2:4.0.4-9+b1), libpsl5t64 (= 0.21.2-1.1+b2), libpython3-stdlib (= 3.13.9-3), libpython3.13-minimal (= 3.13.12-1), libpython3.13-stdlib (= 3.13.12-1), libquadmath0 (= 15.2.0-13), libreadline8t64 (= 8.3-4), librhash1 (= 1.4.6-1.1), librtmp1 (= 2.4+20151223.gitfa8646d.1-3+b1), libsasl2-2 (= 2.1.28+dfsg1-10), libsasl2-modules-db (= 2.1.28+dfsg1-10), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.9-4+b1), libsensors-config (= 1:3.6.2-2), libsensors5 (= 1:3.6.2-2+b1), libseqan2-dev (= 2.5.2-1), libsframe3 (= 2.46-2), libsimbody-dev (= 3.7+dfsg-5), libsimbody3.7 (= 3.7+dfsg-5), libsimtkmolmodel-dev (= 3.1.0-5), libsimtkmolmodel-plugins (= 3.1.0-5), libsimtkmolmodel3.1t64 (= 3.1.0-5), libsm-dev (= 2:1.2.6-1+b1), libsm6 (= 2:1.2.6-1+b1), libsmartcols1 (= 2.41.3-4), libsqlite3-0 (= 3.46.1-9), libssh2-1t64 (= 1.11.1-1+b1), libssl3t64 (= 3.5.5-1), libstb-dev (= 0.0~git20250907.fede005+ds-1+b1), libstb0t64 (= 0.0~git20250907.fede005+ds-1+b1), libstdc++-15-dev (= 15.2.0-13), libstdc++6 (= 15.2.0-13), libsystemd0 (= 259.1-1), libtasn1-6 (= 4.21.0-2), libtinfo6 (= 6.6+20251231-1), libtool (= 2.5.4-9), libtsan2 (= 15.2.0-13), libubsan1 (= 15.2.0-13), libuchardet0 (= 0.0.8-2+b1), libudev1 (= 259.1-1), libunistring5 (= 1.3-2+b1), libuuid1 (= 2.41.3-4), libuv1t64 (= 1.51.0-2+b1), libvulkan1 (= 1.4.341.0-1), libx11-6 (= 2:1.8.12-1+b1), libx11-data (= 2:1.8.12-1), libx11-dev (= 2:1.8.12-1+b1), libx11-xcb1 (= 2:1.8.12-1+b1), libxau-dev (= 1:1.0.11-1+b1), libxau6 (= 1:1.0.11-1+b1), libxcb-dri3-0 (= 1.17.0-2+b2), libxcb-glx0 (= 1.17.0-2+b2), libxcb-present0 (= 1.17.0-2+b2), libxcb-randr0 (= 1.17.0-2+b2), libxcb-shm0 (= 1.17.0-2+b2), libxcb-sync1 (= 1.17.0-2+b2), libxcb-xfixes0 (= 1.17.0-2+b2), libxcb1 (= 1.17.0-2+b2), libxcb1-dev (= 1.17.0-2+b2), libxdmcp-dev (= 1:1.1.5-2), libxdmcp6 (= 1:1.1.5-2), libxext-dev (= 2:1.3.4-1+b4), libxext6 (= 2:1.3.4-1+b4), libxfixes-dev (= 1:6.0.0-2+b5), libxfixes3 (= 1:6.0.0-2+b5), libxi-dev (= 2:1.8.2-2), libxi6 (= 2:1.8.2-2), libxml2-16 (= 2.15.1+dfsg-2+b1), libxml2-utils (= 2.15.1+dfsg-2+b1), libxmu-dev (= 2:1.1.3-4), libxmu-headers (= 2:1.1.3-4), libxmu6 (= 2:1.1.3-4), libxshmfence1 (= 1.3.3-1+b1), libxslt1.1 (= 1.1.43-0.3), libxt-dev (= 1:1.2.1-1.3+b1), libxt6t64 (= 1:1.2.1-1.3+b1), libxxf86vm1 (= 1:1.1.4-2), libxxhash0 (= 0.8.3-2+b1), libz3-4 (= 4.13.3-1+b1), libzstd1 (= 1.5.7+dfsg-3+b1), linux-libc-dev (= 6.18.12-1), m4 (= 1.4.21-1), make (= 4.4.1-3+b1), man-db (= 2.13.1-1+b1), mawk (= 1.3.4.20260129-1), media-types (= 14.0.0), mesa-libgallium (= 26.0.0-1), ncurses-base (= 6.6+20251231-1), ncurses-bin (= 6.6+20251231-1), netbase (= 6.5), openssl-provider-legacy (= 3.5.5-1), patch (= 2.8-2+b1), perl (= 5.40.1-7), perl-base (= 5.40.1-7), perl-modules-5.40 (= 5.40.1-7), po-debconf (= 1.0.22), procps (= 2:4.0.4-9+b1), python3 (= 3.13.9-3), python3-minimal (= 3.13.9-3), python3.13 (= 3.13.12-1), python3.13-minimal (= 3.13.12-1), readline-common (= 8.3-4), rpcsvc-proto (= 1.4.3-1+b2), sed (= 4.9-2+b2), sensible-utils (= 0.0.26), sgml-base (= 1.31+nmu1), sgml-data (= 2.0.11+nmu1), sysvinit-utils (= 3.15-6+b1), tao-pegtl-dev (= 3.2.7-1), tar (= 1.35+dfsg-4), tzdata (= 2025c-3), util-linux (= 2.41.3-4), uuid-dev (= 2.41.3-4), x11-common (= 1:7.7+26), x11proto-dev (= 2025.1-1), xml-core (= 0.19), xorg-sgml-doctools (= 1:1.11-1.1), xsltproc (= 1.1.43-0.3), xtrans-dev (= 1.6.0-1), xz-utils (= 5.8.2-2), zlib1g (= 1:1.3.dfsg+really1.3.1-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-3) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" SOURCE_DATE_EPOCH="1768471505" +------------------------------------------------------------------------------+ | Package contents Sun, 22 Feb 2026 10:50:04 +0000 | +------------------------------------------------------------------------------+ libmmb-dev_4.2+dfsg-2_amd64.deb ------------------------------- new Debian package, version 2.0. size 77088 bytes: control archive=2896 bytes. 770 bytes, 20 lines control 5109 bytes, 72 lines md5sums Package: libmmb-dev Source: macromoleculebuilder Version: 4.2+dfsg-2 Architecture: amd64 Maintainer: Debichem Team Installed-Size: 560 Depends: libmmb4.1 (= 4.2+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 2026-01-15 10:05 ./ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/include/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/include/MMB/ -rw-r--r-- root/root 8108 2025-01-24 10:51 ./usr/include/MMB/AddBackboneOxygenForces.h -rw-r--r-- root/root 6293 2025-01-24 10:51 ./usr/include/MMB/AddNASTForces.h -rw-r--r-- root/root 7278 2026-01-15 10:05 ./usr/include/MMB/AtomSpringContainer.h -rw-r--r-- root/root 3559 2025-01-24 10:51 ./usr/include/MMB/BaseInteractionParameterReader.h -rw-r--r-- root/root 3477 2025-01-24 10:51 ./usr/include/MMB/BasePairContainer.h -rw-r--r-- root/root 42908 2026-01-15 10:05 ./usr/include/MMB/BiopolymerClass.h -rw-r--r-- root/root 2644 2025-01-24 10:51 ./usr/include/MMB/BiopolymerClassTwoTransformForces.h -rw-r--r-- root/root 19309 2025-01-24 10:51 ./usr/include/MMB/CalcTransformCorrection.h -rw-r--r-- root/root 3188 2025-01-24 10:51 ./usr/include/MMB/CenterOfMass.h -rw-r--r-- root/root 1328 2025-01-24 10:51 ./usr/include/MMB/CifOutput.h -rw-r--r-- root/root 188 2025-01-24 10:51 ./usr/include/MMB/Constexpr.h -rw-r--r-- root/root 3848 2025-01-24 10:51 ./usr/include/MMB/ConstraintContainer.h -rw-r--r-- root/root 3295 2025-01-24 10:51 ./usr/include/MMB/ContactContainer.h -rw-r--r-- root/root 1793 2025-01-24 10:51 ./usr/include/MMB/DensityContainer.h -rw-r--r-- root/root 2105 2025-01-24 10:51 ./usr/include/MMB/DensityForce.h -rw-r--r-- root/root 7794 2025-01-24 10:51 ./usr/include/MMB/DensityMap.h -rw-r--r-- root/root 1912 2025-01-24 10:51 ./usr/include/MMB/DisplacementContainer.h -rw-r--r-- root/root 2165 2025-01-24 10:51 ./usr/include/MMB/ElectrostaticPotentialGridForce.h -rw-r--r-- root/root 3001 2025-01-24 10:51 ./usr/include/MMB/ExportMacros.h -rw-r--r-- root/root 752 2025-01-24 10:51 ./usr/include/MMB/ExtraMath.h -rw-r--r-- root/root 1756 2025-01-24 10:51 ./usr/include/MMB/GeometricCenter.h -rw-r--r-- root/root 4613 2025-01-24 10:51 ./usr/include/MMB/HarmonicVelocityRescalingThermostat.h -rw-r--r-- root/root 227 2025-01-24 10:51 ./usr/include/MMB/Impossible.h -rw-r--r-- root/root 4871 2025-01-24 10:51 ./usr/include/MMB/KBBackboneTorsionForce.h -rw-r--r-- root/root 312 2025-01-24 10:51 ./usr/include/MMB/Lepton.h -rw-r--r-- root/root 8211 2025-01-24 10:51 ./usr/include/MMB/LigandDroplet.h -rw-r--r-- root/root 16881 2025-01-24 10:51 ./usr/include/MMB/Ligands.h -rw-r--r-- root/root 16712 2025-01-24 10:51 ./usr/include/MMB/Ligands.sam.h -rw-r--r-- root/root 3130 2025-01-24 10:51 ./usr/include/MMB/MMBLogger.h -rw-r--r-- root/root 91 2026-01-15 10:05 ./usr/include/MMB/MMB_config.h -rw-r--r-- root/root 5172 2025-01-24 10:51 ./usr/include/MMB/MobilizerContainer.h -rw-r--r-- root/root 3821 2025-01-24 10:51 ./usr/include/MMB/MoleculeContainer.h -rw-r--r-- root/root 4156 2025-01-24 10:51 ./usr/include/MMB/MonoAtoms.h -rw-r--r-- root/root 7486 2025-01-24 10:51 ./usr/include/MMB/Mutation.h -rw-r--r-- root/root 328 2025-01-24 10:51 ./usr/include/MMB/NTC_FORCE_CLASS.h -rw-r--r-- root/root 4598 2025-01-24 10:51 ./usr/include/MMB/NTC_PARAMETER_READER.h -rw-r--r-- root/root 4871 2025-01-24 10:51 ./usr/include/MMB/NtCBackboneTorsionForce.h -rw-r--r-- root/root 1747 2025-01-24 10:51 ./usr/include/MMB/NtCForces.h -rw-r--r-- root/root 4568 2025-01-24 10:51 ./usr/include/MMB/NtCInteractionParameterReader.h -rw-r--r-- root/root 2181 2025-01-24 10:51 ./usr/include/MMB/NtC_Class_Container.h -rw-r--r-- root/root 15557 2025-01-24 10:51 ./usr/include/MMB/ParameterReader.h -rw-r--r-- root/root 56249 2025-01-24 10:51 ./usr/include/MMB/ParameterReader_wrapper.h -rw-r--r-- root/root 5300 2025-01-24 10:51 ./usr/include/MMB/PeriodicParameterReaderUpdater.h -rw-r--r-- root/root 5408 2025-01-24 10:51 ./usr/include/MMB/PeriodicPdbAndCOMWriter.h -rw-r--r-- root/root 3151 2025-01-24 10:51 ./usr/include/MMB/PeriodicPdbAndEnergySingleFrameWriter.h -rw-r--r-- root/root 2002 2025-01-24 10:51 ./usr/include/MMB/PeriodicPdbAndEnergyWriter.h -rw-r--r-- root/root 4985 2025-01-24 10:51 ./usr/include/MMB/PeriodicPdbSingleFrameWriter.h -rw-r--r-- root/root 4299 2025-01-24 10:51 ./usr/include/MMB/PeriodicScrubber.h -rw-r--r-- root/root 1615 2025-01-24 10:51 ./usr/include/MMB/ProgressWriter.h -rw-r--r-- root/root 8487 2025-01-24 10:51 ./usr/include/MMB/RandomizeRNACoordinates.h -rw-r--r-- root/root 8587 2025-01-24 10:51 ./usr/include/MMB/Repel.h -rw-r--r-- root/root 23997 2025-01-24 10:51 ./usr/include/MMB/ResidueStretchContainer.h -rw-r--r-- root/root 12884 2025-01-24 10:51 ./usr/include/MMB/RigidifyFormedHelices.h -rw-r--r-- root/root 7179 2025-01-24 10:51 ./usr/include/MMB/SetChiMobility.h -rw-r--r-- root/root 3252 2025-01-24 10:51 ./usr/include/MMB/SetSingleBondMobility.h -rw-r--r-- root/root 3132 2025-01-24 10:51 ./usr/include/MMB/Spiral.h -rw-r--r-- root/root 2359 2025-01-24 10:51 ./usr/include/MMB/StackingForceSubsystem.h -rw-r--r-- root/root 15674 2025-01-24 10:51 ./usr/include/MMB/Sterics.h -rw-r--r-- root/root 1958 2025-01-24 10:51 ./usr/include/MMB/TetherForce.h -rw-r--r-- root/root 13460 2026-01-15 10:05 ./usr/include/MMB/Threading.h -rw-r--r-- root/root 5366 2025-01-24 10:51 ./usr/include/MMB/UnitCellParameters.h -rw-r--r-- root/root 61244 2025-01-24 10:51 ./usr/include/MMB/Utils.h -rw-r--r-- root/root 12299 2025-01-24 10:51 ./usr/include/MMB/WadleyKeatingDuartePyleTorsionForce.h -rw-r--r-- root/root 2817 2025-01-24 10:51 ./usr/include/MMB/Water.h -rw-r--r-- root/root 3544 2025-01-24 10:51 ./usr/include/MMB/WaterDroplet.h -rw-r--r-- root/root 845 2025-01-24 10:51 ./usr/include/MMB/superimposer.h drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/lib/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/lib/x86_64-linux-gnu/cmake/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/lib/x86_64-linux-gnu/cmake/mmb/ -rw-r--r-- root/root 2756 2026-01-15 10:05 ./usr/lib/x86_64-linux-gnu/cmake/mmb/MmbConfigVersion.cmake -rw-r--r-- root/root 818 2026-01-15 10:05 ./usr/lib/x86_64-linux-gnu/cmake/mmb/MmbTargets-release.cmake -rw-r--r-- root/root 4540 2026-01-15 10:05 ./usr/lib/x86_64-linux-gnu/cmake/mmb/MmbTargets.cmake lrwxrwxrwx root/root 0 2026-01-15 10:05 ./usr/lib/x86_64-linux-gnu/libMMB.so -> libMMB.so.4.1 drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/lib/x86_64-linux-gnu/pkgconfig/ -rw-r--r-- root/root 194 2026-01-15 10:05 ./usr/lib/x86_64-linux-gnu/pkgconfig/mmb.pc drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/share/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/share/doc/libmmb-dev/ -rw-r--r-- root/root 1533 2026-01-15 10:05 ./usr/share/doc/libmmb-dev/changelog.Debian.gz -rw-r--r-- root/root 1977 2026-01-15 10:05 ./usr/share/doc/libmmb-dev/copyright libmmb4.1-dbgsym_4.2+dfsg-2_amd64.deb ------------------------------------- new Debian package, version 2.0. size 29116412 bytes: control archive=560 bytes. 396 bytes, 13 lines control 106 bytes, 1 lines md5sums Package: libmmb4.1-dbgsym Source: macromoleculebuilder Version: 4.2+dfsg-2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debichem Team Installed-Size: 30675 Depends: libmmb4.1 (= 4.2+dfsg-2) Section: debug Priority: optional Multi-Arch: same Description: debug symbols for libmmb4.1 Build-Ids: 3dfab6d7d4aa3af4c0ccfafdffc2bf1fd4a31e60 drwxr-xr-x root/root 0 2026-01-15 10:05 ./ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/lib/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/lib/debug/.build-id/3d/ -rw-r--r-- root/root 31400152 2026-01-15 10:05 ./usr/lib/debug/.build-id/3d/fab6d7d4aa3af4c0ccfafdffc2bf1fd4a31e60.debug drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/share/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-01-15 10:05 ./usr/share/doc/libmmb4.1-dbgsym -> libmmb4.1 libmmb4.1_4.2+dfsg-2_amd64.deb ------------------------------ new Debian package, version 2.0. size 1282740 bytes: control archive=1000 bytes. 817 bytes, 18 lines control 219 bytes, 3 lines md5sums 35 bytes, 1 lines shlibs 66 bytes, 2 lines triggers Package: libmmb4.1 Source: macromoleculebuilder Version: 4.2+dfsg-2 Architecture: amd64 Maintainer: Debichem Team Installed-Size: 4996 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libopenmm8.1 (>= 8.1.2+dfsg), libsimbody3.7 (>= 3.7+dfsg), libsimtkmolmodel3.1t64 (>= 3.1.0), libstdc++6 (>= 14) 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 2026-01-15 10:05 ./ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/lib/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 5101000 2026-01-15 10:05 ./usr/lib/x86_64-linux-gnu/libMMB.so.4.1 drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/share/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/share/doc/libmmb4.1/ -rw-r--r-- root/root 1533 2026-01-15 10:05 ./usr/share/doc/libmmb4.1/changelog.Debian.gz -rw-r--r-- root/root 1977 2026-01-15 10:05 ./usr/share/doc/libmmb4.1/copyright mmb-dbgsym_4.2+dfsg-2_amd64.deb ------------------------------- new Debian package, version 2.0. size 1608640 bytes: control archive=540 bytes. 360 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: mmb-dbgsym Source: macromoleculebuilder Version: 4.2+dfsg-2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debichem Team Installed-Size: 1644 Depends: mmb (= 4.2+dfsg-2) Section: debug Priority: optional Description: debug symbols for mmb Build-Ids: 169c857f390a675dfac31c8eb57a13f6187d520f drwxr-xr-x root/root 0 2026-01-15 10:05 ./ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/lib/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/lib/debug/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/lib/debug/.build-id/16/ -rw-r--r-- root/root 1672768 2026-01-15 10:05 ./usr/lib/debug/.build-id/16/9c857f390a675dfac31c8eb57a13f6187d520f.debug drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/share/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/share/doc/ lrwxrwxrwx root/root 0 2026-01-15 10:05 ./usr/share/doc/mmb-dbgsym -> mmb mmb_4.2+dfsg-2_amd64.deb ------------------------ new Debian package, version 2.0. size 30936 bytes: control archive=896 bytes. 792 bytes, 15 lines control 242 bytes, 4 lines md5sums Package: mmb Source: macromoleculebuilder Version: 4.2+dfsg-2 Architecture: amd64 Maintainer: Debichem Team Installed-Size: 114 Depends: mmb-common, libc6 (>= 2.34), libgcc-s1 (>= 3.0), libmmb4.1 (>= 4.2+dfsg), libsimbody3.7 (>= 3.7+dfsg), libsimtkmolmodel3.1t64 (>= 3.1.0), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4) 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 2026-01-15 10:05 ./ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/bin/ -rwxr-xr-x root/root 101616 2026-01-15 10:05 ./usr/bin/MMB drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/share/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/share/doc/mmb/ -rw-r--r-- root/root 1533 2026-01-15 10:05 ./usr/share/doc/mmb/changelog.Debian.gz -rw-r--r-- root/root 1977 2026-01-15 10:05 ./usr/share/doc/mmb/copyright drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/share/man/ drwxr-xr-x root/root 0 2026-01-15 10:05 ./usr/share/man/man1/ -rw-r--r-- root/root 792 2026-01-15 10:05 ./usr/share/man/man1/MMB.1.gz lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:arm64 Filtered Build-Depends: lintian:arm64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/build/reproducible-path/resolver-2NJ4tQ/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/build/reproducible-path/resolver-2NJ4tQ/apt_archive ./ InRelease Get:2 copy:/build/reproducible-path/resolver-2NJ4tQ/apt_archive ./ Release [615 B] Ign:3 copy:/build/reproducible-path/resolver-2NJ4tQ/apt_archive ./ Release.gpg Get:4 copy:/build/reproducible-path/resolver-2NJ4tQ/apt_archive ./ Sources [1563 B] Get:5 copy:/build/reproducible-path/resolver-2NJ4tQ/apt_archive ./ Packages [1643 B] Fetched 3821 B in 0s (151 kB/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... Execute external solver... The following additional packages will be installed: appstream ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libappstream5 libapt-pkg-perl libassuan9 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libcurl3t64-gnutls 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-find-rule-perl libfile-libmagic-perl libfile-listing-perl libfile-sharedir-perl libfont-ttf-perl libfyaml0 libglib2.0-0t64 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 libio-string-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl libksba8 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 libngtcp2-crypto-gnutls8 libnpth0t64 libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libstemmer0d 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-charwidth-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-wrapi18n-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 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxmlb2 libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop openssl patchutils perl-openssl-defaults plzip shared-mime-info t1utils ucf unzip Suggested packages: apt-config-icons isoquery libxml-parser-perl low-memory-monitor libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libmime-base32-perl libregexp-ipv6-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl zip Recommended packages: gnupg libcgi-fast-perl libglib2.0-data xdg-user-dirs libhtml-format-perl libio-compress-brotli-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 libxml-sax-expat-perl The following NEW packages will be installed: appstream ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libappstream5 libapt-pkg-perl libassuan9 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libcurl3t64-gnutls 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-find-rule-perl libfile-libmagic-perl libfile-listing-perl libfile-sharedir-perl libfont-ttf-perl libfyaml0 libglib2.0-0t64 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 libio-string-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl libksba8 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 libngtcp2-crypto-gnutls8 libnpth0t64 libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libstemmer0d 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-charwidth-perl libtext-glob-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-wrapi18n-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 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxmlb2 libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop openssl patchutils perl-openssl-defaults plzip sbuild-build-depends-lintian-dummy:amd64 shared-mime-info t1utils ucf unzip 0 upgraded, 147 newly installed, 0 to remove and 0 not upgraded. Need to get 16.7 MB of archives. After this operation, 76.1 MB of additional disk space will be used. Get:1 copy:/build/reproducible-path/resolver-2NJ4tQ/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [832 B] Get:2 http://mirror.einval.org/debian unstable/main arm64 openssl arm64 3.5.5-1 [1461 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 ca-certificates all 20250419 [162 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libtext-charwidth-perl arm64 0.04-11+b5 [9644 B] Get:5 http://mirror.einval.org/debian unstable/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get:6 http://mirror.einval.org/debian unstable/main arm64 ucf all 3.0052 [43.3 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.87.2-3 [1444 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 shared-mime-info arm64 2.4-5+b4 [754 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.16.0-1 [23.8 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.19.0~rc2-1 [368 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 libfyaml0 arm64 0.9.4-1 [245 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 libstemmer0d arm64 3.0.1-1+b1 [123 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 libxmlb2 arm64 0.3.24-2 [58.5 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 libappstream5 arm64 1.1.2-1 [210 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 appstream arm64 1.1.2-1 [564 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 diffstat arm64 1.68-1+b1 [33.1 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 libassuan9 arm64 3.0.2-2+b1 [59.0 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 gpgconf arm64 2.4.8-5 [121 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 libksba8 arm64 1.6.7-2+b2 [125 kB] Get:20 http://mirror.einval.org/debian unstable/main arm64 libnpth0t64 arm64 1.8-3+b1 [23.1 kB] Get:21 http://mirror.einval.org/debian unstable/main arm64 gpg arm64 2.4.8-5 [572 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 iso-codes all 4.20.1-1 [3319 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 libaliased-perl all 0.34-3 [13.5 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 libapt-pkg-perl arm64 0.1.43 [64.6 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b3 [10.6 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 libdynaloader-functions-perl all 0.004-2 [12.2 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 libdevel-callchecker-perl arm64 0.009-3 [15.5 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 libparams-classify-perl arm64 0.015-2+b5 [22.3 kB] Get:29 http://mirror.einval.org/debian unstable/main arm64 libmodule-runtime-perl all 0.018-1 [17.8 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:33 http://mirror.einval.org/debian unstable/main arm64 libvariable-magic-perl arm64 0.64-1+b2 [43.9 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 libb-hooks-endofscope-perl all 0.28-2 [17.6 kB] Get:35 http://mirror.einval.org/debian unstable/main arm64 libberkeleydb-perl arm64 0.66-2 [116 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 libcapture-tiny-perl all 0.50-1 [24.6 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:38 http://mirror.einval.org/debian unstable/main arm64 liburi-perl all 5.34-2 [111 kB] Get:39 http://mirror.einval.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.83-1+b3 [97.2 kB] Get:40 http://mirror.einval.org/debian unstable/main arm64 libcgi-pm-perl all 4.71-1 [217 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get:42 http://mirror.einval.org/debian unstable/main arm64 libclass-inspector-perl all 1.36-3 [17.5 kB] Get:43 http://mirror.einval.org/debian unstable/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get:44 http://mirror.einval.org/debian unstable/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b6 [35.1 kB] Get:45 http://mirror.einval.org/debian unstable/main arm64 libclone-perl arm64 0.47-1+b2 [13.7 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 libconfig-tiny-perl all 2.30-1 [18.9 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 libparams-util-perl arm64 1.102-3+b2 [23.9 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libsub-install-perl all 0.929-1 [10.5 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 libconst-fast-perl all 0.014-2 [8792 B] Get:52 http://mirror.einval.org/debian unstable/main arm64 libcpanel-json-xs-perl arm64 4.40-1 [129 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 libdata-dpath-perl all 0.60-1 [41.8 kB] Get:58 http://mirror.einval.org/debian unstable/main arm64 libdata-messagepack-perl arm64 1.02-3+b1 [31.5 kB] Get:59 http://mirror.einval.org/debian unstable/main arm64 libnet-domain-tld-perl all 1.75-4 [31.5 kB] Get:60 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-domain-perl all 0.15-1 [11.9 kB] Get:61 http://mirror.einval.org/debian unstable/main arm64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:62 http://mirror.einval.org/debian unstable/main arm64 libnet-netmask-perl all 2.0003-1 [28.5 kB] Get:63 http://mirror.einval.org/debian unstable/main arm64 libnetaddr-ip-perl arm64 4.079+dfsg-2+b6 [97.8 kB] Get:64 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-ip-perl all 0.31-1 [20.6 kB] Get:65 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-uri-perl all 0.07-3 [11.0 kB] Get:66 http://mirror.einval.org/debian unstable/main arm64 libdevel-size-perl arm64 0.86-1 [24.0 kB] Get:67 http://mirror.einval.org/debian unstable/main arm64 libemail-address-xs-perl arm64 1.05-1+b5 [28.2 kB] Get:68 http://mirror.einval.org/debian unstable/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:69 http://mirror.einval.org/debian unstable/main arm64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:70 http://mirror.einval.org/debian unstable/main arm64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:71 http://mirror.einval.org/debian unstable/main arm64 libnumber-compare-perl all 0.03-3 [6332 B] Get:72 http://mirror.einval.org/debian unstable/main arm64 libtext-glob-perl all 0.11-3 [7676 B] Get:73 http://mirror.einval.org/debian unstable/main arm64 libfile-find-rule-perl all 0.35-1 [25.9 kB] Get:74 http://mirror.einval.org/debian unstable/main arm64 libfile-libmagic-perl arm64 1.23-2+b3 [31.1 kB] Get:75 http://mirror.einval.org/debian unstable/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:76 http://mirror.einval.org/debian unstable/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:77 http://mirror.einval.org/debian unstable/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:78 http://mirror.einval.org/debian unstable/main arm64 libfile-sharedir-perl all 1.118-3 [16.0 kB] Get:79 http://mirror.einval.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get:80 http://mirror.einval.org/debian unstable/main arm64 libfont-ttf-perl all 1.06-2 [318 kB] Get:81 http://mirror.einval.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get:82 http://mirror.einval.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:83 http://mirror.einval.org/debian unstable/main arm64 libhttp-message-perl all 7.01-1 [80.0 kB] Get:84 http://mirror.einval.org/debian unstable/main arm64 libhtml-form-perl all 6.13-1 [32.6 kB] Get:85 http://mirror.einval.org/debian unstable/main arm64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:86 http://mirror.einval.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get:87 http://mirror.einval.org/debian unstable/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:88 http://mirror.einval.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:89 http://mirror.einval.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B] Get:90 http://mirror.einval.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.94-3+b1 [326 kB] Get:91 http://mirror.einval.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.098-1 [229 kB] Get:92 http://mirror.einval.org/debian unstable/main arm64 libnet-http-perl all 6.24-1 [23.2 kB] Get:93 http://mirror.einval.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get:94 http://mirror.einval.org/debian unstable/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:95 http://mirror.einval.org/debian unstable/main arm64 libwww-perl all 6.81-1 [186 kB] Get:96 http://mirror.einval.org/debian unstable/main arm64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:97 http://mirror.einval.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:98 http://mirror.einval.org/debian unstable/main arm64 libio-interactive-perl all 1.027-1 [11.8 kB] Get:99 http://mirror.einval.org/debian unstable/main arm64 libipc-run3-perl all 0.049-1 [31.5 kB] Get:100 http://mirror.einval.org/debian unstable/main arm64 libjson-maybexs-perl all 1.004008-1 [12.9 kB] Get:101 http://mirror.einval.org/debian unstable/main arm64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:102 http://mirror.einval.org/debian unstable/main arm64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:103 http://mirror.einval.org/debian unstable/main arm64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:104 http://mirror.einval.org/debian unstable/main arm64 liblz1 arm64 1.16~rc1-3 [38.5 kB] Get:105 http://mirror.einval.org/debian unstable/main arm64 liblzo2-2 arm64 2.10-3+b2 [50.7 kB] Get:106 http://mirror.einval.org/debian unstable/main arm64 libmarkdown2 arm64 2.2.7-2.1+b1 [33.8 kB] Get:107 http://mirror.einval.org/debian unstable/main arm64 libmldbm-perl all 2.05-4 [16.8 kB] Get:108 http://mirror.einval.org/debian unstable/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:109 http://mirror.einval.org/debian unstable/main arm64 libsub-quote-perl all 2.006009-1 [21.3 kB] Get:110 http://mirror.einval.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get:111 http://mirror.einval.org/debian unstable/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:112 http://mirror.einval.org/debian unstable/main arm64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:113 http://mirror.einval.org/debian unstable/main arm64 libmouse-perl arm64 2.6.1-1 [140 kB] Get:114 http://mirror.einval.org/debian unstable/main arm64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:115 http://mirror.einval.org/debian unstable/main arm64 libsub-identify-perl arm64 0.14-4 [10.9 kB] Get:116 http://mirror.einval.org/debian unstable/main arm64 libsub-name-perl arm64 0.28-1+b1 [12.4 kB] Get:117 http://mirror.einval.org/debian unstable/main arm64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:118 http://mirror.einval.org/debian unstable/main arm64 libpath-tiny-perl all 0.148-1 [56.7 kB] Get:119 http://mirror.einval.org/debian unstable/main arm64 libperlio-gzip-perl arm64 0.20-1+b5 [17.4 kB] Get:120 http://mirror.einval.org/debian unstable/main arm64 libperlio-utf8-strict-perl arm64 0.010-1+b4 [11.4 kB] Get:121 http://mirror.einval.org/debian unstable/main arm64 libproc-processtable-perl arm64 0.637-1+b1 [41.6 kB] Get:122 http://mirror.einval.org/debian unstable/main arm64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:123 http://mirror.einval.org/debian unstable/main arm64 libsereal-decoder-perl arm64 5.004+ds-1+b4 [97.1 kB] Get:124 http://mirror.einval.org/debian unstable/main arm64 libsereal-encoder-perl arm64 5.004+ds-1+b4 [99.6 kB] Get:125 http://mirror.einval.org/debian unstable/main arm64 libsort-versions-perl all 1.62-3 [8928 B] Get:126 http://mirror.einval.org/debian unstable/main arm64 libxs-parse-keyword-perl arm64 0.49-1 [64.3 kB] Get:127 http://mirror.einval.org/debian unstable/main arm64 libsyntax-keyword-try-perl arm64 0.31-1 [27.2 kB] Get:128 http://mirror.einval.org/debian unstable/main arm64 libterm-readkey-perl arm64 2.38-2+b5 [24.5 kB] Get:129 http://mirror.einval.org/debian unstable/main arm64 libtext-levenshteinxs-perl arm64 0.03-5+b5 [8792 B] Get:130 http://mirror.einval.org/debian unstable/main arm64 libtext-markdown-discount-perl arm64 0.18-1+b1 [13.5 kB] Get:131 http://mirror.einval.org/debian unstable/main arm64 libtext-xslate-perl arm64 3.5.9-2+b2 [171 kB] Get:132 http://mirror.einval.org/debian unstable/main arm64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:133 http://mirror.einval.org/debian unstable/main arm64 libtime-moment-perl arm64 0.46-1 [77.1 kB] Get:134 http://mirror.einval.org/debian unstable/main arm64 libunicode-utf8-perl arm64 0.63-1 [20.1 kB] Get:135 http://mirror.einval.org/debian unstable/main arm64 libwww-mechanize-perl all 2.20-1 [117 kB] Get:136 http://mirror.einval.org/debian unstable/main arm64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:137 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:138 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-perl all 1.02+dfsg-4 [53.4 kB] Get:139 http://mirror.einval.org/debian unstable/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-7 [300 kB] Get:140 http://mirror.einval.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-2+b1 [47.8 kB] Get:141 http://mirror.einval.org/debian unstable/main arm64 libyaml-libyaml-perl arm64 0.904.0+ds-1 [43.6 kB] Get:142 http://mirror.einval.org/debian unstable/main arm64 plzip arm64 1.13~rc1-3 [61.2 kB] Get:143 http://mirror.einval.org/debian unstable/main arm64 lzop arm64 1.04-2+b2 [82.0 kB] Get:144 http://mirror.einval.org/debian unstable/main arm64 patchutils arm64 0.4.3-1+b1 [74.8 kB] Get:145 http://mirror.einval.org/debian unstable/main arm64 t1utils arm64 1.41-4+b2 [57.5 kB] Get:146 http://mirror.einval.org/debian unstable/main arm64 unzip arm64 6.0-29+b1 [163 kB] Get:147 http://mirror.einval.org/debian unstable/main arm64 lintian all 2.129.0 [1068 kB] Preconfiguring packages ... Fetched 16.7 MB in 0s (56.7 MB/s) Selecting previously unselected package openssl. (Reading database ... 29039 files and directories currently installed.) Preparing to unpack .../000-openssl_3.5.5-1_arm64.deb ... Unpacking openssl (3.5.5-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../001-ca-certificates_20250419_all.deb ... Unpacking ca-certificates (20250419) ... Selecting previously unselected package libtext-charwidth-perl:arm64. Preparing to unpack .../002-libtext-charwidth-perl_0.04-11+b5_arm64.deb ... Unpacking libtext-charwidth-perl:arm64 (0.04-11+b5) ... Selecting previously unselected package libtext-wrapi18n-perl. Preparing to unpack .../003-libtext-wrapi18n-perl_0.06-10_all.deb ... Unpacking libtext-wrapi18n-perl (0.06-10) ... Selecting previously unselected package ucf. Preparing to unpack .../004-ucf_3.0052_all.deb ... Moving old data out of the way Unpacking ucf (3.0052) ... Selecting previously unselected package libglib2.0-0t64:arm64. Preparing to unpack .../005-libglib2.0-0t64_2.87.2-3_arm64.deb ... Unpacking libglib2.0-0t64:arm64 (2.87.2-3) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../006-shared-mime-info_2.4-5+b4_arm64.deb ... Unpacking shared-mime-info (2.4-5+b4) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:arm64. Preparing to unpack .../007-libngtcp2-crypto-gnutls8_1.16.0-1_arm64.deb ... Unpacking libngtcp2-crypto-gnutls8:arm64 (1.16.0-1) ... Selecting previously unselected package libcurl3t64-gnutls:arm64. Preparing to unpack .../008-libcurl3t64-gnutls_8.19.0~rc2-1_arm64.deb ... Unpacking libcurl3t64-gnutls:arm64 (8.19.0~rc2-1) ... Selecting previously unselected package libfyaml0:arm64. Preparing to unpack .../009-libfyaml0_0.9.4-1_arm64.deb ... Unpacking libfyaml0:arm64 (0.9.4-1) ... Selecting previously unselected package libstemmer0d:arm64. 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Unpacking libxml-sax-base-perl (1.09-3) ... Selecting previously unselected package libxml-sax-perl. Preparing to unpack .../136-libxml-sax-perl_1.02+dfsg-4_all.deb ... Unpacking libxml-sax-perl (1.02+dfsg-4) ... Selecting previously unselected package libxml-libxml-perl. Preparing to unpack .../137-libxml-libxml-perl_2.0207+dfsg+really+2.0134-7_arm64.deb ... Unpacking libxml-libxml-perl (2.0207+dfsg+really+2.0134-7) ... Selecting previously unselected package libyaml-0-2:arm64. Preparing to unpack .../138-libyaml-0-2_0.2.5-2+b1_arm64.deb ... Unpacking libyaml-0-2:arm64 (0.2.5-2+b1) ... Selecting previously unselected package libyaml-libyaml-perl. Preparing to unpack .../139-libyaml-libyaml-perl_0.904.0+ds-1_arm64.deb ... Unpacking libyaml-libyaml-perl (0.904.0+ds-1) ... Selecting previously unselected package plzip. Preparing to unpack .../140-plzip_1.13~rc1-3_arm64.deb ... Unpacking plzip (1.13~rc1-3) ... Selecting previously unselected package lzop. 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Setting up libksba8:arm64 (1.6.7-2+b2) ... Setting up libberkeleydb-perl:arm64 (0.66-2) ... Setting up plzip (1.13~rc1-3) ... 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 libtext-charwidth-perl:arm64 (0.04-11+b5) ... Setting up libnpth0t64:arm64 (1.8-3+b1) ... Setting up libunicode-utf8-perl (0.63-1) ... Setting up libmouse-perl:arm64 (2.6.1-1) ... Setting up libdata-messagepack-perl (1.02-3+b1) ... Setting up libclass-inspector-perl (1.36-3) ... Setting up libdynaloader-functions-perl (0.004-2) ... Setting up libtext-glob-perl (0.11-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up liblist-compare-perl (0.55-2) ... Setting up libclone-perl:arm64 (0.47-1+b2) ... Setting up libyaml-0-2:arm64 (0.2.5-2+b1) ... Setting up libsub-identify-perl (0.14-4) ... Setting up libcpanel-json-xs-perl:arm64 (4.40-1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdevel-size-perl (0.86-1) ... Setting up unzip (6.0-29+b1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libyaml-libyaml-perl (0.904.0+ds-1) ... Setting up libio-interactive-perl (1.027-1) ... Setting up libtry-tiny-perl (0.32-1) ... Setting up perl-openssl-defaults:arm64 (7+b2) ... Setting up libmldbm-perl (2.05-4) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up liblzo2-2:arm64 (2.10-3+b2) ... Setting up libtime-moment-perl (0.46-1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libconfig-tiny-perl (2.30-1) ... Setting up libsereal-encoder-perl (5.004+ds-1+b4) ... Setting up liblist-utilsby-perl (0.12-2) ... Setting up libtext-wrapi18n-perl (0.06-10) ... Setting up libnet-netmask-perl (2.0003-1) ... Setting up libsub-install-perl (0.929-1) ... Setting up libfyaml0:arm64 (0.9.4-1) ... Setting up libnumber-compare-perl (0.03-3) ... Setting up patchutils (0.4.3-1+b1) ... Setting up libjson-maybexs-perl (1.004008-1) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2+b6) ... Setting up libglib2.0-0t64:arm64 (2.87.2-3) ... No schema files found: doing nothing. Setting up libclass-data-inheritable-perl (0.10-1) ... Setting up libfile-find-rule-perl (0.35-1) ... Setting up libipc-system-simple-perl (1.30-2) ... Setting up libnet-domain-tld-perl (1.75-4) ... Setting up libperlio-utf8-strict-perl (0.010-1+b4) ... Setting up t1utils (1.41-4+b2) ... Setting up shared-mime-info (2.4-5+b4) ... Setting up diffstat (1.68-1+b1) ... Setting up libvariable-magic-perl (0.64-1+b2) ... Setting up libio-html-perl (1.004-3) ... Setting up libb-hooks-op-check-perl:arm64 (0.22-3+b3) ... Setting up libfile-libmagic-perl (1.23-2+b3) ... Setting up ucf (3.0052) ... Setting up libparams-util-perl (1.102-3+b2) ... Setting up libtime-duration-perl (1.21-2) ... Setting up libtext-xslate-perl:arm64 (3.5.9-2+b2) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libcapture-tiny-perl (0.50-1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libsub-name-perl:arm64 (0.28-1+b1) ... Setting up libdata-validate-domain-perl (0.15-1) ... Setting up libproc-processtable-perl:arm64 (0.637-1+b1) ... Setting up libpath-tiny-perl (0.148-1) ... Setting up lzop (1.04-2+b2) ... Setting up libassuan9:arm64 (3.0.2-2+b1) ... Setting up gpgconf (2.4.8-5) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.049-1) ... Setting up libregexp-wildcards-perl (1.05-3) ... Setting up libfile-sharedir-perl (1.118-3) ... Setting up libaliased-perl (0.34-3) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006009-1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b6) ... Setting up libstemmer0d:arm64 (3.0.1-1+b1) ... Setting up libsort-versions-perl (1.62-3) ... Setting up libterm-readkey-perl (2.38-2+b5) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.5.5-1) ... Setting up libtext-levenshteinxs-perl (0.03-5+b5) ... Setting up libperlio-gzip-perl (0.20-1+b5) ... Setting up libhtml-html5-entities-perl (0.004-3) ... Setting up libsereal-decoder-perl (5.004+ds-1+b4) ... Setting up libmarkdown2:arm64 (2.2.7-2.1+b1) ... Setting up liburi-perl (5.34-2) ... Setting up iso-codes (4.20.1-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up gpg (2.4.8-5) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.16.0-1) ... Setting up libdata-validate-ip-perl (0.31-1) ... Setting up libemail-address-xs-perl (1.05-1+b5) ... Setting up libnet-ssleay-perl:arm64 (1.94-3+b1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libfile-basedir-perl (0.09-2) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libxmlb2:arm64 (0.3.24-2) ... Setting up libcurl3t64-gnutls:arm64 (8.19.0~rc2-1) ... Setting up libnet-http-perl (6.24-1) ... Setting up libtext-markdown-discount-perl (0.18-1+b1) ... Setting up libappstream5:arm64 (1.1.2-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:arm64 (0.009-3) ... Setting up libxml-sax-perl (1.02+dfsg-4) ... 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 ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libdata-validate-uri-perl (0.07-3) ... Setting up libxs-parse-keyword-perl (0.49-1) ... Setting up appstream (1.1.2-1) ... ✔ Metadata cache was updated successfully. Setting up libdata-optlist-perl (0.114-1) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-7) ... 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... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libsyntax-keyword-try-perl (0.31-1) ... Setting up libhtml-parser-perl:arm64 (3.83-1+b3) ... Setting up libio-socket-ssl-perl (2.098-1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libhttp-message-perl (7.01-1) ... Setting up libhtml-form-perl (6.13-1) ... 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 (6.11-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:arm64 (0.015-2+b5) ... Setting up libcgi-pm-perl (4.71-1) ... Setting up libmodule-runtime-perl (0.018-1) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.60-1) ... 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 (0.28-2) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libwww-perl (6.81-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.20-1) ... Processing triggers for sgml-base (1.31+nmu1) ... Processing triggers for libc-bin (2.42-13) ... Setting up lintian (2.129.0) ... Processing triggers for man-db (2.13.1-1+b1) ... Not building database; man-db/auto-update is not 'true'. Setting up sbuild-build-depends-lintian-dummy:amd64 (0.invalid.0) ... Processing triggers for ca-certificates (20250419) ... 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 Sun, 22 Feb 2026 10:53:04 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Sun, 22 Feb 2026 10:53:04 +0000 | +------------------------------------------------------------------------------+ Purging /build/reproducible-path Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Sun, 22 Feb 2026 10:53:08 +0000 | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Build-Space: n/a Build-Time: 2060 Distribution: unstable Foreign Architectures: amd64 Host Architecture: amd64 Install-Time: 95 Job: macromoleculebuilder_4.2+dfsg-2 Lintian: pass Machine Architecture: arm64 Package: macromoleculebuilder Package-Time: 2198 Source-Version: 4.2+dfsg-2 Space: n/a Status: successful Version: 4.2+dfsg-2 -------------------------------------------------------------------------------- Finished at 2026-02-22T10:50:00Z Build needed 00:36:38, no disk space