sbuild (Debian sbuild) 0.85.0 (04 January 2023) on mjolnir.einval.org

+==============================================================================+
| macromoleculebuilder 4.0.0+dfsg-3.1 (amd64)  Wed, 24 Apr 2024 08:31:40 +0000 |
+==============================================================================+

Package: macromoleculebuilder
Version: 4.0.0+dfsg-3.1
Source Version: 4.0.0+dfsg-3.1
Distribution: unstable
Machine Architecture: arm64
Host Architecture: amd64
Build Architecture: arm64
Build Profiles: cross nocheck
Build Type: any

Unpacking /home/helmut/.cache/sbuild/unstable-arm64-sbuild.tar.zst to /tmp/tmp.sbuild.Z5PmqMx0fH...
I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-g823Zu/resolver-FawOld' with '<<RESOLVERDIR>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://mirror.einval.org/debian unstable InRelease [198 kB]
Get:2 http://mirror.einval.org/debian unstable/main Sources [10.6 MB]
Get:3 http://mirror.einval.org/debian unstable/main arm64 Packages [9753 kB]
Get:4 http://mirror.einval.org/debian unstable/main amd64 Packages [9873 kB]
Fetched 30.4 MB in 8s (3928 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages will be upgraded:
  apt libapt-pkg6.0t64
2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 2200 kB of archives.
After this operation, 23.6 kB of additional disk space will be used.
Get:1 http://mirror.einval.org/debian unstable/main arm64 libapt-pkg6.0t64 arm64 2.9.2 [881 kB]
Get:2 http://mirror.einval.org/debian unstable/main arm64 apt arm64 2.9.2 [1319 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 2200 kB in 0s (42.6 MB/s)
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11927 files and directories currently installed.)
Preparing to unpack .../libapt-pkg6.0t64_2.9.2_arm64.deb ...
Unpacking libapt-pkg6.0t64:arm64 (2.9.2) over (2.9.1) ...
Setting up libapt-pkg6.0t64:arm64 (2.9.2) ...
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11927 files and directories currently installed.)
Preparing to unpack .../archives/apt_2.9.2_arm64.deb ...
Unpacking apt (2.9.2) over (2.9.1) ...
Setting up apt (2.9.2) ...
Processing triggers for libc-bin (2.37-18) ...

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'macromoleculebuilder' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/debichem-team/macromoleculebuilder.git
Please use:
git clone https://salsa.debian.org/debichem-team/macromoleculebuilder.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 2575 kB of source archives.
Get:1 http://mirror.einval.org/debian unstable/main macromoleculebuilder 4.0.0+dfsg-3.1 (dsc) [2450 B]
Get:2 http://mirror.einval.org/debian unstable/main macromoleculebuilder 4.0.0+dfsg-3.1 (tar) [2567 kB]
Get:3 http://mirror.einval.org/debian unstable/main macromoleculebuilder 4.0.0+dfsg-3.1 (diff) [5704 B]
Fetched 2575 kB in 0s (8580 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-g823Zu/macromoleculebuilder-4.0.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-g823Zu' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: dpkg-dev (>= 1.22.5), asciidoc-base, cmake, debhelper-compat (= 13), docbook-xml, gemmi-dev (>= 0.6.2+ds-2), libopenmm-dev, libseqan2-dev, libsimbody-dev, libsimtkmolmodel-dev (>= 3.1.0), libsimtkmolmodel-plugins, libstb-dev, tao-pegtl-dev, zlib1g-dev, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64
Filtered Build-Depends: dpkg-dev (>= 1.22.5), asciidoc-base, cmake, debhelper-compat (= 13), docbook-xml, gemmi-dev (>= 0.6.2+ds-2), libopenmm-dev, libseqan2-dev, libsimbody-dev, libsimtkmolmodel-dev (>= 3.1.0), libsimtkmolmodel-plugins, libstb-dev, tao-pegtl-dev, zlib1g-dev, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [942 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [986 B]
Fetched 2537 B in 0s (144 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:
  asciidoc-base asciidoc-common autoconf automake autopoint autotools-dev
  binutils-x86-64-linux-gnu bsdextrautils cmake cmake-data
  cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config
  crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism
  docbook-xml docbook-xsl dpkg-cross dwz fakeroot file freeglut3-dev:amd64
  g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-13-base:amd64
  gcc-13-cross-base gcc-13-x86-64-linux-gnu gcc-13-x86-64-linux-gnu-base
  gcc-14-base:amd64 gcc-14-cross-base gcc-x86-64-linux-gnu gemmi-dev:amd64
  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
  libbsd0:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64
  libc6-dev-amd64-cross libcom-err2 libconfig-auto-perl
  libconfig-inifiles-perl libcrypt-dev:amd64 libcrypt1:amd64 libcurl4t64
  libdebhelper-perl libdebian-dpkgcross-perl libdrm-amdgpu1:amd64
  libdrm-common libdrm-intel1:amd64 libdrm-nouveau2:amd64 libdrm-radeon1:amd64
  libdrm2:amd64 libedit2:amd64 libegl-dev:amd64 libegl-mesa0:amd64
  libegl1:amd64 libelf1t64 libelf1t64:amd64 libexpat1 libexpat1:amd64
  libfakeroot libffi8:amd64 libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libgbm1:amd64
  libgcc-13-dev:amd64 libgcc-13-dev-amd64-cross libgcc-s1:amd64
  libgcc-s1-amd64-cross libgfortran5:amd64 libgl-dev:amd64 libgl1:amd64
  libgl1-mesa-dev:amd64 libgl1-mesa-dri:amd64 libglapi-mesa:amd64
  libgles-dev:amd64 libgles1:amd64 libgles2:amd64 libglu1-mesa:amd64
  libglu1-mesa-dev:amd64 libglut-dev:amd64 libglut3.12:amd64
  libglvnd-core-dev:amd64 libglvnd-dev:amd64 libglvnd0:amd64 libglx-dev:amd64
  libglx-mesa0:amd64 libglx0:amd64 libgomp1:amd64 libgomp1-amd64-cross
  libgssapi-krb5-2 libhwasan0:amd64 libhwasan0-amd64-cross libice-dev:amd64
  libice6:amd64 libicu72 libicu72:amd64 libio-string-perl libitm1:amd64
  libitm1-amd64-cross libjsoncpp25 libk5crypto3 libkeyutils1 libkrb5-3
  libkrb5support0 liblapack-dev:amd64 liblapack3:amd64 libldap-2.5-0
  libllvm17t64:amd64 liblocale-gettext-perl liblsan0:amd64
  liblsan0-amd64-cross liblzma5:amd64 libmagic-mgc libmagic1t64 libmd0:amd64
  libncursesw6 libnghttp2-14 libopengl-dev:amd64 libopengl0:amd64
  libopenmm-dev:amd64 libopenmm8.0t64:amd64 libpciaccess0:amd64 libpipeline1
  libproc2-0 libpsl5t64 libpthread-stubs0-dev libpthread-stubs0-dev:amd64
  libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib
  libquadmath0:amd64 libquadmath0-amd64-cross libreadline8t64 librhash0
  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++-13-dev:amd64
  libstdc++-13-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross
  libsub-override-perl libtinfo6:amd64 libtool libtsan2:amd64
  libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0
  libuuid1:amd64 libuv1t64 libvulkan1:amd64 libwayland-client0:amd64
  libwayland-server0: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-dri2-0: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 libxml-libxml-perl libxml-namespacesupport-perl
  libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2
  libxml2:amd64 libxml2-utils libxmu-dev:amd64 libxmu-headers libxmu6:amd64
  libxshmfence1:amd64 libxslt1.1 libxt-dev:amd64 libxt6t64:amd64
  libxxf86vm1:amd64 libyaml-perl libz3-4:amd64 libzstd1:amd64 m4 man-db
  media-types netbase po-debconf procps python3 python3-minimal python3.11
  python3.11-minimal readline-common sensible-utils sgml-base sgml-data
  tao-pegtl-dev tzdata ucf 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-13-locales cpp-13-doc cpp-doc dh-make docbook docbook-dsssl
  docbook-defguide dbtoepub docbook-xsl-doc-html | docbook-xsl-doc-pdf
  | docbook-xsl-doc-text | docbook-xsl-doc docbook-xsl-saxon fop libsaxon-java
  libxalan2-java libxslthl-java xalan binutils-multiarch gcc-13-doc
  manpages-dev flex bison gdb-x86-64-linux-gnu gcc-doc gettext-doc
  libasprintf-dev libgettextpo-dev groff lrzip liblapack-doc:amd64
  glibc-doc:amd64 libc-l10n:amd64 locales:amd64 libnss-nis:amd64
  libnss-nisplus:amd64 manpages-dev:amd64 krb5-doc krb5-user libice-doc:amd64
  pciutils:amd64 lm-sensors lm-sensors:amd64 libsm-doc:amd64
  libstdc++-13-doc:amd64 libtool-doc gfortran | fortran95-compiler gcj-jdk
  uuid-runtime:amd64 libx11-doc libx11-doc:amd64 libxcb-doc libxcb-doc:amd64
  libxext-doc:amd64 libxt-doc:amd64 libyaml-shell-perl m4-doc apparmor less
  www-browser libmail-box-perl python3-doc python3-tk python3-venv
  python3.11-venv python3.11-doc binfmt-support readline-doc sgml-base-doc
  perlsgml w3-recs opensp
Recommended packages:
  xmlto curl | wget | lynx libidn2-0:amd64 ca-certificates
  libarchive-cpio-perl krb5-locales libldap-common libgpm2 publicsuffix
  libsasl2-modules libltdl-dev mesa-vulkan-drivers:amd64 | vulkan-icd:amd64
  libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl
  libmail-sendmail-perl psmisc
The following NEW packages will be installed:
  asciidoc-base asciidoc-common autoconf automake autopoint autotools-dev
  binutils-x86-64-linux-gnu bsdextrautils cmake cmake-data
  cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config
  crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism
  docbook-xml docbook-xsl dpkg-cross dwz fakeroot file freeglut3-dev:amd64
  g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-13-base:amd64
  gcc-13-cross-base gcc-13-x86-64-linux-gnu gcc-13-x86-64-linux-gnu-base
  gcc-14-base:amd64 gcc-14-cross-base gcc-x86-64-linux-gnu gemmi-dev:amd64
  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
  libbsd0:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64
  libc6-dev-amd64-cross libcom-err2 libconfig-auto-perl
  libconfig-inifiles-perl libcrypt-dev:amd64 libcrypt1:amd64 libcurl4t64
  libdebhelper-perl libdebian-dpkgcross-perl libdrm-amdgpu1:amd64
  libdrm-common libdrm-intel1:amd64 libdrm-nouveau2:amd64 libdrm-radeon1:amd64
  libdrm2:amd64 libedit2:amd64 libegl-dev:amd64 libegl-mesa0:amd64
  libegl1:amd64 libelf1t64 libelf1t64:amd64 libexpat1 libexpat1:amd64
  libfakeroot libffi8:amd64 libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libgbm1:amd64
  libgcc-13-dev:amd64 libgcc-13-dev-amd64-cross libgcc-s1:amd64
  libgcc-s1-amd64-cross libgfortran5:amd64 libgl-dev:amd64 libgl1:amd64
  libgl1-mesa-dev:amd64 libgl1-mesa-dri:amd64 libglapi-mesa:amd64
  libgles-dev:amd64 libgles1:amd64 libgles2:amd64 libglu1-mesa:amd64
  libglu1-mesa-dev:amd64 libglut-dev:amd64 libglut3.12:amd64
  libglvnd-core-dev:amd64 libglvnd-dev:amd64 libglvnd0:amd64 libglx-dev:amd64
  libglx-mesa0:amd64 libglx0:amd64 libgomp1:amd64 libgomp1-amd64-cross
  libgssapi-krb5-2 libhwasan0:amd64 libhwasan0-amd64-cross libice-dev:amd64
  libice6:amd64 libicu72 libicu72:amd64 libio-string-perl libitm1:amd64
  libitm1-amd64-cross libjsoncpp25 libk5crypto3 libkeyutils1 libkrb5-3
  libkrb5support0 liblapack-dev:amd64 liblapack3:amd64 libldap-2.5-0
  libllvm17t64:amd64 liblocale-gettext-perl liblsan0:amd64
  liblsan0-amd64-cross liblzma5:amd64 libmagic-mgc libmagic1t64 libmd0:amd64
  libncursesw6 libnghttp2-14 libopengl-dev:amd64 libopengl0:amd64
  libopenmm-dev:amd64 libopenmm8.0t64:amd64 libpciaccess0:amd64 libpipeline1
  libproc2-0 libpsl5t64 libpthread-stubs0-dev libpthread-stubs0-dev:amd64
  libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib
  libquadmath0:amd64 libquadmath0-amd64-cross libreadline8t64 librhash0
  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++-13-dev:amd64
  libstdc++-13-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross
  libsub-override-perl libtinfo6:amd64 libtool libtsan2:amd64
  libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0
  libuuid1:amd64 libuv1t64 libvulkan1:amd64 libwayland-client0:amd64
  libwayland-server0: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-dri2-0: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 libxml-libxml-perl libxml-namespacesupport-perl
  libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2
  libxml2:amd64 libxml2-utils libxmu-dev:amd64 libxmu-headers libxmu6:amd64
  libxshmfence1:amd64 libxslt1.1 libxt-dev:amd64 libxt6t64:amd64
  libxxf86vm1:amd64 libyaml-perl libz3-4:amd64 libzstd1:amd64 m4 man-db
  media-types netbase po-debconf procps python3 python3-minimal python3.11
  python3.11-minimal readline-common sbuild-build-depends-main-dummy:amd64
  sensible-utils sgml-base sgml-data tao-pegtl-dev tzdata ucf x11-common
  x11proto-dev xml-core xorg-sgml-doctools xsltproc xtrans-dev zlib1g:amd64
  zlib1g-dev:amd64
0 upgraded, 262 newly installed, 0 to remove and 0 not upgraded.
Need to get 204 MB of archives.
After this operation, 868 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1028 B]
Get:2 http://mirror.einval.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7 [14.8 kB]
Get:3 http://mirror.einval.org/debian unstable/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB]
Get:4 http://mirror.einval.org/debian unstable/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB]
Get:5 http://mirror.einval.org/debian unstable/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB]
Get:6 http://mirror.einval.org/debian unstable/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB]
Get:7 http://mirror.einval.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB]
Get:8 http://mirror.einval.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB]
Get:9 http://mirror.einval.org/debian unstable/main arm64 tzdata all 2024a-3 [255 kB]
Get:10 http://mirror.einval.org/debian unstable/main arm64 libncursesw6 arm64 6.4+20240414-1 [124 kB]
Get:11 http://mirror.einval.org/debian unstable/main arm64 readline-common all 8.2-4 [69.3 kB]
Get:12 http://mirror.einval.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-4 [157 kB]
Get:13 http://mirror.einval.org/debian unstable/main arm64 libsqlite3-0 arm64 3.45.3-1 [837 kB]
Get:14 http://mirror.einval.org/debian unstable/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB]
Get:15 http://mirror.einval.org/debian unstable/main arm64 python3.11 arm64 3.11.9-1 [602 kB]
Get:16 http://mirror.einval.org/debian unstable/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B]
Get:17 http://mirror.einval.org/debian unstable/main arm64 python3 arm64 3.11.8-1 [27.4 kB]
Get:18 http://mirror.einval.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB]
Get:19 http://mirror.einval.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-4 [61.7 kB]
Get:20 http://mirror.einval.org/debian unstable/main arm64 procps arm64 2:4.0.4-4 [869 kB]
Get:21 http://mirror.einval.org/debian unstable/main arm64 sensible-utils all 0.0.22 [22.4 kB]
Get:22 http://mirror.einval.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB]
Get:23 http://mirror.einval.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB]
Get:24 http://mirror.einval.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB]
Get:25 http://mirror.einval.org/debian unstable/main arm64 gettext-base arm64 0.21-14+b1 [160 kB]
Get:26 http://mirror.einval.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB]
Get:27 http://mirror.einval.org/debian unstable/main arm64 groff-base arm64 1.23.0-3+b1 [1126 kB]
Get:28 http://mirror.einval.org/debian unstable/main arm64 bsdextrautils arm64 2.40-6 [92.6 kB]
Get:29 http://mirror.einval.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB]
Get:30 http://mirror.einval.org/debian unstable/main arm64 man-db arm64 2.12.1-1 [1394 kB]
Get:31 http://mirror.einval.org/debian unstable/main arm64 ucf all 3.0043+nmu1 [55.2 kB]
Get:32 http://mirror.einval.org/debian unstable/main arm64 asciidoc-common all 10.2.0-2 [104 kB]
Get:33 http://mirror.einval.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB]
Get:34 http://mirror.einval.org/debian unstable/main arm64 docbook-xsl all 1.79.2+dfsg-7 [1221 kB]
Get:35 http://mirror.einval.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB]
Get:36 http://mirror.einval.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b2 [624 kB]
Get:37 http://mirror.einval.org/debian unstable/main arm64 libxml2-utils arm64 2.9.14+dfsg-1.3+b2 [97.5 kB]
Get:38 http://mirror.einval.org/debian unstable/main arm64 libxslt1.1 arm64 1.1.35-1 [231 kB]
Get:39 http://mirror.einval.org/debian unstable/main arm64 xsltproc arm64 1.1.35-1 [126 kB]
Get:40 http://mirror.einval.org/debian unstable/main arm64 asciidoc-base all 10.2.0-2 [85.3 kB]
Get:41 http://mirror.einval.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB]
Get:42 http://mirror.einval.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB]
Get:43 http://mirror.einval.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get:44 http://mirror.einval.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get:45 http://mirror.einval.org/debian unstable/main arm64 autopoint all 0.21-14 [496 kB]
Get:46 http://mirror.einval.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.2-2 [321 kB]
Get:47 http://mirror.einval.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB]
Get:48 http://mirror.einval.org/debian unstable/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB]
Get:49 http://mirror.einval.org/debian unstable/main arm64 libcom-err2 arm64 1.47.0-2.4 [20.1 kB]
Get:50 http://mirror.einval.org/debian unstable/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB]
Get:51 http://mirror.einval.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B]
Get:52 http://mirror.einval.org/debian unstable/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB]
Get:53 http://mirror.einval.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB]
Get:54 http://mirror.einval.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB]
Get:55 http://mirror.einval.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB]
Get:56 http://mirror.einval.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.16+dfsg-2 [173 kB]
Get:57 http://mirror.einval.org/debian unstable/main arm64 libnghttp2-14 arm64 1.61.0-1+b1 [71.0 kB]
Get:58 http://mirror.einval.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB]
Get:59 http://mirror.einval.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB]
Get:60 http://mirror.einval.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB]
Get:61 http://mirror.einval.org/debian unstable/main arm64 libcurl4t64 arm64 8.7.1-3 [412 kB]
Get:62 http://mirror.einval.org/debian unstable/main arm64 libjsoncpp25 arm64 1.9.5-6+b2 [73.2 kB]
Get:63 http://mirror.einval.org/debian unstable/main arm64 librhash0 arm64 1.4.3-3+b1 [127 kB]
Get:64 http://mirror.einval.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-1.1 [142 kB]
Get:65 http://mirror.einval.org/debian unstable/main arm64 cmake-data all 3.28.3-1 [2128 kB]
Get:66 http://mirror.einval.org/debian unstable/main arm64 cmake arm64 3.28.3-1+b1 [8896 kB]
Get:67 http://mirror.einval.org/debian unstable/main arm64 gcc-13-x86-64-linux-gnu-base arm64 13.2.0-12cross1 [42.6 kB]
Get:68 http://mirror.einval.org/debian unstable/main arm64 cpp-13-x86-64-linux-gnu arm64 13.2.0-12cross1 [9273 kB]
Get:69 http://mirror.einval.org/debian unstable/main arm64 cpp-x86-64-linux-gnu arm64 4:13.2.0-7 [4732 B]
Get:70 http://mirror.einval.org/debian unstable/main arm64 cross-config all 2.6.20 [16.3 kB]
Get:71 http://mirror.einval.org/debian unstable/main arm64 binutils-x86-64-linux-gnu arm64 2.42-4 [2376 kB]
Get:72 http://mirror.einval.org/debian unstable/main arm64 gcc-13-cross-base all 13.2.0-12cross1 [38.1 kB]
Get:73 http://mirror.einval.org/debian unstable/main arm64 gcc-14-cross-base all 14-20240127-1cross1 [37.9 kB]
Get:74 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1-amd64-cross all 14-20240127-1cross1 [71.7 kB]
Get:75 http://mirror.einval.org/debian unstable/main arm64 libgomp1-amd64-cross all 14-20240127-1cross1 [128 kB]
Get:76 http://mirror.einval.org/debian unstable/main arm64 libitm1-amd64-cross all 14-20240127-1cross1 [25.2 kB]
Get:77 http://mirror.einval.org/debian unstable/main arm64 libatomic1-amd64-cross all 14-20240127-1cross1 [8996 B]
Get:78 http://mirror.einval.org/debian unstable/main arm64 libasan8-amd64-cross all 14-20240127-1cross1 [2716 kB]
Get:79 http://mirror.einval.org/debian unstable/main arm64 liblsan0-amd64-cross all 14-20240127-1cross1 [1199 kB]
Get:80 http://mirror.einval.org/debian unstable/main arm64 libtsan2-amd64-cross all 14-20240127-1cross1 [2444 kB]
Get:81 http://mirror.einval.org/debian unstable/main arm64 libc6-amd64-cross all 2.37-12cross1 [1478 kB]
Get:82 http://mirror.einval.org/debian unstable/main arm64 libstdc++6-amd64-cross all 14-20240127-1cross1 [667 kB]
Get:83 http://mirror.einval.org/debian unstable/main arm64 libubsan1-amd64-cross all 14-20240127-1cross1 [1070 kB]
Get:84 http://mirror.einval.org/debian unstable/main arm64 libhwasan0-amd64-cross all 14-20240127-1cross1 [1434 kB]
Get:85 http://mirror.einval.org/debian unstable/main arm64 libquadmath0-amd64-cross all 14-20240127-1cross1 [146 kB]
Get:86 http://mirror.einval.org/debian unstable/main arm64 libgcc-13-dev-amd64-cross all 13.2.0-12cross1 [2536 kB]
Get:87 http://mirror.einval.org/debian unstable/main arm64 gcc-13-x86-64-linux-gnu arm64 13.2.0-12cross1 [17.8 MB]
Get:88 http://mirror.einval.org/debian unstable/main arm64 gcc-x86-64-linux-gnu arm64 4:13.2.0-7 [1452 B]
Get:89 http://mirror.einval.org/debian unstable/main arm64 libc6-dev-amd64-cross all 2.37-12cross1 [1898 kB]
Get:90 http://mirror.einval.org/debian unstable/main arm64 libstdc++-13-dev-amd64-cross all 13.2.0-12cross1 [2210 kB]
Get:91 http://mirror.einval.org/debian unstable/main arm64 g++-13-x86-64-linux-gnu arm64 13.2.0-12cross1 [10.1 MB]
Get:92 http://mirror.einval.org/debian unstable/main arm64 g++-x86-64-linux-gnu arm64 4:13.2.0-7 [1204 B]
Get:93 http://mirror.einval.org/debian unstable/main arm64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB]
Get:94 http://mirror.einval.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB]
Get:95 http://mirror.einval.org/debian unstable/main arm64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB]
Get:96 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-base-perl all 1.09-3 [20.6 kB]
Get:97 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB]
Get:98 http://mirror.einval.org/debian unstable/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-1+b3 [299 kB]
Get:99 http://mirror.einval.org/debian unstable/main arm64 libxml-simple-perl all 2.25-2 [69.8 kB]
Get:100 http://mirror.einval.org/debian unstable/main arm64 libyaml-perl all 1.31-1 [64.8 kB]
Get:101 http://mirror.einval.org/debian unstable/main arm64 libconfig-auto-perl all 0.44-2 [19.2 kB]
Get:102 http://mirror.einval.org/debian unstable/main arm64 libfile-which-perl all 1.27-2 [15.1 kB]
Get:103 http://mirror.einval.org/debian unstable/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB]
Get:104 http://mirror.einval.org/debian unstable/main arm64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB]
Get:105 http://mirror.einval.org/debian unstable/main arm64 dpkg-cross all 2.6.20 [25.8 kB]
Get:106 http://mirror.einval.org/debian unstable/main arm64 crossbuild-essential-amd64 all 12.10 [3488 B]
Get:107 http://mirror.einval.org/debian unstable/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB]
Get:108 http://mirror.einval.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB]
Get:109 http://mirror.einval.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 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 libsub-override-perl all 0.10-1 [10.6 kB]
Get:112 http://mirror.einval.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:113 http://mirror.einval.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:114 http://mirror.einval.org/debian unstable/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB]
Get:115 http://mirror.einval.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get:116 http://mirror.einval.org/debian unstable/main arm64 gettext arm64 0.21-14+b1 [1249 kB]
Get:117 http://mirror.einval.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:118 http://mirror.einval.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:119 http://mirror.einval.org/debian unstable/main arm64 debhelper all 13.15.3 [901 kB]
Get:120 http://mirror.einval.org/debian unstable/main arm64 sgml-data all 2.0.11+nmu1 [179 kB]
Get:121 http://mirror.einval.org/debian unstable/main arm64 docbook-xml all 4.5-12 [85.2 kB]
Get:122 http://mirror.einval.org/debian unstable/main arm64 libfakeroot arm64 1.34-1 [28.4 kB]
Get:123 http://mirror.einval.org/debian unstable/main arm64 fakeroot arm64 1.34-1 [73.5 kB]
Get:124 http://mirror.einval.org/debian unstable/main amd64 gcc-14-base amd64 14-20240330-1 [43.2 kB]
Get:125 http://mirror.einval.org/debian unstable/main amd64 libgcc-s1 amd64 14-20240330-1 [71.9 kB]
Get:126 http://mirror.einval.org/debian unstable/main amd64 libc6 amd64 2.37-18 [2757 kB]
Get:127 http://mirror.einval.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1 [51.3 kB]
Get:128 http://mirror.einval.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB]
Get:129 http://mirror.einval.org/debian unstable/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB]
Get:130 http://mirror.einval.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB]
Get:131 http://mirror.einval.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB]
Get:132 http://mirror.einval.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-1 [144 kB]
Get:133 http://mirror.einval.org/debian unstable/main arm64 libx11-data all 2:1.8.7-1 [328 kB]
Get:134 http://mirror.einval.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB]
Get:135 http://mirror.einval.org/debian unstable/main arm64 libdrm-common all 2.4.120-2 [7688 B]
Get:136 http://mirror.einval.org/debian unstable/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB]
Get:137 http://mirror.einval.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB]
Get:138 http://mirror.einval.org/debian unstable/main amd64 libglapi-mesa amd64 24.0.5-1 [36.3 kB]
Get:139 http://mirror.einval.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.7-1 [232 kB]
Get:140 http://mirror.einval.org/debian unstable/main amd64 libxcb-dri2-0 amd64 1.17.0-1 [106 kB]
Get:141 http://mirror.einval.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-1 [106 kB]
Get:142 http://mirror.einval.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-1 [122 kB]
Get:143 http://mirror.einval.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-1 [105 kB]
Get:144 http://mirror.einval.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-1 [116 kB]
Get:145 http://mirror.einval.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-1 [105 kB]
Get:146 http://mirror.einval.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-1 [108 kB]
Get:147 http://mirror.einval.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-1 [109 kB]
Get:148 http://mirror.einval.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB]
Get:149 http://mirror.einval.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB]
Get:150 http://mirror.einval.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1 [8820 B]
Get:151 http://mirror.einval.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB]
Get:152 http://mirror.einval.org/debian unstable/main amd64 libvulkan1 amd64 1.3.280.0-1 [123 kB]
Get:153 http://mirror.einval.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB]
Get:154 http://mirror.einval.org/debian unstable/main amd64 zlib1g amd64 1:1.3.dfsg-3.1 [87.6 kB]
Get:155 http://mirror.einval.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3 [51.6 kB]
Get:156 http://mirror.einval.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB]
Get:157 http://mirror.einval.org/debian unstable/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [19.3 kB]
Get:158 http://mirror.einval.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB]
Get:159 http://mirror.einval.org/debian unstable/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB]
Get:160 http://mirror.einval.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB]
Get:161 http://mirror.einval.org/debian unstable/main amd64 libtinfo6 amd64 6.4+20240414-1 [344 kB]
Get:162 http://mirror.einval.org/debian unstable/main amd64 libedit2 amd64 3.1-20230828-1 [93.1 kB]
Get:163 http://mirror.einval.org/debian unstable/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB]
Get:164 http://mirror.einval.org/debian unstable/main amd64 libstdc++6 amd64 14-20240330-1 [713 kB]
Get:165 http://mirror.einval.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB]
Get:166 http://mirror.einval.org/debian unstable/main amd64 liblzma5 amd64 5.6.1+really5.4.5-1 [240 kB]
Get:167 http://mirror.einval.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB]
Get:168 http://mirror.einval.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB]
Get:169 http://mirror.einval.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-9+b2 [23.7 MB]
Get:170 http://mirror.einval.org/debian unstable/main arm64 libsensors-config all 1:3.6.0-9 [14.6 kB]
Get:171 http://mirror.einval.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB]
Get:172 http://mirror.einval.org/debian unstable/main amd64 libgl1-mesa-dri amd64 24.0.5-1 [8278 kB]
Get:173 http://mirror.einval.org/debian unstable/main amd64 libglx-mesa0 amd64 24.0.5-1 [151 kB]
Get:174 http://mirror.einval.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1 [34.7 kB]
Get:175 http://mirror.einval.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1 [89.7 kB]
Get:176 http://mirror.einval.org/debian unstable/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB]
Get:177 http://mirror.einval.org/debian unstable/main amd64 libglut3.12 amd64 3.4.0-1+b1 [139 kB]
Get:178 http://mirror.einval.org/debian unstable/main arm64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get:179 http://mirror.einval.org/debian unstable/main arm64 x11proto-dev all 2024.1-1 [603 kB]
Get:180 http://mirror.einval.org/debian unstable/main amd64 libxau-dev amd64 1:1.0.9-1 [22.9 kB]
Get:181 http://mirror.einval.org/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [42.2 kB]
Get:182 http://mirror.einval.org/debian unstable/main arm64 xtrans-dev all 1.4.0-1 [98.7 kB]
Get:183 http://mirror.einval.org/debian unstable/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B]
Get:184 http://mirror.einval.org/debian unstable/main amd64 libxcb1-dev amd64 1.17.0-1 [181 kB]
Get:185 http://mirror.einval.org/debian unstable/main amd64 libx11-dev amd64 2:1.8.7-1 [875 kB]
Get:186 http://mirror.einval.org/debian unstable/main amd64 libglx-dev amd64 1.7.0-1 [15.5 kB]
Get:187 http://mirror.einval.org/debian unstable/main amd64 libgl-dev amd64 1.7.0-1 [100 kB]
Get:188 http://mirror.einval.org/debian unstable/main amd64 libglvnd-core-dev amd64 1.7.0-1 [13.1 kB]
Get:189 http://mirror.einval.org/debian unstable/main amd64 libwayland-server0 amd64 1.22.0-2.1+b1 [33.0 kB]
Get:190 http://mirror.einval.org/debian unstable/main amd64 libgbm1 amd64 24.0.5-1 [40.8 kB]
Get:191 http://mirror.einval.org/debian unstable/main amd64 libwayland-client0 amd64 1.22.0-2.1+b1 [25.7 kB]
Get:192 http://mirror.einval.org/debian unstable/main amd64 libegl-mesa0 amd64 24.0.5-1 [119 kB]
Get:193 http://mirror.einval.org/debian unstable/main amd64 libegl1 amd64 1.7.0-1 [34.0 kB]
Get:194 http://mirror.einval.org/debian unstable/main amd64 libegl-dev amd64 1.7.0-1 [19.2 kB]
Get:195 http://mirror.einval.org/debian unstable/main amd64 libgles1 amd64 1.7.0-1 [11.9 kB]
Get:196 http://mirror.einval.org/debian unstable/main amd64 libgles2 amd64 1.7.0-1 [16.9 kB]
Get:197 http://mirror.einval.org/debian unstable/main amd64 libgles-dev amd64 1.7.0-1 [50.5 kB]
Get:198 http://mirror.einval.org/debian unstable/main amd64 libopengl0 amd64 1.7.0-1 [30.8 kB]
Get:199 http://mirror.einval.org/debian unstable/main amd64 libopengl-dev amd64 1.7.0-1 [5104 B]
Get:200 http://mirror.einval.org/debian unstable/main amd64 libglvnd-dev amd64 1.7.0-1 [4868 B]
Get:201 http://mirror.einval.org/debian unstable/main amd64 libgl1-mesa-dev amd64 24.0.5-1 [17.0 kB]
Get:202 http://mirror.einval.org/debian unstable/main amd64 libglu1-mesa amd64 9.0.2-1.1 [178 kB]
Get:203 http://mirror.einval.org/debian unstable/main amd64 libglu1-mesa-dev amd64 9.0.2-1.1 [216 kB]
Get:204 http://mirror.einval.org/debian unstable/main amd64 libxext-dev amd64 2:1.3.4-1+b1 [107 kB]
Get:205 http://mirror.einval.org/debian unstable/main arm64 x11-common all 1:7.7+23 [252 kB]
Get:206 http://mirror.einval.org/debian unstable/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB]
Get:207 http://mirror.einval.org/debian unstable/main amd64 libuuid1 amd64 2.40-6 [32.0 kB]
Get:208 http://mirror.einval.org/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB]
Get:209 http://mirror.einval.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB]
Get:210 http://mirror.einval.org/debian unstable/main amd64 libice-dev amd64 2:1.0.10-1 [67.1 kB]
Get:211 http://mirror.einval.org/debian unstable/main amd64 libsm-dev amd64 2:1.2.3-1 [38.0 kB]
Get:212 http://mirror.einval.org/debian unstable/main amd64 libxt-dev amd64 1:1.2.1-1.2 [406 kB]
Get:213 http://mirror.einval.org/debian unstable/main amd64 libglut-dev amd64 3.4.0-1+b1 [163 kB]
Get:214 http://mirror.einval.org/debian unstable/main amd64 freeglut3-dev amd64 3.4.0-1+b1 [53.4 kB]
Get:215 http://mirror.einval.org/debian unstable/main amd64 gcc-13-base amd64 13.2.0-23 [44.6 kB]
Get:216 http://mirror.einval.org/debian unstable/main amd64 gemmi-dev amd64 0.6.4+ds-1 [1115 kB]
Get:217 http://mirror.einval.org/debian unstable/main amd64 libasan8 amd64 14-20240330-1 [2724 kB]
Get:218 http://mirror.einval.org/debian unstable/main amd64 libatomic1 amd64 14-20240330-1 [9216 B]
Get:219 http://mirror.einval.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3 [148 kB]
Get:220 http://mirror.einval.org/debian unstable/main amd64 libblas-dev amd64 3.12.0-3 [159 kB]
Get:221 http://mirror.einval.org/debian unstable/main arm64 libbsd0 arm64 0.12.2-1 [129 kB]
Get:222 http://mirror.einval.org/debian unstable/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB]
Get:223 http://mirror.einval.org/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.36-4 [119 kB]
Get:224 http://mirror.einval.org/debian unstable/main amd64 libc6-dev amd64 2.37-18 [1906 kB]
Get:225 http://mirror.einval.org/debian unstable/main amd64 libgomp1 amd64 14-20240330-1 [136 kB]
Get:226 http://mirror.einval.org/debian unstable/main amd64 libitm1 amd64 14-20240330-1 [25.8 kB]
Get:227 http://mirror.einval.org/debian unstable/main amd64 liblsan0 amd64 14-20240330-1 [1201 kB]
Get:228 http://mirror.einval.org/debian unstable/main amd64 libtsan2 amd64 14-20240330-1 [2454 kB]
Get:229 http://mirror.einval.org/debian unstable/main amd64 libubsan1 amd64 14-20240330-1 [1071 kB]
Get:230 http://mirror.einval.org/debian unstable/main amd64 libhwasan0 amd64 14-20240330-1 [1485 kB]
Get:231 http://mirror.einval.org/debian unstable/main amd64 libquadmath0 amd64 14-20240330-1 [147 kB]
Get:232 http://mirror.einval.org/debian unstable/main amd64 libgcc-13-dev amd64 13.2.0-23 [2537 kB]
Get:233 http://mirror.einval.org/debian unstable/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB]
Get:234 http://mirror.einval.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB]
Get:235 http://mirror.einval.org/debian unstable/main amd64 liblapack-dev amd64 3.12.0-3 [4880 kB]
Get:236 http://mirror.einval.org/debian unstable/main amd64 libopenmm8.0t64 amd64 8.0.0+dfsg-6.1 [1018 kB]
Get:237 http://mirror.einval.org/debian unstable/main amd64 libopenmm-dev amd64 8.0.0+dfsg-6.1 [338 kB]
Get:238 http://mirror.einval.org/debian unstable/main arm64 libpthread-stubs0-dev arm64 0.4-1 [5336 B]
Get:239 http://mirror.einval.org/debian unstable/main arm64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB]
Get:240 http://mirror.einval.org/debian unstable/main amd64 libxfixes-dev amd64 1:6.0.0-2 [24.7 kB]
Get:241 http://mirror.einval.org/debian unstable/main amd64 libxi-dev amd64 2:1.8.1-1 [241 kB]
Get:242 http://mirror.einval.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b2 [58.7 kB]
Get:243 http://mirror.einval.org/debian unstable/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB]
Get:244 http://mirror.einval.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB]
Get:245 http://mirror.einval.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-1 [143 kB]
Get:246 http://mirror.einval.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.7-1 [772 kB]
Get:247 http://mirror.einval.org/debian unstable/main arm64 libxau-dev arm64 1:1.0.9-1 [23.2 kB]
Get:248 http://mirror.einval.org/debian unstable/main arm64 libxdmcp-dev arm64 1:1.1.2-3 [41.2 kB]
Get:249 http://mirror.einval.org/debian unstable/main arm64 libxcb1-dev arm64 1.17.0-1 [182 kB]
Get:250 http://mirror.einval.org/debian unstable/main arm64 libx11-dev arm64 2:1.8.7-1 [864 kB]
Get:251 http://mirror.einval.org/debian unstable/main arm64 libxmu-headers all 2:1.1.3-3 [68.5 kB]
Get:252 http://mirror.einval.org/debian unstable/main amd64 libxmu-dev amd64 2:1.1.3-3+b2 [65.1 kB]
Get:253 http://mirror.einval.org/debian unstable/main amd64 libsimbody3.7 amd64 3.7+dfsg-3 [3230 kB]
Get:254 http://mirror.einval.org/debian unstable/main amd64 libsimbody-dev amd64 3.7+dfsg-3 [2727 kB]
Get:255 http://mirror.einval.org/debian unstable/main amd64 libsimtkmolmodel3.1t64 amd64 3.1.0-4.1+b1 [672 kB]
Get:256 http://mirror.einval.org/debian unstable/main amd64 libsimtkmolmodel-dev amd64 3.1.0-4.1+b1 [1864 kB]
Get:257 http://mirror.einval.org/debian unstable/main amd64 libsimtkmolmodel-plugins amd64 3.1.0-4.1+b1 [20.1 kB]
Get:258 http://mirror.einval.org/debian unstable/main amd64 libstb0t64 amd64 0.0~git20230129.5736b15+ds-1.2 [214 kB]
Get:259 http://mirror.einval.org/debian unstable/main amd64 libstb-dev amd64 0.0~git20230129.5736b15+ds-1.2 [595 kB]
Get:260 http://mirror.einval.org/debian unstable/main amd64 libstdc++-13-dev amd64 13.2.0-23 [2264 kB]
Get:261 http://mirror.einval.org/debian unstable/main arm64 tao-pegtl-dev all 3.2.7-1 [69.4 kB]
Get:262 http://mirror.einval.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 204 MB in 3s (73.3 MB/s)
Selecting previously unselected package liblocale-gettext-perl.
(Reading database ... 11927 files and directories currently installed.)
Preparing to unpack .../liblocale-gettext-perl_1.07-7_arm64.deb ...
Unpacking liblocale-gettext-perl (1.07-7) ...
Selecting previously unselected package libpython3.11-minimal:arm64.
Preparing to unpack .../libpython3.11-minimal_3.11.9-1_arm64.deb ...
Unpacking libpython3.11-minimal:arm64 (3.11.9-1) ...
Selecting previously unselected package libexpat1:arm64.
Preparing to unpack .../libexpat1_2.6.2-1_arm64.deb ...
Unpacking libexpat1:arm64 (2.6.2-1) ...
Selecting previously unselected package python3.11-minimal.
Preparing to unpack .../python3.11-minimal_3.11.9-1_arm64.deb ...
Unpacking python3.11-minimal (3.11.9-1) ...
Setting up libpython3.11-minimal:arm64 (3.11.9-1) ...
Setting up libexpat1:arm64 (2.6.2-1) ...
Setting up python3.11-minimal (3.11.9-1) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 12257 files and directories currently installed.)
Preparing to unpack .../00-python3-minimal_3.11.8-1_arm64.deb ...
Unpacking python3-minimal (3.11.8-1) ...
Selecting previously unselected package media-types.
Preparing to unpack .../01-media-types_10.1.0_all.deb ...
Unpacking media-types (10.1.0) ...
Selecting previously unselected package netbase.
Preparing to unpack .../02-netbase_6.4_all.deb ...
Unpacking netbase (6.4) ...
Selecting previously unselected package tzdata.
Preparing to unpack .../03-tzdata_2024a-3_all.deb ...
Unpacking tzdata (2024a-3) ...
Selecting previously unselected package libncursesw6:arm64.
Preparing to unpack .../04-libncursesw6_6.4+20240414-1_arm64.deb ...
Unpacking libncursesw6:arm64 (6.4+20240414-1) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../05-readline-common_8.2-4_all.deb ...
Unpacking readline-common (8.2-4) ...
Selecting previously unselected package libreadline8t64:arm64.
Preparing to unpack .../06-libreadline8t64_8.2-4_arm64.deb ...
Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
Unpacking libreadline8t64:arm64 (8.2-4) ...
Selecting previously unselected package libsqlite3-0:arm64.
Preparing to unpack .../07-libsqlite3-0_3.45.3-1_arm64.deb ...
Unpacking libsqlite3-0:arm64 (3.45.3-1) ...
Selecting previously unselected package libpython3.11-stdlib:arm64.
Preparing to unpack .../08-libpython3.11-stdlib_3.11.9-1_arm64.deb ...
Unpacking libpython3.11-stdlib:arm64 (3.11.9-1) ...
Selecting previously unselected package python3.11.
Preparing to unpack .../09-python3.11_3.11.9-1_arm64.deb ...
Unpacking python3.11 (3.11.9-1) ...
Selecting previously unselected package libpython3-stdlib:arm64.
Preparing to unpack .../10-libpython3-stdlib_3.11.8-1_arm64.deb ...
Unpacking libpython3-stdlib:arm64 (3.11.8-1) ...
Setting up python3-minimal (3.11.8-1) ...
Selecting previously unselected package python3.
(Reading database ... 13266 files and directories currently installed.)
Preparing to unpack .../000-python3_3.11.8-1_arm64.deb ...
Unpacking python3 (3.11.8-1) ...
Selecting previously unselected package sgml-base.
Preparing to unpack .../001-sgml-base_1.31_all.deb ...
Unpacking sgml-base (1.31) ...
Selecting previously unselected package libproc2-0:arm64.
Preparing to unpack .../002-libproc2-0_2%3a4.0.4-4_arm64.deb ...
Unpacking libproc2-0:arm64 (2:4.0.4-4) ...
Selecting previously unselected package procps.
Preparing to unpack .../003-procps_2%3a4.0.4-4_arm64.deb ...
Unpacking procps (2:4.0.4-4) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../004-sensible-utils_0.0.22_all.deb ...
Unpacking sensible-utils (0.0.22) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../005-libmagic-mgc_1%3a5.45-3_arm64.deb ...
Unpacking libmagic-mgc (1:5.45-3) ...
Selecting previously unselected package libmagic1t64:arm64.
Preparing to unpack .../006-libmagic1t64_1%3a5.45-3_arm64.deb ...
Unpacking libmagic1t64:arm64 (1:5.45-3) ...
Selecting previously unselected package file.
Preparing to unpack .../007-file_1%3a5.45-3_arm64.deb ...
Unpacking file (1:5.45-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../008-gettext-base_0.21-14+b1_arm64.deb ...
Unpacking gettext-base (0.21-14+b1) ...
Selecting previously unselected package libuchardet0:arm64.
Preparing to unpack .../009-libuchardet0_0.0.8-1+b1_arm64.deb ...
Unpacking libuchardet0:arm64 (0.0.8-1+b1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../010-groff-base_1.23.0-3+b1_arm64.deb ...
Unpacking groff-base (1.23.0-3+b1) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../011-bsdextrautils_2.40-6_arm64.deb ...
Unpacking bsdextrautils (2.40-6) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../012-libpipeline1_1.5.7-2_arm64.deb ...
Unpacking libpipeline1:arm64 (1.5.7-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../013-man-db_2.12.1-1_arm64.deb ...
Unpacking man-db (2.12.1-1) ...
Selecting previously unselected package ucf.
Preparing to unpack .../014-ucf_3.0043+nmu1_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0043+nmu1) ...
Selecting previously unselected package asciidoc-common.
Preparing to unpack .../015-asciidoc-common_10.2.0-2_all.deb ...
Unpacking asciidoc-common (10.2.0-2) ...
Selecting previously unselected package xml-core.
Preparing to unpack .../016-xml-core_0.19_all.deb ...
Unpacking xml-core (0.19) ...
Selecting previously unselected package docbook-xsl.
Preparing to unpack .../017-docbook-xsl_1.79.2+dfsg-7_all.deb ...
Unpacking docbook-xsl (1.79.2+dfsg-7) ...
Selecting previously unselected package libicu72:arm64.
Preparing to unpack .../018-libicu72_72.1-4+b1_arm64.deb ...
Unpacking libicu72:arm64 (72.1-4+b1) ...
Selecting previously unselected package libxml2:arm64.
Preparing to unpack .../019-libxml2_2.9.14+dfsg-1.3+b2_arm64.deb ...
Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b2) ...
Selecting previously unselected package libxml2-utils.
Preparing to unpack .../020-libxml2-utils_2.9.14+dfsg-1.3+b2_arm64.deb ...
Unpacking libxml2-utils (2.9.14+dfsg-1.3+b2) ...
Selecting previously unselected package libxslt1.1:arm64.
Preparing to unpack .../021-libxslt1.1_1.1.35-1_arm64.deb ...
Unpacking libxslt1.1:arm64 (1.1.35-1) ...
Selecting previously unselected package xsltproc.
Preparing to unpack .../022-xsltproc_1.1.35-1_arm64.deb ...
Unpacking xsltproc (1.1.35-1) ...
Selecting previously unselected package asciidoc-base.
Preparing to unpack .../023-asciidoc-base_10.2.0-2_all.deb ...
Unpacking asciidoc-base (10.2.0-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../024-m4_1.4.19-4_arm64.deb ...
Unpacking m4 (1.4.19-4) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../025-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../026-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../027-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../028-autopoint_0.21-14_all.deb ...
Unpacking autopoint (0.21-14) ...
Selecting previously unselected package libarchive13t64:arm64.
Preparing to unpack .../029-libarchive13t64_3.7.2-2_arm64.deb ...
Unpacking libarchive13t64:arm64 (3.7.2-2) ...
Selecting previously unselected package libbrotli1:arm64.
Preparing to unpack .../030-libbrotli1_1.1.0-2+b3_arm64.deb ...
Unpacking libbrotli1:arm64 (1.1.0-2+b3) ...
Selecting previously unselected package libkrb5support0:arm64.
Preparing to unpack .../031-libkrb5support0_1.20.1-6+b1_arm64.deb ...
Unpacking libkrb5support0:arm64 (1.20.1-6+b1) ...
Selecting previously unselected package libcom-err2:arm64.
Preparing to unpack .../032-libcom-err2_1.47.0-2.4_arm64.deb ...
Unpacking libcom-err2:arm64 (1.47.0-2.4) ...
Selecting previously unselected package libk5crypto3:arm64.
Preparing to unpack .../033-libk5crypto3_1.20.1-6+b1_arm64.deb ...
Unpacking libk5crypto3:arm64 (1.20.1-6+b1) ...
Selecting previously unselected package libkeyutils1:arm64.
Preparing to unpack .../034-libkeyutils1_1.6.3-3_arm64.deb ...
Unpacking libkeyutils1:arm64 (1.6.3-3) ...
Selecting previously unselected package libkrb5-3:arm64.
Preparing to unpack .../035-libkrb5-3_1.20.1-6+b1_arm64.deb ...
Unpacking libkrb5-3:arm64 (1.20.1-6+b1) ...
Selecting previously unselected package libgssapi-krb5-2:arm64.
Preparing to unpack .../036-libgssapi-krb5-2_1.20.1-6+b1_arm64.deb ...
Unpacking libgssapi-krb5-2:arm64 (1.20.1-6+b1) ...
Selecting previously unselected package libsasl2-modules-db:arm64.
Preparing to unpack .../037-libsasl2-modules-db_2.1.28+dfsg1-6_arm64.deb ...
Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-6) ...
Selecting previously unselected package libsasl2-2:arm64.
Preparing to unpack .../038-libsasl2-2_2.1.28+dfsg1-6_arm64.deb ...
Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-6) ...
Selecting previously unselected package libldap-2.5-0:arm64.
Preparing to unpack .../039-libldap-2.5-0_2.5.16+dfsg-2_arm64.deb ...
Unpacking libldap-2.5-0:arm64 (2.5.16+dfsg-2) ...
Selecting previously unselected package libnghttp2-14:arm64.
Preparing to unpack .../040-libnghttp2-14_1.61.0-1+b1_arm64.deb ...
Unpacking libnghttp2-14:arm64 (1.61.0-1+b1) ...
Selecting previously unselected package libpsl5t64:arm64.
Preparing to unpack .../041-libpsl5t64_0.21.2-1.1_arm64.deb ...
Unpacking libpsl5t64:arm64 (0.21.2-1.1) ...
Selecting previously unselected package librtmp1:arm64.
Preparing to unpack .../042-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_arm64.deb ...
Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ...
Selecting previously unselected package libssh2-1t64:arm64.
Preparing to unpack .../043-libssh2-1t64_1.11.0-4.1+b2_arm64.deb ...
Unpacking libssh2-1t64:arm64 (1.11.0-4.1+b2) ...
Selecting previously unselected package libcurl4t64:arm64.
Preparing to unpack .../044-libcurl4t64_8.7.1-3_arm64.deb ...
Unpacking libcurl4t64:arm64 (8.7.1-3) ...
Selecting previously unselected package libjsoncpp25:arm64.
Preparing to unpack .../045-libjsoncpp25_1.9.5-6+b2_arm64.deb ...
Unpacking libjsoncpp25:arm64 (1.9.5-6+b2) ...
Selecting previously unselected package librhash0:arm64.
Preparing to unpack .../046-librhash0_1.4.3-3+b1_arm64.deb ...
Unpacking librhash0:arm64 (1.4.3-3+b1) ...
Selecting previously unselected package libuv1t64:arm64.
Preparing to unpack .../047-libuv1t64_1.48.0-1.1_arm64.deb ...
Unpacking libuv1t64:arm64 (1.48.0-1.1) ...
Selecting previously unselected package cmake-data.
Preparing to unpack .../048-cmake-data_3.28.3-1_all.deb ...
Unpacking cmake-data (3.28.3-1) ...
Selecting previously unselected package cmake.
Preparing to unpack .../049-cmake_3.28.3-1+b1_arm64.deb ...
Unpacking cmake (3.28.3-1+b1) ...
Selecting previously unselected package gcc-13-x86-64-linux-gnu-base:arm64.
Preparing to unpack .../050-gcc-13-x86-64-linux-gnu-base_13.2.0-12cross1_arm64.deb ...
Unpacking gcc-13-x86-64-linux-gnu-base:arm64 (13.2.0-12cross1) ...
Selecting previously unselected package cpp-13-x86-64-linux-gnu.
Preparing to unpack .../051-cpp-13-x86-64-linux-gnu_13.2.0-12cross1_arm64.deb ...
Unpacking cpp-13-x86-64-linux-gnu (13.2.0-12cross1) ...
Selecting previously unselected package cpp-x86-64-linux-gnu.
Preparing to unpack .../052-cpp-x86-64-linux-gnu_4%3a13.2.0-7_arm64.deb ...
Unpacking cpp-x86-64-linux-gnu (4:13.2.0-7) ...
Selecting previously unselected package cross-config.
Preparing to unpack .../053-cross-config_2.6.20_all.deb ...
Unpacking cross-config (2.6.20) ...
Selecting previously unselected package binutils-x86-64-linux-gnu.
Preparing to unpack .../054-binutils-x86-64-linux-gnu_2.42-4_arm64.deb ...
Unpacking binutils-x86-64-linux-gnu (2.42-4) ...
Selecting previously unselected package gcc-13-cross-base.
Preparing to unpack .../055-gcc-13-cross-base_13.2.0-12cross1_all.deb ...
Unpacking gcc-13-cross-base (13.2.0-12cross1) ...
Selecting previously unselected package gcc-14-cross-base.
Preparing to unpack .../056-gcc-14-cross-base_14-20240127-1cross1_all.deb ...
Unpacking gcc-14-cross-base (14-20240127-1cross1) ...
Selecting previously unselected package libgcc-s1-amd64-cross.
Preparing to unpack .../057-libgcc-s1-amd64-cross_14-20240127-1cross1_all.deb ...
Unpacking libgcc-s1-amd64-cross (14-20240127-1cross1) ...
Selecting previously unselected package libgomp1-amd64-cross.
Preparing to unpack .../058-libgomp1-amd64-cross_14-20240127-1cross1_all.deb ...
Unpacking libgomp1-amd64-cross (14-20240127-1cross1) ...
Selecting previously unselected package libitm1-amd64-cross.
Preparing to unpack .../059-libitm1-amd64-cross_14-20240127-1cross1_all.deb ...
Unpacking libitm1-amd64-cross (14-20240127-1cross1) ...
Selecting previously unselected package libatomic1-amd64-cross.
Preparing to unpack .../060-libatomic1-amd64-cross_14-20240127-1cross1_all.deb ...
Unpacking libatomic1-amd64-cross (14-20240127-1cross1) ...
Selecting previously unselected package libasan8-amd64-cross.
Preparing to unpack .../061-libasan8-amd64-cross_14-20240127-1cross1_all.deb ...
Unpacking libasan8-amd64-cross (14-20240127-1cross1) ...
Selecting previously unselected package liblsan0-amd64-cross.
Preparing to unpack .../062-liblsan0-amd64-cross_14-20240127-1cross1_all.deb ...
Unpacking liblsan0-amd64-cross (14-20240127-1cross1) ...
Selecting previously unselected package libtsan2-amd64-cross.
Preparing to unpack .../063-libtsan2-amd64-cross_14-20240127-1cross1_all.deb ...
Unpacking libtsan2-amd64-cross (14-20240127-1cross1) ...
Selecting previously unselected package libc6-amd64-cross.
Preparing to unpack .../064-libc6-amd64-cross_2.37-12cross1_all.deb ...
Unpacking libc6-amd64-cross (2.37-12cross1) ...
Selecting previously unselected package libstdc++6-amd64-cross.
Preparing to unpack .../065-libstdc++6-amd64-cross_14-20240127-1cross1_all.deb ...
Unpacking libstdc++6-amd64-cross (14-20240127-1cross1) ...
Selecting previously unselected package libubsan1-amd64-cross.
Preparing to unpack .../066-libubsan1-amd64-cross_14-20240127-1cross1_all.deb ...
Unpacking libubsan1-amd64-cross (14-20240127-1cross1) ...
Selecting previously unselected package libhwasan0-amd64-cross.
Preparing to unpack .../067-libhwasan0-amd64-cross_14-20240127-1cross1_all.deb ...
Unpacking libhwasan0-amd64-cross (14-20240127-1cross1) ...
Selecting previously unselected package libquadmath0-amd64-cross.
Preparing to unpack .../068-libquadmath0-amd64-cross_14-20240127-1cross1_all.deb ...
Unpacking libquadmath0-amd64-cross (14-20240127-1cross1) ...
Selecting previously unselected package libgcc-13-dev-amd64-cross.
Preparing to unpack .../069-libgcc-13-dev-amd64-cross_13.2.0-12cross1_all.deb ...
Unpacking libgcc-13-dev-amd64-cross (13.2.0-12cross1) ...
Selecting previously unselected package gcc-13-x86-64-linux-gnu.
Preparing to unpack .../070-gcc-13-x86-64-linux-gnu_13.2.0-12cross1_arm64.deb ...
Unpacking gcc-13-x86-64-linux-gnu (13.2.0-12cross1) ...
Selecting previously unselected package gcc-x86-64-linux-gnu.
Preparing to unpack .../071-gcc-x86-64-linux-gnu_4%3a13.2.0-7_arm64.deb ...
Unpacking gcc-x86-64-linux-gnu (4:13.2.0-7) ...
Selecting previously unselected package libc6-dev-amd64-cross.
Preparing to unpack .../072-libc6-dev-amd64-cross_2.37-12cross1_all.deb ...
Unpacking libc6-dev-amd64-cross (2.37-12cross1) ...
Selecting previously unselected package libstdc++-13-dev-amd64-cross.
Preparing to unpack .../073-libstdc++-13-dev-amd64-cross_13.2.0-12cross1_all.deb ...
Unpacking libstdc++-13-dev-amd64-cross (13.2.0-12cross1) ...
Selecting previously unselected package g++-13-x86-64-linux-gnu.
Preparing to unpack .../074-g++-13-x86-64-linux-gnu_13.2.0-12cross1_arm64.deb ...
Unpacking g++-13-x86-64-linux-gnu (13.2.0-12cross1) ...
Selecting previously unselected package g++-x86-64-linux-gnu.
Preparing to unpack .../075-g++-x86-64-linux-gnu_4%3a13.2.0-7_arm64.deb ...
Unpacking g++-x86-64-linux-gnu (4:13.2.0-7) ...
Selecting previously unselected package libconfig-inifiles-perl.
Preparing to unpack .../076-libconfig-inifiles-perl_3.000003-2_all.deb ...
Unpacking libconfig-inifiles-perl (3.000003-2) ...
Selecting previously unselected package libio-string-perl.
Preparing to unpack .../077-libio-string-perl_1.08-4_all.deb ...
Unpacking libio-string-perl (1.08-4) ...
Selecting previously unselected package libxml-namespacesupport-perl.
Preparing to unpack .../078-libxml-namespacesupport-perl_1.12-2_all.deb ...
Unpacking libxml-namespacesupport-perl (1.12-2) ...
Selecting previously unselected package libxml-sax-base-perl.
Preparing to unpack .../079-libxml-sax-base-perl_1.09-3_all.deb ...
Unpacking libxml-sax-base-perl (1.09-3) ...
Selecting previously unselected package libxml-sax-perl.
Preparing to unpack .../080-libxml-sax-perl_1.02+dfsg-3_all.deb ...
Unpacking libxml-sax-perl (1.02+dfsg-3) ...
Selecting previously unselected package libxml-libxml-perl.
Preparing to unpack .../081-libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b3_arm64.deb ...
Unpacking libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b3) ...
Selecting previously unselected package libxml-simple-perl.
Preparing to unpack .../082-libxml-simple-perl_2.25-2_all.deb ...
Unpacking libxml-simple-perl (2.25-2) ...
Selecting previously unselected package libyaml-perl.
Preparing to unpack .../083-libyaml-perl_1.31-1_all.deb ...
Unpacking libyaml-perl (1.31-1) ...
Selecting previously unselected package libconfig-auto-perl.
Preparing to unpack .../084-libconfig-auto-perl_0.44-2_all.deb ...
Unpacking libconfig-auto-perl (0.44-2) ...
Selecting previously unselected package libfile-which-perl.
Preparing to unpack .../085-libfile-which-perl_1.27-2_all.deb ...
Unpacking libfile-which-perl (1.27-2) ...
Selecting previously unselected package libfile-homedir-perl.
Preparing to unpack .../086-libfile-homedir-perl_1.006-2_all.deb ...
Unpacking libfile-homedir-perl (1.006-2) ...
Selecting previously unselected package libdebian-dpkgcross-perl.
Preparing to unpack .../087-libdebian-dpkgcross-perl_2.6.20_all.deb ...
Unpacking libdebian-dpkgcross-perl (2.6.20) ...
Selecting previously unselected package dpkg-cross.
Preparing to unpack .../088-dpkg-cross_2.6.20_all.deb ...
Unpacking dpkg-cross (2.6.20) ...
Selecting previously unselected package crossbuild-essential-amd64.
Preparing to unpack .../089-crossbuild-essential-amd64_12.10_all.deb ...
Unpacking crossbuild-essential-amd64 (12.10) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../090-libdebhelper-perl_13.15.3_all.deb ...
Unpacking libdebhelper-perl (13.15.3) ...
Selecting previously unselected package libtool.
Preparing to unpack .../091-libtool_2.4.7-7_all.deb ...
Unpacking libtool (2.4.7-7) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../092-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../093-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../094-libsub-override-perl_0.10-1_all.deb ...
Unpacking libsub-override-perl (0.10-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../095-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../096-dh-strip-nondeterminism_1.13.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1t64:arm64.
Preparing to unpack .../097-libelf1t64_0.191-1+b1_arm64.deb ...
Unpacking libelf1t64:arm64 (0.191-1+b1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../098-dwz_0.15-1+b1_arm64.deb ...
Unpacking dwz (0.15-1+b1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../099-gettext_0.21-14+b1_arm64.deb ...
Unpacking gettext (0.21-14+b1) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../100-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../101-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../102-debhelper_13.15.3_all.deb ...
Unpacking debhelper (13.15.3) ...
Selecting previously unselected package sgml-data.
Preparing to unpack .../103-sgml-data_2.0.11+nmu1_all.deb ...
Unpacking sgml-data (2.0.11+nmu1) ...
Selecting previously unselected package docbook-xml.
Preparing to unpack .../104-docbook-xml_4.5-12_all.deb ...
Unpacking docbook-xml (4.5-12) ...
Selecting previously unselected package libfakeroot:arm64.
Preparing to unpack .../105-libfakeroot_1.34-1_arm64.deb ...
Unpacking libfakeroot:arm64 (1.34-1) ...
Selecting previously unselected package fakeroot.
Preparing to unpack .../106-fakeroot_1.34-1_arm64.deb ...
Unpacking fakeroot (1.34-1) ...
Selecting previously unselected package gcc-14-base:amd64.
Preparing to unpack .../107-gcc-14-base_14-20240330-1_amd64.deb ...
Unpacking gcc-14-base:amd64 (14-20240330-1) ...
Selecting previously unselected package libgcc-s1:amd64.
Preparing to unpack .../108-libgcc-s1_14-20240330-1_amd64.deb ...
Unpacking libgcc-s1:amd64 (14-20240330-1) ...
Selecting previously unselected package libc6:amd64.
Preparing to unpack .../109-libc6_2.37-18_amd64.deb ...
Unpacking libc6:amd64 (2.37-18) ...
Selecting previously unselected package libglvnd0:amd64.
Preparing to unpack .../110-libglvnd0_1.7.0-1_amd64.deb ...
Unpacking libglvnd0:amd64 (1.7.0-1) ...
Selecting previously unselected package libxau6:amd64.
Preparing to unpack .../111-libxau6_1%3a1.0.9-1_amd64.deb ...
Unpacking libxau6:amd64 (1:1.0.9-1) ...
Selecting previously unselected package libmd0:amd64.
Preparing to unpack .../112-libmd0_1.1.0-2_amd64.deb ...
Unpacking libmd0:amd64 (1.1.0-2) ...
Selecting previously unselected package libbsd0:amd64.
Preparing to unpack .../113-libbsd0_0.12.2-1_amd64.deb ...
Unpacking libbsd0:amd64 (0.12.2-1) ...
Selecting previously unselected package libxdmcp6:amd64.
Preparing to unpack .../114-libxdmcp6_1%3a1.1.2-3_amd64.deb ...
Unpacking libxdmcp6:amd64 (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:amd64.
Preparing to unpack .../115-libxcb1_1.17.0-1_amd64.deb ...
Unpacking libxcb1:amd64 (1.17.0-1) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../116-libx11-data_2%3a1.8.7-1_all.deb ...
Unpacking libx11-data (2:1.8.7-1) ...
Selecting previously unselected package libx11-6:amd64.
Preparing to unpack .../117-libx11-6_2%3a1.8.7-1_amd64.deb ...
Unpacking libx11-6:amd64 (2:1.8.7-1) ...
Selecting previously unselected package libdrm-common.
Preparing to unpack .../118-libdrm-common_2.4.120-2_all.deb ...
Unpacking libdrm-common (2.4.120-2) ...
Selecting previously unselected package libdrm2:amd64.
Preparing to unpack .../119-libdrm2_2.4.120-2_amd64.deb ...
Unpacking libdrm2:amd64 (2.4.120-2) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../120-libexpat1_2.6.2-1_amd64.deb ...
Unpacking libexpat1:amd64 (2.6.2-1) ...
Selecting previously unselected package libglapi-mesa:amd64.
Preparing to unpack .../121-libglapi-mesa_24.0.5-1_amd64.deb ...
Unpacking libglapi-mesa:amd64 (24.0.5-1) ...
Selecting previously unselected package libx11-xcb1:amd64.
Preparing to unpack .../122-libx11-xcb1_2%3a1.8.7-1_amd64.deb ...
Unpacking libx11-xcb1:amd64 (2:1.8.7-1) ...
Selecting previously unselected package libxcb-dri2-0:amd64.
Preparing to unpack .../123-libxcb-dri2-0_1.17.0-1_amd64.deb ...
Unpacking libxcb-dri2-0:amd64 (1.17.0-1) ...
Selecting previously unselected package libxcb-dri3-0:amd64.
Preparing to unpack .../124-libxcb-dri3-0_1.17.0-1_amd64.deb ...
Unpacking libxcb-dri3-0:amd64 (1.17.0-1) ...
Selecting previously unselected package libxcb-glx0:amd64.
Preparing to unpack .../125-libxcb-glx0_1.17.0-1_amd64.deb ...
Unpacking libxcb-glx0:amd64 (1.17.0-1) ...
Selecting previously unselected package libxcb-present0:amd64.
Preparing to unpack .../126-libxcb-present0_1.17.0-1_amd64.deb ...
Unpacking libxcb-present0:amd64 (1.17.0-1) ...
Selecting previously unselected package libxcb-randr0:amd64.
Preparing to unpack .../127-libxcb-randr0_1.17.0-1_amd64.deb ...
Unpacking libxcb-randr0:amd64 (1.17.0-1) ...
Selecting previously unselected package libxcb-shm0:amd64.
Preparing to unpack .../128-libxcb-shm0_1.17.0-1_amd64.deb ...
Unpacking libxcb-shm0:amd64 (1.17.0-1) ...
Selecting previously unselected package libxcb-sync1:amd64.
Preparing to unpack .../129-libxcb-sync1_1.17.0-1_amd64.deb ...
Unpacking libxcb-sync1:amd64 (1.17.0-1) ...
Selecting previously unselected package libxcb-xfixes0:amd64.
Preparing to unpack .../130-libxcb-xfixes0_1.17.0-1_amd64.deb ...
Unpacking libxcb-xfixes0:amd64 (1.17.0-1) ...
Selecting previously unselected package libxext6:amd64.
Preparing to unpack .../131-libxext6_2%3a1.3.4-1+b1_amd64.deb ...
Unpacking libxext6:amd64 (2:1.3.4-1+b1) ...
Selecting previously unselected package libxfixes3:amd64.
Preparing to unpack .../132-libxfixes3_1%3a6.0.0-2_amd64.deb ...
Unpacking libxfixes3:amd64 (1:6.0.0-2) ...
Selecting previously unselected package libxshmfence1:amd64.
Preparing to unpack .../133-libxshmfence1_1.3-1_amd64.deb ...
Unpacking libxshmfence1:amd64 (1.3-1) ...
Selecting previously unselected package libxxf86vm1:amd64.
Preparing to unpack .../134-libxxf86vm1_1%3a1.1.4-1+b2_amd64.deb ...
Unpacking libxxf86vm1:amd64 (1:1.1.4-1+b2) ...
Selecting previously unselected package libvulkan1:amd64.
Preparing to unpack .../135-libvulkan1_1.3.280.0-1_amd64.deb ...
Unpacking libvulkan1:amd64 (1.3.280.0-1) ...
Selecting previously unselected package libdrm-amdgpu1:amd64.
Preparing to unpack .../136-libdrm-amdgpu1_2.4.120-2_amd64.deb ...
Unpacking libdrm-amdgpu1:amd64 (2.4.120-2) ...
Selecting previously unselected package zlib1g:amd64.
Preparing to unpack .../137-zlib1g_1%3a1.3.dfsg-3.1_amd64.deb ...
Unpacking zlib1g:amd64 (1:1.3.dfsg-3.1) ...
Selecting previously unselected package libpciaccess0:amd64.
Preparing to unpack .../138-libpciaccess0_0.17-3_amd64.deb ...
Unpacking libpciaccess0:amd64 (0.17-3) ...
Selecting previously unselected package libdrm-intel1:amd64.
Preparing to unpack .../139-libdrm-intel1_2.4.120-2_amd64.deb ...
Unpacking libdrm-intel1:amd64 (2.4.120-2) ...
Selecting previously unselected package libdrm-nouveau2:amd64.
Preparing to unpack .../140-libdrm-nouveau2_2.4.120-2_amd64.deb ...
Unpacking libdrm-nouveau2:amd64 (2.4.120-2) ...
Selecting previously unselected package libdrm-radeon1:amd64.
Preparing to unpack .../141-libdrm-radeon1_2.4.120-2_amd64.deb ...
Unpacking libdrm-radeon1:amd64 (2.4.120-2) ...
Selecting previously unselected package libzstd1:amd64.
Preparing to unpack .../142-libzstd1_1.5.5+dfsg2-2_amd64.deb ...
Unpacking libzstd1:amd64 (1.5.5+dfsg2-2) ...
Selecting previously unselected package libelf1t64:amd64.
Preparing to unpack .../143-libelf1t64_0.191-1+b1_amd64.deb ...
Unpacking libelf1t64:amd64 (0.191-1+b1) ...
Selecting previously unselected package libtinfo6:amd64.
Preparing to unpack .../144-libtinfo6_6.4+20240414-1_amd64.deb ...
Unpacking libtinfo6:amd64 (6.4+20240414-1) ...
Selecting previously unselected package libedit2:amd64.
Preparing to unpack .../145-libedit2_3.1-20230828-1_amd64.deb ...
Unpacking libedit2:amd64 (3.1-20230828-1) ...
Selecting previously unselected package libffi8:amd64.
Preparing to unpack .../146-libffi8_3.4.6-1_amd64.deb ...
Unpacking libffi8:amd64 (3.4.6-1) ...
Selecting previously unselected package libstdc++6:amd64.
Preparing to unpack .../147-libstdc++6_14-20240330-1_amd64.deb ...
Unpacking libstdc++6:amd64 (14-20240330-1) ...
Selecting previously unselected package libicu72:amd64.
Preparing to unpack .../148-libicu72_72.1-4+b1_amd64.deb ...
Unpacking libicu72:amd64 (72.1-4+b1) ...
Selecting previously unselected package liblzma5:amd64.
Preparing to unpack .../149-liblzma5_5.6.1+really5.4.5-1_amd64.deb ...
Unpacking liblzma5:amd64 (5.6.1+really5.4.5-1) ...
Selecting previously unselected package libxml2:amd64.
Preparing to unpack .../150-libxml2_2.9.14+dfsg-1.3+b2_amd64.deb ...
Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b2) ...
Selecting previously unselected package libz3-4:amd64.
Preparing to unpack .../151-libz3-4_4.8.12-3.1+b2_amd64.deb ...
Unpacking libz3-4:amd64 (4.8.12-3.1+b2) ...
Selecting previously unselected package libllvm17t64:amd64.
Preparing to unpack .../152-libllvm17t64_1%3a17.0.6-9+b2_amd64.deb ...
Unpacking libllvm17t64:amd64 (1:17.0.6-9+b2) ...
Selecting previously unselected package libsensors-config.
Preparing to unpack .../153-libsensors-config_1%3a3.6.0-9_all.deb ...
Unpacking libsensors-config (1:3.6.0-9) ...
Selecting previously unselected package libsensors5:amd64.
Preparing to unpack .../154-libsensors5_1%3a3.6.0-9_amd64.deb ...
Unpacking libsensors5:amd64 (1:3.6.0-9) ...
Selecting previously unselected package libgl1-mesa-dri:amd64.
Preparing to unpack .../155-libgl1-mesa-dri_24.0.5-1_amd64.deb ...
Unpacking libgl1-mesa-dri:amd64 (24.0.5-1) ...
Selecting previously unselected package libglx-mesa0:amd64.
Preparing to unpack .../156-libglx-mesa0_24.0.5-1_amd64.deb ...
Unpacking libglx-mesa0:amd64 (24.0.5-1) ...
Selecting previously unselected package libglx0:amd64.
Preparing to unpack .../157-libglx0_1.7.0-1_amd64.deb ...
Unpacking libglx0:amd64 (1.7.0-1) ...
Selecting previously unselected package libgl1:amd64.
Preparing to unpack .../158-libgl1_1.7.0-1_amd64.deb ...
Unpacking libgl1:amd64 (1.7.0-1) ...
Selecting previously unselected package libxi6:amd64.
Preparing to unpack .../159-libxi6_2%3a1.8.1-1_amd64.deb ...
Unpacking libxi6:amd64 (2:1.8.1-1) ...
Selecting previously unselected package libglut3.12:amd64.
Preparing to unpack .../160-libglut3.12_3.4.0-1+b1_amd64.deb ...
Unpacking libglut3.12:amd64 (3.4.0-1+b1) ...
Selecting previously unselected package xorg-sgml-doctools.
Preparing to unpack .../161-xorg-sgml-doctools_1%3a1.11-1.1_all.deb ...
Unpacking xorg-sgml-doctools (1:1.11-1.1) ...
Selecting previously unselected package x11proto-dev.
Preparing to unpack .../162-x11proto-dev_2024.1-1_all.deb ...
Unpacking x11proto-dev (2024.1-1) ...
Selecting previously unselected package libxau-dev:amd64.
Preparing to unpack .../163-libxau-dev_1%3a1.0.9-1_amd64.deb ...
Unpacking libxau-dev:amd64 (1:1.0.9-1) ...
Selecting previously unselected package libxdmcp-dev:amd64.
Preparing to unpack .../164-libxdmcp-dev_1%3a1.1.2-3_amd64.deb ...
Unpacking libxdmcp-dev:amd64 (1:1.1.2-3) ...
Selecting previously unselected package xtrans-dev.
Preparing to unpack .../165-xtrans-dev_1.4.0-1_all.deb ...
Unpacking xtrans-dev (1.4.0-1) ...
Selecting previously unselected package libpthread-stubs0-dev:amd64.
Preparing to unpack .../166-libpthread-stubs0-dev_0.4-1_amd64.deb ...
Unpacking libpthread-stubs0-dev:amd64 (0.4-1) ...
Selecting previously unselected package libxcb1-dev:amd64.
Preparing to unpack .../167-libxcb1-dev_1.17.0-1_amd64.deb ...
Unpacking libxcb1-dev:amd64 (1.17.0-1) ...
Selecting previously unselected package libx11-dev:amd64.
Preparing to unpack .../168-libx11-dev_2%3a1.8.7-1_amd64.deb ...
Unpacking libx11-dev:amd64 (2:1.8.7-1) ...
Selecting previously unselected package libglx-dev:amd64.
Preparing to unpack .../169-libglx-dev_1.7.0-1_amd64.deb ...
Unpacking libglx-dev:amd64 (1.7.0-1) ...
Selecting previously unselected package libgl-dev:amd64.
Preparing to unpack .../170-libgl-dev_1.7.0-1_amd64.deb ...
Unpacking libgl-dev:amd64 (1.7.0-1) ...
Selecting previously unselected package libglvnd-core-dev:amd64.
Preparing to unpack .../171-libglvnd-core-dev_1.7.0-1_amd64.deb ...
Unpacking libglvnd-core-dev:amd64 (1.7.0-1) ...
Selecting previously unselected package libwayland-server0:amd64.
Preparing to unpack .../172-libwayland-server0_1.22.0-2.1+b1_amd64.deb ...
Unpacking libwayland-server0:amd64 (1.22.0-2.1+b1) ...
Selecting previously unselected package libgbm1:amd64.
Preparing to unpack .../173-libgbm1_24.0.5-1_amd64.deb ...
Unpacking libgbm1:amd64 (24.0.5-1) ...
Selecting previously unselected package libwayland-client0:amd64.
Preparing to unpack .../174-libwayland-client0_1.22.0-2.1+b1_amd64.deb ...
Unpacking libwayland-client0:amd64 (1.22.0-2.1+b1) ...
Selecting previously unselected package libegl-mesa0:amd64.
Preparing to unpack .../175-libegl-mesa0_24.0.5-1_amd64.deb ...
Unpacking libegl-mesa0:amd64 (24.0.5-1) ...
Selecting previously unselected package libegl1:amd64.
Preparing to unpack .../176-libegl1_1.7.0-1_amd64.deb ...
Unpacking libegl1:amd64 (1.7.0-1) ...
Selecting previously unselected package libegl-dev:amd64.
Preparing to unpack .../177-libegl-dev_1.7.0-1_amd64.deb ...
Unpacking libegl-dev:amd64 (1.7.0-1) ...
Selecting previously unselected package libgles1:amd64.
Preparing to unpack .../178-libgles1_1.7.0-1_amd64.deb ...
Unpacking libgles1:amd64 (1.7.0-1) ...
Selecting previously unselected package libgles2:amd64.
Preparing to unpack .../179-libgles2_1.7.0-1_amd64.deb ...
Unpacking libgles2:amd64 (1.7.0-1) ...
Selecting previously unselected package libgles-dev:amd64.
Preparing to unpack .../180-libgles-dev_1.7.0-1_amd64.deb ...
Unpacking libgles-dev:amd64 (1.7.0-1) ...
Selecting previously unselected package libopengl0:amd64.
Preparing to unpack .../181-libopengl0_1.7.0-1_amd64.deb ...
Unpacking libopengl0:amd64 (1.7.0-1) ...
Selecting previously unselected package libopengl-dev:amd64.
Preparing to unpack .../182-libopengl-dev_1.7.0-1_amd64.deb ...
Unpacking libopengl-dev:amd64 (1.7.0-1) ...
Selecting previously unselected package libglvnd-dev:amd64.
Preparing to unpack .../183-libglvnd-dev_1.7.0-1_amd64.deb ...
Unpacking libglvnd-dev:amd64 (1.7.0-1) ...
Selecting previously unselected package libgl1-mesa-dev:amd64.
Preparing to unpack .../184-libgl1-mesa-dev_24.0.5-1_amd64.deb ...
Unpacking libgl1-mesa-dev:amd64 (24.0.5-1) ...
Selecting previously unselected package libglu1-mesa:amd64.
Preparing to unpack .../185-libglu1-mesa_9.0.2-1.1_amd64.deb ...
Unpacking libglu1-mesa:amd64 (9.0.2-1.1) ...
Selecting previously unselected package libglu1-mesa-dev:amd64.
Preparing to unpack .../186-libglu1-mesa-dev_9.0.2-1.1_amd64.deb ...
Unpacking libglu1-mesa-dev:amd64 (9.0.2-1.1) ...
Selecting previously unselected package libxext-dev:amd64.
Preparing to unpack .../187-libxext-dev_2%3a1.3.4-1+b1_amd64.deb ...
Unpacking libxext-dev:amd64 (2:1.3.4-1+b1) ...
Selecting previously unselected package x11-common.
Preparing to unpack .../188-x11-common_1%3a7.7+23_all.deb ...
Unpacking x11-common (1:7.7+23) ...
Selecting previously unselected package libice6:amd64.
Preparing to unpack .../189-libice6_2%3a1.0.10-1_amd64.deb ...
Unpacking libice6:amd64 (2:1.0.10-1) ...
Selecting previously unselected package libuuid1:amd64.
Preparing to unpack .../190-libuuid1_2.40-6_amd64.deb ...
Unpacking libuuid1:amd64 (2.40-6) ...
Selecting previously unselected package libsm6:amd64.
Preparing to unpack .../191-libsm6_2%3a1.2.3-1_amd64.deb ...
Unpacking libsm6:amd64 (2:1.2.3-1) ...
Selecting previously unselected package libxt6t64:amd64.
Preparing to unpack .../192-libxt6t64_1%3a1.2.1-1.2_amd64.deb ...
Unpacking libxt6t64:amd64 (1:1.2.1-1.2) ...
Selecting previously unselected package libice-dev:amd64.
Preparing to unpack .../193-libice-dev_2%3a1.0.10-1_amd64.deb ...
Unpacking libice-dev:amd64 (2:1.0.10-1) ...
Selecting previously unselected package libsm-dev:amd64.
Preparing to unpack .../194-libsm-dev_2%3a1.2.3-1_amd64.deb ...
Unpacking libsm-dev:amd64 (2:1.2.3-1) ...
Selecting previously unselected package libxt-dev:amd64.
Preparing to unpack .../195-libxt-dev_1%3a1.2.1-1.2_amd64.deb ...
Unpacking libxt-dev:amd64 (1:1.2.1-1.2) ...
Selecting previously unselected package libglut-dev:amd64.
Preparing to unpack .../196-libglut-dev_3.4.0-1+b1_amd64.deb ...
Unpacking libglut-dev:amd64 (3.4.0-1+b1) ...
Selecting previously unselected package freeglut3-dev:amd64.
Preparing to unpack .../197-freeglut3-dev_3.4.0-1+b1_amd64.deb ...
Unpacking freeglut3-dev:amd64 (3.4.0-1+b1) ...
Selecting previously unselected package gcc-13-base:amd64.
Preparing to unpack .../198-gcc-13-base_13.2.0-23_amd64.deb ...
Unpacking gcc-13-base:amd64 (13.2.0-23) ...
Selecting previously unselected package gemmi-dev:amd64.
Preparing to unpack .../199-gemmi-dev_0.6.4+ds-1_amd64.deb ...
Unpacking gemmi-dev:amd64 (0.6.4+ds-1) ...
Selecting previously unselected package libasan8:amd64.
Preparing to unpack .../200-libasan8_14-20240330-1_amd64.deb ...
Unpacking libasan8:amd64 (14-20240330-1) ...
Selecting previously unselected package libatomic1:amd64.
Preparing to unpack .../201-libatomic1_14-20240330-1_amd64.deb ...
Unpacking libatomic1:amd64 (14-20240330-1) ...
Selecting previously unselected package libblas3:amd64.
Preparing to unpack .../202-libblas3_3.12.0-3_amd64.deb ...
Unpacking libblas3:amd64 (3.12.0-3) ...
Selecting previously unselected package libblas-dev:amd64.
Preparing to unpack .../203-libblas-dev_3.12.0-3_amd64.deb ...
Unpacking libblas-dev:amd64 (3.12.0-3) ...
Selecting previously unselected package libbsd0:arm64.
Preparing to unpack .../204-libbsd0_0.12.2-1_arm64.deb ...
Unpacking libbsd0:arm64 (0.12.2-1) ...
Selecting previously unselected package libcrypt1:amd64.
Preparing to unpack .../205-libcrypt1_1%3a4.4.36-4_amd64.deb ...
Unpacking libcrypt1:amd64 (1:4.4.36-4) ...
Selecting previously unselected package libcrypt-dev:amd64.
Preparing to unpack .../206-libcrypt-dev_1%3a4.4.36-4_amd64.deb ...
Unpacking libcrypt-dev:amd64 (1:4.4.36-4) ...
Selecting previously unselected package libc6-dev:amd64.
Preparing to unpack .../207-libc6-dev_2.37-18_amd64.deb ...
Unpacking libc6-dev:amd64 (2.37-18) ...
Selecting previously unselected package libgomp1:amd64.
Preparing to unpack .../208-libgomp1_14-20240330-1_amd64.deb ...
Unpacking libgomp1:amd64 (14-20240330-1) ...
Selecting previously unselected package libitm1:amd64.
Preparing to unpack .../209-libitm1_14-20240330-1_amd64.deb ...
Unpacking libitm1:amd64 (14-20240330-1) ...
Selecting previously unselected package liblsan0:amd64.
Preparing to unpack .../210-liblsan0_14-20240330-1_amd64.deb ...
Unpacking liblsan0:amd64 (14-20240330-1) ...
Selecting previously unselected package libtsan2:amd64.
Preparing to unpack .../211-libtsan2_14-20240330-1_amd64.deb ...
Unpacking libtsan2:amd64 (14-20240330-1) ...
Selecting previously unselected package libubsan1:amd64.
Preparing to unpack .../212-libubsan1_14-20240330-1_amd64.deb ...
Unpacking libubsan1:amd64 (14-20240330-1) ...
Selecting previously unselected package libhwasan0:amd64.
Preparing to unpack .../213-libhwasan0_14-20240330-1_amd64.deb ...
Unpacking libhwasan0:amd64 (14-20240330-1) ...
Selecting previously unselected package libquadmath0:amd64.
Preparing to unpack .../214-libquadmath0_14-20240330-1_amd64.deb ...
Unpacking libquadmath0:amd64 (14-20240330-1) ...
Selecting previously unselected package libgcc-13-dev:amd64.
Preparing to unpack .../215-libgcc-13-dev_13.2.0-23_amd64.deb ...
Unpacking libgcc-13-dev:amd64 (13.2.0-23) ...
Selecting previously unselected package libgfortran5:amd64.
Preparing to unpack .../216-libgfortran5_14-20240330-1_amd64.deb ...
Unpacking libgfortran5:amd64 (14-20240330-1) ...
Selecting previously unselected package liblapack3:amd64.
Preparing to unpack .../217-liblapack3_3.12.0-3_amd64.deb ...
Unpacking liblapack3:amd64 (3.12.0-3) ...
Selecting previously unselected package liblapack-dev:amd64.
Preparing to unpack .../218-liblapack-dev_3.12.0-3_amd64.deb ...
Unpacking liblapack-dev:amd64 (3.12.0-3) ...
Selecting previously unselected package libopenmm8.0t64:amd64.
Preparing to unpack .../219-libopenmm8.0t64_8.0.0+dfsg-6.1_amd64.deb ...
Unpacking libopenmm8.0t64:amd64 (8.0.0+dfsg-6.1) ...
Selecting previously unselected package libopenmm-dev:amd64.
Preparing to unpack .../220-libopenmm-dev_8.0.0+dfsg-6.1_amd64.deb ...
Unpacking libopenmm-dev:amd64 (8.0.0+dfsg-6.1) ...
Selecting previously unselected package libpthread-stubs0-dev:arm64.
Preparing to unpack .../221-libpthread-stubs0-dev_0.4-1_arm64.deb ...
Unpacking libpthread-stubs0-dev:arm64 (0.4-1) ...
Selecting previously unselected package libseqan2-dev.
Preparing to unpack .../222-libseqan2-dev_2.4.0+dfsg-16_all.deb ...
Unpacking libseqan2-dev (2.4.0+dfsg-16) ...
Selecting previously unselected package libxfixes-dev:amd64.
Preparing to unpack .../223-libxfixes-dev_1%3a6.0.0-2_amd64.deb ...
Unpacking libxfixes-dev:amd64 (1:6.0.0-2) ...
Selecting previously unselected package libxi-dev:amd64.
Preparing to unpack .../224-libxi-dev_2%3a1.8.1-1_amd64.deb ...
Unpacking libxi-dev:amd64 (2:1.8.1-1) ...
Selecting previously unselected package libxmu6:amd64.
Preparing to unpack .../225-libxmu6_2%3a1.1.3-3+b2_amd64.deb ...
Unpacking libxmu6:amd64 (2:1.1.3-3+b2) ...
Selecting previously unselected package libxau6:arm64.
Preparing to unpack .../226-libxau6_1%3a1.0.9-1_arm64.deb ...
Unpacking libxau6:arm64 (1:1.0.9-1) ...
Selecting previously unselected package libxdmcp6:arm64.
Preparing to unpack .../227-libxdmcp6_1%3a1.1.2-3_arm64.deb ...
Unpacking libxdmcp6:arm64 (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:arm64.
Preparing to unpack .../228-libxcb1_1.17.0-1_arm64.deb ...
Unpacking libxcb1:arm64 (1.17.0-1) ...
Selecting previously unselected package libx11-6:arm64.
Preparing to unpack .../229-libx11-6_2%3a1.8.7-1_arm64.deb ...
Unpacking libx11-6:arm64 (2:1.8.7-1) ...
Selecting previously unselected package libxau-dev:arm64.
Preparing to unpack .../230-libxau-dev_1%3a1.0.9-1_arm64.deb ...
Unpacking libxau-dev:arm64 (1:1.0.9-1) ...
Selecting previously unselected package libxdmcp-dev:arm64.
Preparing to unpack .../231-libxdmcp-dev_1%3a1.1.2-3_arm64.deb ...
Unpacking libxdmcp-dev:arm64 (1:1.1.2-3) ...
Selecting previously unselected package libxcb1-dev:arm64.
Preparing to unpack .../232-libxcb1-dev_1.17.0-1_arm64.deb ...
Unpacking libxcb1-dev:arm64 (1.17.0-1) ...
Selecting previously unselected package libx11-dev:arm64.
Preparing to unpack .../233-libx11-dev_2%3a1.8.7-1_arm64.deb ...
Unpacking libx11-dev:arm64 (2:1.8.7-1) ...
Selecting previously unselected package libxmu-headers.
Preparing to unpack .../234-libxmu-headers_2%3a1.1.3-3_all.deb ...
Unpacking libxmu-headers (2:1.1.3-3) ...
Selecting previously unselected package libxmu-dev:amd64.
Preparing to unpack .../235-libxmu-dev_2%3a1.1.3-3+b2_amd64.deb ...
Unpacking libxmu-dev:amd64 (2:1.1.3-3+b2) ...
Selecting previously unselected package libsimbody3.7:amd64.
Preparing to unpack .../236-libsimbody3.7_3.7+dfsg-3_amd64.deb ...
Unpacking libsimbody3.7:amd64 (3.7+dfsg-3) ...
Selecting previously unselected package libsimbody-dev:amd64.
Preparing to unpack .../237-libsimbody-dev_3.7+dfsg-3_amd64.deb ...
Unpacking libsimbody-dev:amd64 (3.7+dfsg-3) ...
Selecting previously unselected package libsimtkmolmodel3.1t64:amd64.
Preparing to unpack .../238-libsimtkmolmodel3.1t64_3.1.0-4.1+b1_amd64.deb ...
Unpacking libsimtkmolmodel3.1t64:amd64 (3.1.0-4.1+b1) ...
Selecting previously unselected package libsimtkmolmodel-dev:amd64.
Preparing to unpack .../239-libsimtkmolmodel-dev_3.1.0-4.1+b1_amd64.deb ...
Unpacking libsimtkmolmodel-dev:amd64 (3.1.0-4.1+b1) ...
Selecting previously unselected package libsimtkmolmodel-plugins:amd64.
Preparing to unpack .../240-libsimtkmolmodel-plugins_3.1.0-4.1+b1_amd64.deb ...
Unpacking libsimtkmolmodel-plugins:amd64 (3.1.0-4.1+b1) ...
Selecting previously unselected package libstb0t64:amd64.
Preparing to unpack .../241-libstb0t64_0.0~git20230129.5736b15+ds-1.2_amd64.deb ...
Unpacking libstb0t64:amd64 (0.0~git20230129.5736b15+ds-1.2) ...
Selecting previously unselected package libstb-dev:amd64.
Preparing to unpack .../242-libstb-dev_0.0~git20230129.5736b15+ds-1.2_amd64.deb ...
Unpacking libstb-dev:amd64 (0.0~git20230129.5736b15+ds-1.2) ...
Selecting previously unselected package libstdc++-13-dev:amd64.
Preparing to unpack .../243-libstdc++-13-dev_13.2.0-23_amd64.deb ...
Unpacking libstdc++-13-dev:amd64 (13.2.0-23) ...
Selecting previously unselected package tao-pegtl-dev.
Preparing to unpack .../244-tao-pegtl-dev_3.2.7-1_all.deb ...
Unpacking tao-pegtl-dev (3.2.7-1) ...
Selecting previously unselected package zlib1g-dev:amd64.
Preparing to unpack .../245-zlib1g-dev_1%3a1.3.dfsg-3.1_amd64.deb ...
Unpacking zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ...
Selecting previously unselected package sbuild-build-depends-main-dummy:amd64.
Preparing to unpack .../246-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ...
Unpacking sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ...
Setting up libconfig-inifiles-perl (3.000003-2) ...
Setting up media-types (10.1.0) ...
Setting up libpipeline1:arm64 (1.5.7-2) ...
Setting up libfile-which-perl (1.27-2) ...
Setting up libxau6:arm64 (1:1.0.9-1) ...
Setting up libkeyutils1:arm64 (1.6.3-3) ...
Setting up libicu72:arm64 (72.1-4+b1) ...
Setting up bsdextrautils (2.40-6) ...
Setting up libglvnd-core-dev:amd64 (1.7.0-1) ...
Setting up libmagic-mgc (1:5.45-3) ...
Setting up gcc-14-base:amd64 (14-20240330-1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.15.3) ...
Setting up libbrotli1:arm64 (1.1.0-2+b3) ...
Setting up gemmi-dev:amd64 (0.6.4+ds-1) ...
Setting up libsqlite3-0:arm64 (3.45.3-1) ...
Setting up libuv1t64:arm64 (1.48.0-1.1) ...
Setting up libmagic1t64:arm64 (1:5.45-3) ...
Setting up x11-common (1:7.7+23) ...
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 (1:3.6.0-9) ...
Setting up libpsl5t64:arm64 (0.21.2-1.1) ...
Setting up libnghttp2-14:arm64 (1.61.0-1+b1) ...
Setting up libxml-namespacesupport-perl (1.12-2) ...
Setting up gettext-base (0.21-14+b1) ...
Setting up m4 (1.4.19-4) ...
Setting up gcc-14-cross-base (14-20240127-1cross1) ...
Setting up libcom-err2:arm64 (1.47.0-2.4) ...
Setting up file (1:5.45-3) ...
Setting up libyaml-perl (1.31-1) ...
Setting up libgomp1-amd64-cross (14-20240127-1cross1) ...
Setting up libpthread-stubs0-dev:amd64 (0.4-1) ...
Setting up libpthread-stubs0-dev:arm64 (0.4-1) ...
Setting up libfakeroot:arm64 (1.34-1) ...
Setting up libelf1t64:arm64 (0.191-1+b1) ...
Setting up libkrb5support0:arm64 (1.20.1-6+b1) ...
Setting up libseqan2-dev (2.4.0+dfsg-16) ...
Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-6) ...
Setting up tzdata (2024a-3) ...

Current default time zone: 'Etc/UTC'
Local time is now:      Wed Apr 24 08:33:38 UTC 2024.
Universal Time is now:  Wed Apr 24 08:33:38 UTC 2024.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

Setting up fakeroot (1.34-1) ...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
Setting up libitm1-amd64-cross (14-20240127-1cross1) ...
Setting up libxml-sax-base-perl (1.09-3) ...
Setting up libio-string-perl (1.08-4) ...
Setting up xtrans-dev (1.4.0-1) ...
Setting up autotools-dev (20220109.1) ...
Setting up cross-config (2.6.20) ...
Setting up gcc-13-base:amd64 (13.2.0-23) ...
Setting up libatomic1-amd64-cross (14-20240127-1cross1) ...
Setting up libx11-data (2:1.8.7-1) ...
Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ...
Setting up gcc-13-cross-base (13.2.0-12cross1) ...
Setting up libproc2-0:arm64 (2:4.0.4-4) ...
Setting up libquadmath0-amd64-cross (14-20240127-1cross1) ...
Setting up autopoint (0.21-14) ...
Setting up libjsoncpp25:arm64 (1.9.5-6+b2) ...
Setting up libc6-amd64-cross (2.37-12cross1) ...
Setting up libncursesw6:arm64 (6.4+20240414-1) ...
Setting up libk5crypto3:arm64 (1.20.1-6+b1) ...
Setting up libsasl2-2:arm64 (2.1.28+dfsg1-6) ...
Setting up autoconf (2.71-3) ...
Setting up gcc-13-x86-64-linux-gnu-base:arm64 (13.2.0-12cross1) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.22) ...
Setting up librhash0:arm64 (1.4.3-3+b1) ...
Setting up libuchardet0:arm64 (0.0.8-1+b1) ...
Setting up procps (2:4.0.4-4) ...
Setting up libsub-override-perl (0.10-1) ...
Setting up xorg-sgml-doctools (1:1.11-1.1) ...
Setting up netbase (6.4) ...
Setting up sgml-base (1.31) ...
Setting up cmake-data (3.28.3-1) ...
Setting up libkrb5-3:arm64 (1.20.1-6+b1) ...
Setting up libssh2-1t64:arm64 (1.11.0-4.1+b2) ...
Setting up libgcc-s1-amd64-cross (14-20240127-1cross1) ...
Setting up libfile-homedir-perl (1.006-2) ...
Setting up libbsd0:arm64 (0.12.2-1) ...
Setting up libdrm-common (2.4.120-2) ...
Setting up readline-common (8.2-4) ...
Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b2) ...
Setting up liblocale-gettext-perl (1.07-7) ...
Setting up tao-pegtl-dev (3.2.7-1) ...
Setting up binutils-x86-64-linux-gnu (2.42-4) ...
Setting up libstdc++6-amd64-cross (14-20240127-1cross1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up x11proto-dev (2024.1-1) ...
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up libxdmcp6:arm64 (1:1.1.2-3) ...
Setting up libxcb1:arm64 (1.17.0-1) ...
Setting up gettext (0.21-14+b1) ...
Setting up libxau-dev:arm64 (1:1.0.9-1) ...
Setting up libtool (2.4.7-7) ...
Setting up cpp-13-x86-64-linux-gnu (13.2.0-12cross1) ...
Setting up libasan8-amd64-cross (14-20240127-1cross1) ...
Setting up liblsan0-amd64-cross (14-20240127-1cross1) ...
Setting up libc6-dev-amd64-cross (2.37-12cross1) ...
Setting up libtsan2-amd64-cross (14-20240127-1cross1) ...
Setting up libldap-2.5-0:arm64 (2.5.16+dfsg-2) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up libxdmcp-dev:arm64 (1:1.1.2-3) ...
Setting up libhwasan0-amd64-cross (14-20240127-1cross1) ...
Setting up libgssapi-krb5-2:arm64 (1.20.1-6+b1) ...
Setting up libubsan1-amd64-cross (14-20240127-1cross1) ...
Setting up ucf (3.0043+nmu1) ...
Setting up libreadline8t64:arm64 (8.2-4) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up groff-base (1.23.0-3+b1) ...
Setting up xml-core (0.19) ...
Setting up libxslt1.1:arm64 (1.1.35-1) ...
Setting up libx11-6:arm64 (2:1.8.7-1) ...
Setting up libxml2-utils (2.9.14+dfsg-1.3+b2) ...
Setting up libarchive13t64:arm64 (3.7.2-2) ...
Setting up cpp-x86-64-linux-gnu (4:13.2.0-7) ...
Setting up libxcb1-dev:arm64 (1.17.0-1) ...
Setting up libcurl4t64:arm64 (8.7.1-3) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libpython3.11-stdlib:arm64 (3.11.9-1) ...
Setting up xsltproc (1.1.35-1) ...
Setting up libx11-dev:arm64 (2:1.8.7-1) ...
Setting up man-db (2.12.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxml-sax-perl (1.02+dfsg-3) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...

Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up libgcc-13-dev-amd64-cross (13.2.0-12cross1) ...
Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b3) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up libstdc++-13-dev-amd64-cross (13.2.0-12cross1) ...
Setting up cmake (3.28.3-1+b1) ...
Setting up libpython3-stdlib:arm64 (3.11.8-1) ...
Setting up python3.11 (3.11.9-1) ...
Setting up libxmu-headers (2:1.1.3-3) ...
Setting up gcc-13-x86-64-linux-gnu (13.2.0-12cross1) ...
Setting up debhelper (13.15.3) ...
Setting up python3 (3.11.8-1) ...
Setting up asciidoc-common (10.2.0-2) ...
Setting up libxml-simple-perl (2.25-2) ...
Setting up g++-13-x86-64-linux-gnu (13.2.0-12cross1) ...
Setting up gcc-x86-64-linux-gnu (4:13.2.0-7) ...
Setting up libconfig-auto-perl (0.44-2) ...
Setting up g++-x86-64-linux-gnu (4:13.2.0-7) ...
Setting up libdebian-dpkgcross-perl (2.6.20) ...
Setting up dpkg-cross (2.6.20) ...
Setting up crossbuild-essential-amd64 (12.10) ...
Setting up libgcc-s1:amd64 (14-20240330-1) ...
Setting up libc6:amd64 (2.37-18) ...
Setting up libffi8:amd64 (3.4.6-1) ...
Setting up libdrm2:amd64 (2.4.120-2) ...
Setting up libmd0:amd64 (1.1.0-2) ...
Setting up libxshmfence1:amd64 (1.3-1) ...
Setting up libhwasan0:amd64 (14-20240330-1) ...
Setting up libasan8:amd64 (14-20240330-1) ...
Setting up libtsan2:amd64 (14-20240330-1) ...
Setting up libstb0t64:amd64 (0.0~git20230129.5736b15+ds-1.2) ...
Setting up libbsd0:amd64 (0.12.2-1) ...
Setting up libstdc++6:amd64 (14-20240330-1) ...
Setting up liblsan0:amd64 (14-20240330-1) ...
Setting up libitm1:amd64 (14-20240330-1) ...
Setting up libtinfo6:amd64 (6.4+20240414-1) ...
Setting up libopenmm8.0t64:amd64 (8.0.0+dfsg-6.1) ...
Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ...
Setting up libwayland-client0:amd64 (1.22.0-2.1+b1) ...
Setting up libexpat1:amd64 (2.6.2-1) ...
Setting up libwayland-server0:amd64 (1.22.0-2.1+b1) ...
Setting up libzstd1:amd64 (1.5.5+dfsg2-2) ...
Setting up libice6:amd64 (2:1.0.10-1) ...
Setting up libxau6:amd64 (1:1.0.9-1) ...
Setting up libxdmcp6:amd64 (1:1.1.2-3) ...
Setting up libdrm-nouveau2:amd64 (2.4.120-2) ...
Setting up libxcb1:amd64 (1.17.0-1) ...
Setting up libicu72:amd64 (72.1-4+b1) ...
Setting up libxcb-xfixes0:amd64 (1.17.0-1) ...
Setting up libxau-dev:amd64 (1:1.0.9-1) ...
Setting up liblzma5:amd64 (5.6.1+really5.4.5-1) ...
Setting up libice-dev:amd64 (2:1.0.10-1) ...
Setting up libdrm-radeon1:amd64 (2.4.120-2) ...
Setting up libglvnd0:amd64 (1.7.0-1) ...
Setting up libxcb-glx0:amd64 (1.17.0-1) ...
Setting up libedit2:amd64 (3.1-20230828-1) ...
Setting up zlib1g:amd64 (1:1.3.dfsg-3.1) ...
Setting up libcrypt1:amd64 (1:4.4.36-4) ...
Setting up libxcb-shm0:amd64 (1.17.0-1) ...
Setting up libgomp1:amd64 (14-20240330-1) ...
Setting up libopenmm-dev:amd64 (8.0.0+dfsg-6.1) ...
Setting up libopengl0:amd64 (1.7.0-1) ...
Setting up libelf1t64:amd64 (0.191-1+b1) ...
Setting up libxcb-present0:amd64 (1.17.0-1) ...
Setting up libxdmcp-dev:amd64 (1:1.1.2-3) ...
Setting up libz3-4:amd64 (4.8.12-3.1+b2) ...
Setting up libblas3:amd64 (3.12.0-3) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
Setting up libgles2:amd64 (1.7.0-1) ...
Setting up libxcb-sync1:amd64 (1.17.0-1) ...
Setting up libgles1:amd64 (1.7.0-1) ...
Setting up libquadmath0:amd64 (14-20240330-1) ...
Setting up libatomic1:amd64 (14-20240330-1) ...
Setting up libuuid1:amd64 (2.40-6) ...
Setting up libsensors5:amd64 (1:3.6.0-9) ...
Setting up libglapi-mesa:amd64 (24.0.5-1) ...
Setting up libgfortran5:amd64 (14-20240330-1) ...
Setting up libvulkan1:amd64 (1.3.280.0-1) ...
Setting up libubsan1:amd64 (14-20240330-1) ...
Setting up libxcb-dri2-0:amd64 (1.17.0-1) ...
Setting up libstb-dev:amd64 (0.0~git20230129.5736b15+ds-1.2) ...
Setting up libgcc-13-dev:amd64 (13.2.0-23) ...
Setting up libcrypt-dev:amd64 (1:4.4.36-4) ...
Setting up libxcb-randr0:amd64 (1.17.0-1) ...
Setting up libc6-dev:amd64 (2.37-18) ...
Setting up libx11-6:amd64 (2:1.8.7-1) ...
Setting up libglu1-mesa:amd64 (9.0.2-1.1) ...
Setting up libopengl-dev:amd64 (1.7.0-1) ...
Setting up libsm6:amd64 (2:1.2.3-1) ...
Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b2) ...
Setting up libblas-dev:amd64 (3.12.0-3) ...
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 libstdc++-13-dev:amd64 (13.2.0-23) ...
Setting up libxcb-dri3-0:amd64 (1.17.0-1) ...
Setting up libx11-xcb1:amd64 (2:1.8.7-1) ...
Setting up libpciaccess0:amd64 (0.17-3) ...
Setting up liblapack3:amd64 (3.12.0-3) ...
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 libxcb1-dev:amd64 (1.17.0-1) ...
Setting up libgbm1:amd64 (24.0.5-1) ...
Setting up libsm-dev:amd64 (2:1.2.3-1) ...
Setting up libdrm-intel1:amd64 (2.4.120-2) ...
Setting up libx11-dev:amd64 (2:1.8.7-1) ...
Setting up libxext6:amd64 (2:1.3.4-1+b1) ...
Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ...
Setting up libegl-mesa0:amd64 (24.0.5-1) ...
Setting up libllvm17t64:amd64 (1:17.0.6-9+b2) ...
Setting up libxfixes3:amd64 (1:6.0.0-2) ...
Setting up libxt6t64:amd64 (1:1.2.1-1.2) ...
Setting up liblapack-dev:amd64 (3.12.0-3) ...
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 libxext-dev:amd64 (2:1.3.4-1+b1) ...
Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ...
Setting up libegl1:amd64 (1.7.0-1) ...
Setting up libxmu6:amd64 (2:1.1.3-3+b2) ...
Setting up libxi6:amd64 (2:1.8.1-1) ...
Setting up libgl1-mesa-dri:amd64 (24.0.5-1) ...
Setting up libxfixes-dev:amd64 (1:6.0.0-2) ...
Setting up libxt-dev:amd64 (1:1.2.1-1.2) ...
Setting up libxi-dev:amd64 (2:1.8.1-1) ...
Setting up libglx-mesa0:amd64 (24.0.5-1) ...
Setting up libglx0:amd64 (1.7.0-1) ...
Setting up libxmu-dev:amd64 (2:1.1.3-3+b2) ...
Setting up libgl1:amd64 (1.7.0-1) ...
Setting up libglut3.12:amd64 (3.4.0-1+b1) ...
Setting up libsimbody3.7:amd64 (3.7+dfsg-3) ...
Setting up libglx-dev:amd64 (1.7.0-1) ...
Setting up libgl-dev:amd64 (1.7.0-1) ...
Setting up libegl-dev:amd64 (1.7.0-1) ...
Setting up libsimtkmolmodel3.1t64:amd64 (3.1.0-4.1+b1) ...
Setting up libglu1-mesa-dev:amd64 (9.0.2-1.1) ...
Setting up libgles-dev:amd64 (1.7.0-1) ...
Setting up libsimtkmolmodel-plugins:amd64 (3.1.0-4.1+b1) ...
Setting up libsimtkmolmodel-dev:amd64 (3.1.0-4.1+b1) ...
Setting up libglvnd-dev:amd64 (1.7.0-1) ...
Setting up libgl1-mesa-dev:amd64 (24.0.5-1) ...
Setting up libglut-dev:amd64 (3.4.0-1+b1) ...
Setting up freeglut3-dev:amd64 (3.4.0-1+b1) ...
Setting up libsimbody-dev:amd64 (3.7+dfsg-3) ...
Processing triggers for libc-bin (2.37-18) ...
Processing triggers for sgml-base (1.31) ...
Setting up docbook-xsl (1.79.2+dfsg-7) ...
Setting up sgml-data (2.0.11+nmu1) ...
Setting up asciidoc-base (10.2.0-2) ...
Processing triggers for sgml-base (1.31) ...
Setting up docbook-xml (4.5-12) ...
Processing triggers for sgml-base (1.31) ...
Setting up sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ...

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (amd64 included in any all)

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 6.1.0-7-arm64 #1 SMP Debian 6.1.20-1 (2023-03-19) arm64 (aarch64)
Toolchain package versions: binutils_2.42-4 dpkg-dev_1.22.6 g++-13_13.2.0-23 gcc-13_13.2.0-23 libc6-dev_2.37-18 libstdc++-13-dev_13.2.0-23 libstdc++-13-dev-amd64-cross_13.2.0-12cross1 libstdc++6_14-20240330-1 libstdc++6-amd64-cross_14-20240127-1cross1 linux-libc-dev_6.7.9-2
Package versions: apt_2.9.2 asciidoc-base_10.2.0-2 asciidoc-common_10.2.0-2 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13.1 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.42-4 binutils-aarch64-linux-gnu_2.42-4 binutils-common_2.42-4 binutils-x86-64-linux-gnu_2.42-4 bsdextrautils_2.40-6 bsdutils_1:2.40-6 build-essential_12.10 bzip2_1.0.8-5.1 cmake_3.28.3-1+b1 cmake-data_3.28.3-1 coreutils_9.4-3.1 cpp_4:13.2.0-7 cpp-13_13.2.0-23 cpp-13-aarch64-linux-gnu_13.2.0-23 cpp-13-x86-64-linux-gnu_13.2.0-12cross1 cpp-aarch64-linux-gnu_4:13.2.0-7 cpp-x86-64-linux-gnu_4:13.2.0-7 cross-config_2.6.20 crossbuild-essential-amd64_12.10 dash_0.5.12-6 debconf_1.5.86 debhelper_13.15.3 debian-archive-keyring_2023.4 debianutils_5.17 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 docbook-xml_4.5-12 docbook-xsl_1.79.2+dfsg-7 dpkg_1.22.6 dpkg-cross_2.6.20 dpkg-dev_1.22.6 dwz_0.15-1+b1 fakeroot_1.34-1 file_1:5.45-3 findutils_4.9.0-5 freeglut3-dev_3.4.0-1+b1 g++_4:13.2.0-7 g++-13_13.2.0-23 g++-13-aarch64-linux-gnu_13.2.0-23 g++-13-x86-64-linux-gnu_13.2.0-12cross1 g++-aarch64-linux-gnu_4:13.2.0-7 g++-x86-64-linux-gnu_4:13.2.0-7 gcc_4:13.2.0-7 gcc-13_13.2.0-23 gcc-13-aarch64-linux-gnu_13.2.0-23 gcc-13-base_13.2.0-23 gcc-13-cross-base_13.2.0-12cross1 gcc-13-x86-64-linux-gnu_13.2.0-12cross1 gcc-13-x86-64-linux-gnu-base_13.2.0-12cross1 gcc-14-base_14-20240330-1 gcc-14-cross-base_14-20240127-1cross1 gcc-aarch64-linux-gnu_4:13.2.0-7 gcc-x86-64-linux-gnu_4:13.2.0-7 gemmi-dev_0.6.4+ds-1 gettext_0.21-14+b1 gettext-base_0.21-14+b1 gpgv_2.2.40-3 grep_3.11-4 groff-base_1.23.0-3+b1 gzip_1.12-1.1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-1 libapt-pkg6.0t64_2.9.2 libarchive-zip-perl_1.68-1 libarchive13t64_3.7.2-2 libasan8_14-20240330-1 libasan8-amd64-cross_14-20240127-1cross1 libatomic1_14-20240330-1 libatomic1-amd64-cross_14-20240127-1cross1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1 libaudit1_1:3.1.2-2.1 libbinutils_2.42-4 libblas-dev_3.12.0-3 libblas3_3.12.0-3 libblkid1_2.40-6 libbrotli1_1.1.0-2+b3 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-5.1 libc-bin_2.37-18 libc-dev-bin_2.37-18 libc6_2.37-18 libc6-amd64-cross_2.37-12cross1 libc6-dev_2.37-18 libc6-dev-amd64-cross_2.37-12cross1 libcap-ng0_0.8.5-1 libcap2_1:2.66-5 libcc1-0_14-20240330-1 libcom-err2_1.47.0-2.4 libconfig-auto-perl_0.44-2 libconfig-inifiles-perl_3.000003-2 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.42-4 libctf0_2.42-4 libcurl4t64_8.7.1-3 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.271+b3 libdebhelper-perl_13.15.3 libdebian-dpkgcross-perl_2.6.20 libdpkg-perl_1.22.6 libdrm-amdgpu1_2.4.120-2 libdrm-common_2.4.120-2 libdrm-intel1_2.4.120-2 libdrm-nouveau2_2.4.120-2 libdrm-radeon1_2.4.120-2 libdrm2_2.4.120-2 libedit2_3.1-20230828-1 libegl-dev_1.7.0-1 libegl-mesa0_24.0.5-1 libegl1_1.7.0-1 libelf1t64_0.191-1+b1 libexpat1_2.6.2-1 libfakeroot_1.34-1 libffi8_3.4.6-1 libfile-find-rule-perl_0.34-3 libfile-homedir-perl_1.006-2 libfile-stripnondeterminism-perl_1.13.1-1 libfile-which-perl_1.27-2 libgbm1_24.0.5-1 libgcc-13-dev_13.2.0-23 libgcc-13-dev-amd64-cross_13.2.0-12cross1 libgcc-s1_14-20240330-1 libgcc-s1-amd64-cross_14-20240127-1cross1 libgcrypt20_1.10.3-2 libgdbm-compat4t64_1.23-5.1+b1 libgdbm6t64_1.23-5.1+b1 libgfortran5_14-20240330-1 libgl-dev_1.7.0-1 libgl1_1.7.0-1 libgl1-mesa-dev_24.0.5-1 libgl1-mesa-dri_24.0.5-1 libglapi-mesa_24.0.5-1 libgles-dev_1.7.0-1 libgles1_1.7.0-1 libgles2_1.7.0-1 libglu1-mesa_9.0.2-1.1 libglu1-mesa-dev_9.0.2-1.1 libglut-dev_3.4.0-1+b1 libglut3.12_3.4.0-1+b1 libglvnd-core-dev_1.7.0-1 libglvnd-dev_1.7.0-1 libglvnd0_1.7.0-1 libglx-dev_1.7.0-1 libglx-mesa0_24.0.5-1 libglx0_1.7.0-1 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.5-2 libgomp1_14-20240330-1 libgomp1-amd64-cross_14-20240127-1cross1 libgpg-error0_1.47-3 libgprofng0_2.42-4 libgssapi-krb5-2_1.20.1-6+b1 libhogweed6t64_3.9.1-2.2 libhwasan0_14-20240330-1 libhwasan0-amd64-cross_14-20240127-1cross1 libice-dev_2:1.0.10-1 libice6_2:1.0.10-1 libicu72_72.1-4+b1 libidn2-0_2.3.7-2 libio-string-perl_1.08-4 libisl23_0.26-3+b2 libitm1_14-20240330-1 libitm1-amd64-cross_14-20240127-1cross1 libjansson4_2.14-2+b2 libjsoncpp25_1.9.5-6+b2 libk5crypto3_1.20.1-6+b1 libkeyutils1_1.6.3-3 libkrb5-3_1.20.1-6+b1 libkrb5support0_1.20.1-6+b1 liblapack-dev_3.12.0-3 liblapack3_3.12.0-3 libldap-2.5-0_2.5.16+dfsg-2 libllvm17t64_1:17.0.6-9+b2 liblocale-gettext-perl_1.07-7 liblsan0_14-20240330-1 liblsan0-amd64-cross_14-20240127-1cross1 liblz4-1_1.9.4-2 liblzma5_5.6.1+really5.4.5-1 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40-6 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncursesw6_6.4+20240414-1 libnettle8t64_3.9.1-2.2 libnghttp2-14_1.61.0-1+b1 libnumber-compare-perl_0.03-3 libopengl-dev_1.7.0-1 libopengl0_1.7.0-1 libopenmm-dev_8.0.0+dfsg-6.1 libopenmm8.0t64_8.0.0+dfsg-6.1 libp11-kit0_0.25.3-4 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpciaccess0_0.17-3 libpcre2-8-0_10.42-4+b1 libperl5.38t64_5.38.2-3.2+b2 libpipeline1_1.5.7-2 libproc2-0_2:4.0.4-4 libpsl5t64_0.21.2-1.1 libpthread-stubs0-dev_0.4-1 libpython3-stdlib_3.11.8-1 libpython3.11-minimal_3.11.9-1 libpython3.11-stdlib_3.11.9-1 libquadmath0_14-20240330-1 libquadmath0-amd64-cross_14-20240127-1cross1 libreadline8t64_8.2-4 librhash0_1.4.3-3+b1 librtmp1_2.4+20151223.gitfa8646d.1-2+b4 libsasl2-2_2.1.28+dfsg1-6 libsasl2-modules-db_2.1.28+dfsg1-6 libseccomp2_2.5.5-1 libselinux1_3.5-2+b2 libsensors-config_1:3.6.0-9 libsensors5_1:3.6.0-9 libseqan2-dev_2.4.0+dfsg-16 libsframe1_2.42-4 libsimbody-dev_3.7+dfsg-3 libsimbody3.7_3.7+dfsg-3 libsimtkmolmodel-dev_3.1.0-4.1+b1 libsimtkmolmodel-plugins_3.1.0-4.1+b1 libsimtkmolmodel3.1t64_3.1.0-4.1+b1 libsm-dev_2:1.2.3-1 libsm6_2:1.2.3-1 libsmartcols1_2.40-6 libsqlite3-0_3.45.3-1 libssh2-1t64_1.11.0-4.1+b2 libssl3t64_3.2.1-3 libstb-dev_0.0~git20230129.5736b15+ds-1.2 libstb0t64_0.0~git20230129.5736b15+ds-1.2 libstdc++-13-dev_13.2.0-23 libstdc++-13-dev-amd64-cross_13.2.0-12cross1 libstdc++6_14-20240330-1 libstdc++6-amd64-cross_14-20240127-1cross1 libsub-override-perl_0.10-1 libsystemd0_255.4-1+b1 libtasn1-6_4.19.0-3+b2 libtext-glob-perl_0.11-3 libtinfo6_6.4+20240414-1 libtool_2.4.7-7 libtsan2_14-20240330-1 libtsan2-amd64-cross_14-20240127-1cross1 libubsan1_14-20240330-1 libubsan1-amd64-cross_14-20240127-1cross1 libuchardet0_0.0.8-1+b1 libudev1_255.4-1+b1 libunistring5_1.2-1 libuuid1_2.40-6 libuv1t64_1.48.0-1.1 libvulkan1_1.3.280.0-1 libwayland-client0_1.22.0-2.1+b1 libwayland-server0_1.22.0-2.1+b1 libx11-6_2:1.8.7-1 libx11-data_2:1.8.7-1 libx11-dev_2:1.8.7-1 libx11-xcb1_2:1.8.7-1 libxau-dev_1:1.0.9-1 libxau6_1:1.0.9-1 libxcb-dri2-0_1.17.0-1 libxcb-dri3-0_1.17.0-1 libxcb-glx0_1.17.0-1 libxcb-present0_1.17.0-1 libxcb-randr0_1.17.0-1 libxcb-shm0_1.17.0-1 libxcb-sync1_1.17.0-1 libxcb-xfixes0_1.17.0-1 libxcb1_1.17.0-1 libxcb1-dev_1.17.0-1 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext-dev_2:1.3.4-1+b1 libxext6_2:1.3.4-1+b1 libxfixes-dev_1:6.0.0-2 libxfixes3_1:6.0.0-2 libxi-dev_2:1.8.1-1 libxi6_2:1.8.1-1 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b3 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-2 libxml2_2.9.14+dfsg-1.3+b2 libxml2-utils_2.9.14+dfsg-1.3+b2 libxmu-dev_2:1.1.3-3+b2 libxmu-headers_2:1.1.3-3 libxmu6_2:1.1.3-3+b2 libxshmfence1_1.3-1 libxslt1.1_1.1.35-1 libxt-dev_1:1.2.1-1.2 libxt6t64_1:1.2.1-1.2 libxxf86vm1_1:1.1.4-1+b2 libxxhash0_0.8.2-2+b1 libyaml-perl_1.31-1 libz3-4_4.8.12-3.1+b2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.7.9-2 login_1:4.13+dfsg1-4 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-1 mawk_1.3.4.20240123-1 media-types_10.1.0 ncurses-base_6.4+20240414-1 ncurses-bin_6.4+20240414-1 netbase_6.4 patch_2.7.6-7 perl_5.38.2-3.2+b2 perl-base_5.38.2-3.2+b2 perl-modules-5.38_5.38.2-3.2 po-debconf_1.0.21+nmu1 procps_2:4.0.4-4 python3_3.11.8-1 python3-minimal_3.11.8-1 python3.11_3.11.9-1 python3.11-minimal_3.11.9-1 readline-common_8.2-4 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 sgml-base_1.31 sgml-data_2.0.11+nmu1 sysvinit-utils_3.09-1 tao-pegtl-dev_3.2.7-1 tar_1.35+dfsg-3 tzdata_2024a-3 ucf_3.0043+nmu1 usrmerge_39 util-linux_2.40-6 x11-common_1:7.7+23 x11proto-dev_2024.1-1 xml-core_0.19 xorg-sgml-doctools_1:1.11-1.1 xsltproc_1.1.35-1 xtrans-dev_1.4.0-1 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg-3.1 zlib1g-dev_1:1.3.dfsg-3.1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 3.0 (quilt)
Source: macromoleculebuilder
Binary: libmmb-dev, libmmb4.0t64, mmb, mmb-common
Architecture: any all
Version: 4.0.0+dfsg-3.1
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Uploaders:  Andrius Merkys <merkys@debian.org>,
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: dpkg-dev (>= 1.22.5), asciidoc-base, cmake, debhelper-compat (= 13), docbook-xml, gemmi-dev (>= 0.6.2+ds-2), libopenmm-dev, libseqan2-dev, libsimbody-dev, libsimtkmolmodel-dev (>= 3.1.0), libsimtkmolmodel-plugins, libstb-dev, tao-pegtl-dev, zlib1g-dev
Package-List:
 libmmb-dev deb libdevel optional arch=any
 libmmb4.0t64 deb libs optional arch=any
 mmb deb science optional arch=any
 mmb-common deb science optional arch=all
Checksums-Sha1:
 c37eccceb961f3e78d5b7145faf79ce425cf104e 2567256 macromoleculebuilder_4.0.0+dfsg.orig.tar.xz
 c82774e385d6321bd759afff89ece9410f14b900 5704 macromoleculebuilder_4.0.0+dfsg-3.1.debian.tar.xz
Checksums-Sha256:
 2f50d11c886c36fd18476f942d7521536ded599584e0d83462a63ba5f9ccc449 2567256 macromoleculebuilder_4.0.0+dfsg.orig.tar.xz
 9d9017215e057dc5e5d94790768437e85310c3fd9490c9725a18f264dcb50e31 5704 macromoleculebuilder_4.0.0+dfsg-3.1.debian.tar.xz
Files:
 951370d06adf03fb858edccdee43c075 2567256 macromoleculebuilder_4.0.0+dfsg.orig.tar.xz
 223e4362c776e4e14645a97fce35096b 5704 macromoleculebuilder_4.0.0+dfsg-3.1.debian.tar.xz

-----BEGIN PGP SIGNATURE-----
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=nrtL
-----END PGP SIGNATURE-----

gpgv: Signature made Thu Feb 29 11:03:57 2024 UTC
gpgv:                using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./macromoleculebuilder_4.0.0+dfsg-3.1.dsc: no acceptable signature found
dpkg-source: info: extracting macromoleculebuilder in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking macromoleculebuilder_4.0.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking macromoleculebuilder_4.0.0+dfsg-3.1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying drop-CMAKE_CXX_STANDARD.patch
dpkg-source: info: applying 96da444290ab1af4385013c566079d381d8051b4.patch
dpkg-source: info: applying bf1ab1ebf49bb9e48f4f133e155f9315cc37079d.patch

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=/var/lib/sbuild
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=helmut
OLDPWD=/
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/<<PKGBUILDDIR>>
SHELL=/bin/sh
USER=helmut

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage --sanitize-env -aamd64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1
dpkg-buildpackage: info: source package macromoleculebuilder
dpkg-buildpackage: info: source version 4.0.0+dfsg-3.1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Graham Inggs <ginggs@debian.org>
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 '/<<PKGBUILDDIR>>'
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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0"
	cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb 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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0" ..
-- The CXX compiler identification is GNU 13.2.0
-- 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")  
-- Found gemmi version 0.6.4
-- Looking for copy_file_range
-- Looking for copy_file_range - found
-- Looking for sendfile
-- Looking for sendfile - found
-- Configuring done (1.7s)
-- 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: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_auto_build -a
	cd obj-x86_64-linux-gnu && make -j1 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks
make  -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/MMB.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/Utils.cpp
In file included from /<<PKGBUILDDIR>>/src/Utils.cpp:12:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
[  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/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20,
                 from /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:14:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In function ‘bool letterIsPurine(char)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:51:14: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   51 |     return c == 'A' | c == 'G';
      |            ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In function ‘bool letterIsRNA(char)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:57:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   57 |         c == 'A' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:59:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   59 |         c == 'G' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:60:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   60 |         c == 'U'
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In function ‘bool letterIsDNA(char)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:67:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   67 |         c == 'A' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:69:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   69 |         c == 'G' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:70:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   70 |         c == 'T'
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In function ‘bool letterIsProtein(char)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:77:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   77 |         c == 'C' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:79:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   79 |         c == 'H' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:80:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   80 |         c == 'I'
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:86:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   86 |         c == 'M' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:88:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   88 |         c == 'V' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:89:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   89 |         c == 'A'
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:95:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   95 |         c == 'G' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:97:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   97 |         c == 'P' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:98:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   98 |         c == 'T'
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:104:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  104 |         c == 'R' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:106:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  106 |         c == 'Y' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:107:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  107 |         c == 'W'
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:113:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  113 |         c == 'D' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:115:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  115 |         c == 'E' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:116:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  116 |         c == 'Q' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:117:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  117 |         c == 'K'
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClass::modifyResidue(BiopolymerModification, SimTK::Compound, SimTK::DuMMForceFieldSubsystem&)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:127:41: warning: variable ‘myChargedAtomTypeIndex’ set but not used [-Wunused-but-set-variable]
  127 |         DuMM::ChargedAtomTypeIndex      myChargedAtomTypeIndex = dumm.getBiotypeChargedAtomType( compoundToAdd.getAtomBiotypeIndex(Compound::AtomIndex( 0)));
      |                                         ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:135:29: warning: unused variable ‘myOrdinality’ [-Wunused-variable]
  135 |         Ordinality::Residue myOrdinality(SimTK::Ordinality::Any);
      |                             ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:147:32: warning: unused variable ‘myBondMobility’ [-Wunused-variable]
  147 |         BondMobility::Mobility myBondMobility = stringToBondMobility("Rigid");
      |                                ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::checkResidueNumbersAndInsertionCodes()’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:244:15: warning: variable ‘myResidueID’ set but not used [-Wunused-but-set-variable]
  244 |     ResidueID myResidueID = getFirstResidueID();
      |               ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClass::setPdbResidueNumbersFromResidueIDVector()’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:518:15: warning: variable ‘myFirstResidueID’ set but not used [-Wunused-but-set-variable]
  518 |     ResidueID myFirstResidueID = getFirstResidueID() ;
      |               ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:520:9: warning: unused variable ‘numResidues’ [-Wunused-variable]
  520 |     int numResidues = -1;
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClass::renumberPdbResidues(ResidueID)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:551:9: warning: unused variable ‘myNewResidueNumberWithoutInsertionCode’ [-Wunused-variable]
  551 |     int myNewResidueNumberWithoutInsertionCode = firstResidueID.getResidueNumber() ;
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::matchCoordinates(const SimTK::PdbStructure&, bool, bool, bool, bool, bool, bool, double, double)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:669:45: warning: variable ‘biopolymerAtomTargetsIterator’ set but not used [-Wunused-but-set-variable]
  669 |     Compound::AtomTargetLocations::iterator biopolymerAtomTargetsIterator = biopolymerAtomTargets.begin();
      |                                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘bool BiopolymerClass::hasAtom(ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:1053:9: warning: unused variable ‘myResidueIndex’ [-Wunused-variable]
 1053 |     int myResidueIndex = getResidueIndex(myResidueID);
      |         ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘SimTK::Vec3 BiopolymerClass::calcDefaultAtomLocationInGroundFrame(const ResidueID&, const SimTK::String&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:1316:25: warning: variable ‘myAtomIndex’ set but not used [-Wunused-but-set-variable]
 1316 |     Compound::AtomIndex myAtomIndex = atomIndex(myResidueID,atomName);
      |                         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClass::addGeneralSterics(SimTK::GeneralContactSubsystem&, SimTK::ContactSetIndex, SimTK::HuntCrossleyForce&, SimTK::SimbodyMatterSubsystem&, double, double, ResidueID, ResidueID, bool, bool)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:1437:12: warning: unused variable ‘huntCrossleyDissipation’ [-Wunused-variable]
 1437 |     double huntCrossleyDissipation  =.0;
      |            ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘ResidueID BiopolymerClass::sum(ResidueID, int) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:2172:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2172 |         if ((newResidueIndex < 0) || (newResidueIndex >= residueIDVector.size())) {
      |                                       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClassContainer::waterDropletAboutResidues(std::vector<WaterDropletAboutResidueStruct>, WaterDropletContainer&)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:3577:23: warning: variable ‘myLocation’ set but not used [-Wunused-but-set-variable]
 3577 |                  Vec3 myLocation = (primaryBiopolymerClass.calcDefaultAtomLocationInGroundFrame(waterDropletAboutResidueVector[i].residue, primaryBiopolymerClass.getRepresentativeAtomName()))*(1.0); // used to convert to Å, now using nm
      |                       ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClassContainer::substituteResidue(SimTK::String, ResidueID, SimTK::String, bool)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:4130:15: warning: variable ‘myFirstResidueNumber’ set but not used [-Wunused-but-set-variable]
 4130 |     ResidueID myFirstResidueNumber = myOldBiopolymerClass.getFirstResidueID();
      |               ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClassContainer::substituteResidue(Mutation, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:4519:15: warning: variable ‘myFirstResidueNumber’ set but not used [-Wunused-but-set-variable]
 4519 |     ResidueID myFirstResidueNumber = myOldBiopolymerClass.getFirstResidueID();
      |               ^~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:16:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:4682:61:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:283:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  283 |             for (int i = 0; i < chainAtomInfoVector.size() ; i++) {
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:300:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<unsigned int, unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  300 |             for ( int j = 0 ; j < neighborList.size(); j++) {
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = MobilizerStretch]’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:2584:54:   required from ‘void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch&, ResidueStretchContainer<ResidueStretchType>&) [with ResidueStretchType = MobilizerStretch]’
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:2588:181:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MobilizerStretch>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘bool ResidueStretchContainer<ResidueStretchType>::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]’:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:320:27:   required from ‘void ResidueStretchContainer<ResidueStretchType>::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:4682:61:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:104:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SingleResidue>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  104 |                 for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:4827:54:   required from ‘void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer&, ResidueStretchContainer<ResidueStretchType>&) [with ResidueStretchType = DensityStretch]’
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:4830:213:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93,
                 from /usr/include/simbody/SimTKcommon/Simmatrix.h:37,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /usr/include/molmodel/molmodel/internal/Compound.h:36,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:16:
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::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<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’ at /<<PKGBUILDDIR>>/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_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72
  875 |     Rotation myRotation;
      |              ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::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<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’ at /<<PKGBUILDDIR>>/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_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72
  875 |     Rotation myRotation;
      |              ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::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<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’ at /<<PKGBUILDDIR>>/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_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72
  875 |     Rotation myRotation;
      |              ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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_<P>& SimTK::Rotation_<P>::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<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’ at /<<PKGBUILDDIR>>/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_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72
  875 |     Rotation myRotation;
      |              ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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_<P>& SimTK::Rotation_<P>::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<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’ at /<<PKGBUILDDIR>>/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_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72
  875 |     Rotation myRotation;
      |              ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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_<P>& SimTK::Rotation_<P>::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<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’ at /<<PKGBUILDDIR>>/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_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’:
/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:12:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘double AtomSpringContainer::calcRmsd(SimTK::State&, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:65:12: warning: unused variable ‘myExtension’ [-Wunused-variable]
   65 |     double myExtension = 0.0;
      |            ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::deleteAtomSpring(int)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:194:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<AtomSpring>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  194 |     if(id < 0 || id >= atomSpringVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateAtomSpring(int, const AtomSpring&, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:201:21: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::vector<AtomSpring>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  201 |     if(id < 0 || id >= atomSpringVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::deleteThreading(int)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:260:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  260 |     if(id < 0 || id >= threadingStructVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateThreading(int, const ThreadingStruct&, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:268:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  268 |     if(id < 0 || id >= threadingStructVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateThreading(int, SimTK::String, ResidueID, ResidueID, SimTK::String, ResidueID, ResidueID, double, bool, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:279:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  279 |     if(id < 0 || id >= threadingStructVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::deleteGappedThreading(int)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:441:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  441 |     if(id < 0 || id >= gappedThreadingStructVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateGappedThreading(int, const ThreadingStruct&, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:449:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  449 |     if(id < 0 || id >= gappedThreadingStructVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateGappedThreading(int, SimTK::String, SimTK::String, double, bool, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:458:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  458 |     if(id < 0 || id >= gappedThreadingStructVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::createSpringsFromGappedThreading(BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:488:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘seqan::Size<seqan::String<char, seqan::Alloc<> > >::Type’ {aka ‘long unsigned int’} [-Wsign-compare]
  488 |         while ((aIndex < length(thread.updThreadingPartner(0).sequence)) &&
      |                 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:489:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘seqan::Size<seqan::String<char, seqan::Alloc<> > >::Type’ {aka ‘long unsigned int’} [-Wsign-compare]
  489 |                (bIndex < length(thread.updThreadingPartner(1).sequence)))
      |                 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93,
                 from /usr/include/simbody/SimTKcommon/Simmatrix.h:37,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /<<PKGBUILDDIR>>/include/Utils.h:22:
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
In file included from /usr/include/molmodel/molmodel/internal/Compound.h:41,
                 from /usr/include/molmodel/SimTKmolmodel.h:53,
                 from /<<PKGBUILDDIR>>/include/Utils.h:23:
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’:
/usr/include/molmodel/molmodel/internal/Superpose.h:107:18: note: object ‘R’ of size 72
  107 |         Mat<3,3> R(0.0);
      |                  ^
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’:
/usr/include/molmodel/molmodel/internal/Superpose.h:107:18: note: object ‘R’ of size 72
  107 |         Mat<3,3> R(0.0);
      |                  ^
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’:
/usr/include/molmodel/molmodel/internal/Superpose.h:107:18: note: object ‘R’ of size 72
  107 |         Mat<3,3> R(0.0);
      |                  ^
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’:
/usr/include/molmodel/molmodel/internal/Superpose.h:183:18: note: object ‘U’ of size 72
  183 |         Mat<3,3> U(0.0);   // initialize 2-d array
      |                  ^
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’:
/usr/include/molmodel/molmodel/internal/Superpose.h:183:18: note: object ‘U’ of size 72
  183 |         Mat<3,3> U(0.0);   // initialize 2-d array
      |                  ^
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’:
/usr/include/molmodel/molmodel/internal/Superpose.h:183:18: note: object ‘U’ of size 72
  183 |         Mat<3,3> U(0.0);   // initialize 2-d array
      |                  ^
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:201:24:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’:
/usr/include/molmodel/molmodel/internal/Superpose.h:201:33: note: object ‘<anonymous>’ of size 72
  201 |             rotation = Rotation();
      |                                 ^
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:201:24:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’:
/usr/include/molmodel/molmodel/internal/Superpose.h:201:33: note: object ‘<anonymous>’ of size 72
  201 |             rotation = Rotation();
      |                                 ^
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:201:24:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’:
/usr/include/molmodel/molmodel/internal/Superpose.h:201:33: note: object ‘<anonymous>’ 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/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/DisplacementContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20,
                 from /<<PKGBUILDDIR>>/include/DisplacementContainer.h:14,
                 from /<<PKGBUILDDIR>>/src/DisplacementContainer.cpp:12:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 18%] Building CXX object CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/MobilizerContainer.cpp
In file included from /<<PKGBUILDDIR>>/src/MobilizerContainer.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/MobilizerContainer.cpp:12:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/MobilizerContainer.cpp: In member function ‘void MobilizerContainer::addMobilizerDomainsInterfacesToVector(const std::vector<MobilizerDomainsInterface>&, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/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)) ||
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 21%] Building CXX object CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/MoleculeContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/ConstraintContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/MoleculeContainer.h:8,
                 from /<<PKGBUILDDIR>>/src/MoleculeContainer.cpp:3:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/MoleculeContainer.cpp: In constructor ‘CustomMolecule::CustomMolecule(std::vector<std::vector<SimTK::String> >, SimTK::DuMMForceFieldSubsystem&)’:
/<<PKGBUILDDIR>>/src/MoleculeContainer.cpp:324:15: warning: unused variable ‘myAngle1’ [-Wunused-variable]
  324 |         Angle myAngle1 = 180*Deg2Rad; // this is a bond angle
      |               ^~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 25%] Building CXX object CMakeFiles/MMB.dir/src/DensityContainer.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/DensityContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20,
                 from /<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:4,
                 from /<<PKGBUILDDIR>>/include/DensityContainer.h:14,
                 from /<<PKGBUILDDIR>>/src/DensityContainer.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityContainer.cpp: In member function ‘void DensityContainer::updateDensityStretch(int, const DensityStretch&, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/DensityContainer.cpp:18:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   18 |     if(id < 0 || id >= residueStretchVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 28%] Building CXX object CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/BasePairContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20,
                 from /<<PKGBUILDDIR>>/include/BasePairContainer.h:17,
                 from /<<PKGBUILDDIR>>/src/BasePairContainer.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 31%] Building CXX object CMakeFiles/MMB.dir/src/ContactContainer.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/ContactContainer.cpp
In file included from /<<PKGBUILDDIR>>/src/ContactContainer.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/ContactContainer.cpp:12:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ContactContainer.cpp: In member function ‘void ContactContainer::validateContact(ContactStretch, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/ContactContainer.cpp:26:10: warning: variable ‘myEndCapsOn’ set but not used [-Wunused-but-set-variable]
   26 |     bool myEndCapsOn;
      |          ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ContactContainer.cpp: In member function ‘void ContactContainer::deleteContactWithin(int)’:
/<<PKGBUILDDIR>>/src/ContactContainer.cpp:70:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ContactWithin>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   70 |     if(id < 0 || id >= contactWithinVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ContactContainer.cpp: In member function ‘void ContactContainer::updateContactWithin(int, SimTK::String, int, double, SimTK::String, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/ContactContainer.cpp:77:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ContactWithin>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   77 |     if(id < 0 || id >= contactWithinVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ContactContainer.cpp: In member function ‘void ContactContainer::deleteContact(int)’:
/<<PKGBUILDDIR>>/src/ContactContainer.cpp:275:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ContactStretch, std::allocator<ContactStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  275 |     if(id < 0 || id >= residueStretchVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ContactContainer.cpp: In member function ‘void ContactContainer::updateContact(int, std::string, int, int, std::string, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/ContactContainer.cpp:283:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ContactStretch, std::allocator<ContactStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  283 |     if(id < 0 || id >= residueStretchVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ContactContainer.cpp: In member function ‘bool ContactContainer::hasSharedContact(SimTK::String, ResidueID, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/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).
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 34%] Building CXX object CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/ConstraintContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/ConstraintContainer.h:14,
                 from /<<PKGBUILDDIR>>/src/ConstraintContainer.cpp:10:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/ConstraintContainer.cpp:11:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ConstraintContainer.cpp: In member function ‘void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/ConstraintContainer.cpp:129:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ConstraintClass>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  129 |     if(index < 0 || index >= constraintClassVector.size())
      |                     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ConstraintContainer.cpp: In member function ‘void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/ConstraintContainer.cpp:146:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ConstraintClass>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  146 |     if(index < 0 || index >= constraintClassVector.size())
      |                     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 37%] Building CXX object CMakeFiles/MMB.dir/src/Repel.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/Repel.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/PeriodicScrubber.h:16,
                 from /<<PKGBUILDDIR>>/include/Repel.h:24,
                 from /<<PKGBUILDDIR>>/src/Repel.cpp:12:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Repel.cpp: In member function ‘void ConstrainedDynamics::constraintsAndRestraints(ParameterReader&, BiopolymerClassContainer&, SimTK::GeneralForceSubsystem&, SimTK::SimbodyMatterSubsystem&, SimTK::State&, SimTK::CompoundSystem&)’:
/<<PKGBUILDDIR>>/src/Repel.cpp:172:31: warning: variable ‘myResidueID’ set but not used [-Wunused-but-set-variable]
  172 |                     ResidueID myResidueID = myConstraintClass.getResidueID1();
      |                               ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Repel.h: In constructor ‘ConstrainedDynamics::ConstrainedDynamics(ParameterReader*)’:
/<<PKGBUILDDIR>>/include/Repel.h:269:29: warning: ‘ConstrainedDynamics::_parameterReader’ will be initialized after [-Wreorder]
  269 |     ParameterReader *       _parameterReader;
      |                             ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Repel.h:259:29: warning:   ‘SimTK::SimbodyMatterSubsystem ConstrainedDynamics::_matter’ [-Wreorder]
  259 |     SimbodyMatterSubsystem  _matter;
      |                             ^~~~~~~
/<<PKGBUILDDIR>>/src/Repel.cpp:342:1: warning:   when initialized here [-Wreorder]
  342 | ConstrainedDynamics::ConstrainedDynamics(ParameterReader * myParameterReader) : _parameterReader(myParameterReader),
      | ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Repel.cpp: In member function ‘void ConstrainedDynamics::initializeBiopolymer(SimTK::String, SimTK::String)’:
/<<PKGBUILDDIR>>/src/Repel.cpp:405:10: warning: variable ‘readFromFile’ set but not used [-Wunused-but-set-variable]
  405 |     bool readFromFile = false;
      |          ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Repel.cpp: In member function ‘void ConstrainedDynamics::runAllSteps()’:
/<<PKGBUILDDIR>>/src/Repel.cpp:1027:22: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1027 |     for(; _nextFrame <= _parameterReader->numReportingIntervals; _nextFrame++){
      |           ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::addAllMutualChainResidues(double, std::vector<SimTK::String>, std::vector<SimTK::String>, BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]’:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:210:4:   required from ‘void ResidueStretchContainer<ResidueStretchType>::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]’
/<<PKGBUILDDIR>>/src/Repel.cpp:470:84:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:232:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  232 |             for (int i = 0; i < concatenatedAtomInfoVector.size() ; i++) {
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:244:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<unsigned int, unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  244 |             for ( int j = 0 ; j < neighborList.size(); j++) {
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::addAllMutualChainResidues(double, std::vector<SimTK::String>, std::vector<SimTK::String>, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:210:4:   required from ‘void ResidueStretchContainer<ResidueStretchType>::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’
/<<PKGBUILDDIR>>/src/Repel.cpp:573:84:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:232:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  232 |             for (int i = 0; i < concatenatedAtomInfoVector.size() ; i++) {
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:244:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<unsigned int, unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  244 |             for ( int j = 0 ; j < neighborList.size(); j++) {
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘bool ResidueStretchContainer<ResidueStretchType>::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = MobilizerStretch]’:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:264:27:   required from ‘void ResidueStretchContainer<ResidueStretchType>::addAllMutualChainResidues(double, std::vector<SimTK::String>, std::vector<SimTK::String>, BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]’
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:210:4:   required from ‘void ResidueStretchContainer<ResidueStretchType>::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]’
/<<PKGBUILDDIR>>/src/Repel.cpp:470:84:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:104:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MobilizerStretch>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  104 |                 for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘bool ResidueStretchContainer<ResidueStretchType>::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]’:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:264:27:   required from ‘void ResidueStretchContainer<ResidueStretchType>::addAllMutualChainResidues(double, std::vector<SimTK::String>, std::vector<SimTK::String>, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:210:4:   required from ‘void ResidueStretchContainer<ResidueStretchType>::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’
/<<PKGBUILDDIR>>/src/Repel.cpp:573:84:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:104:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SingleResidue>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
/<<PKGBUILDDIR>>/src/Repel.cpp: At global scope:
/<<PKGBUILDDIR>>/src/Repel.cpp:97:17: warning: ‘bool compareUpper(const std::string&, const char*)’ defined but not used [-Wunused-function]
   97 |     static bool compareUpper( const string& param, const char* symbol ) {
      |                 ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 40%] Building CXX object CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/MonoAtoms.cpp.o -MF CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o.d -o CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o -c /<<PKGBUILDDIR>>/src/MonoAtoms.cpp
In file included from /<<PKGBUILDDIR>>/src/MonoAtoms.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 43%] Building CXX object CMakeFiles/MMB.dir/src/Spiral.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/Spiral.cpp
In file included from /<<PKGBUILDDIR>>/include/Spiral.h:16,
                 from /<<PKGBUILDDIR>>/src/Spiral.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Spiral.cpp: In member function ‘void Spiral::clear()’:
/<<PKGBUILDDIR>>/src/Spiral.cpp:92:12: warning: unused variable ‘helixAdvancePerBasePair’ [-Wunused-variable]
   92 |     double helixAdvancePerBasePair = -11111. ;  // in nm // should be user specified.
      |            ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Spiral.cpp: In member function ‘double Spiral::harmonicThetaAdjustment(double)’:
/<<PKGBUILDDIR>>/src/Spiral.cpp:124:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<frequencyPhaseAmplitude>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  124 |     for (int i =0; i < frequencyPhaseAmplitudeVector.size(); i++){
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Spiral.cpp: In member function ‘void Spiral::writeCylindricalSpiralCommandFile(MonoAtomsContainer&)’:
/<<PKGBUILDDIR>>/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 ;
      |          ^~~~~~
/<<PKGBUILDDIR>>/src/Spiral.cpp: In member function ‘void Spiral::writeSphericalSpiralCommandFile(MonoAtomsContainer&)’:
/<<PKGBUILDDIR>>/src/Spiral.cpp:238:16: warning: unused variable ‘currentPhi’ [-Wunused-variable]
  238 |         double currentPhi = priorPhi + deltaPhi ; // phiFromTheta(currentTheta, pitch, radius, phiOffset);
      |                ^~~~~~~~~~
/<<PKGBUILDDIR>>/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
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 46%] Building CXX object CMakeFiles/MMB.dir/src/ParameterReader.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/ParameterReader.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/src/ParameterReader.cpp:17:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::removeNonPriorityBasePairs(int)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:727:9: warning: unused variable ‘oldDutyCyclePriority’ [-Wunused-variable]
  727 |     int oldDutyCyclePriority=0;
      |         ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::updateAllResiduesWithin(int, SimTK::String, int, double)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:776:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<AllResiduesWithin>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  776 |     if(index < 0 || index >= includeAllResiduesWithinVector.size()){
      |                     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::deleteAllResiduesWithin(int)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:785:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<AllResiduesWithin>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  785 |     if(index < 0 || index >= includeAllResiduesWithinVector.size()){
      |                     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:1582:17: warning: unused variable ‘myForceConstant’ [-Wunused-variable]
 1582 |          double myForceConstant = 1000000000.0; // set to super high value just to make sure it's being reset later.
      |                 ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2069:16: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
 2069 |             if ((parameterStringClass.getString(0).compare("constraint") == 0) || (parameterStringClass.getString(0).compare("restraint") == 0))
      |                ^
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2658:27: warning: variable ‘residueID1’ set but not used [-Wunused-but-set-variable]
 2658 |                 ResidueID residueID1 = ResidueID(-11111,'X');
      |                           ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2659:27: warning: variable ‘residueID2’ set but not used [-Wunused-but-set-variable]
 2659 |                 ResidueID residueID2 = ResidueID(-11111,'X');
      |                           ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2735:16: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
 2735 |             if ((parameterStringClass.getString(0).compare("constraint") == 0) || (parameterStringClass.getString(0).compare("restraint") == 0))
      |                ^
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = SingleResidue]’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:814:42:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SingleResidue>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93,
                 from /usr/include/simbody/SimTKcommon/Simmatrix.h:37,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /<<PKGBUILDDIR>>/include/Utils.h:22:
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘Displacement::Displacement()’ at /<<PKGBUILDDIR>>/include/Utils.h:544:8,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2223:19:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘Displacement [1]’ [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2223:26: note: at offset 56 into object ‘myDisplacement’ of size 128
 2223 |             Displacement myDisplacement;
      |                          ^~~~~~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘Displacement::Displacement()’ at /<<PKGBUILDDIR>>/include/Utils.h:544:8,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2223:19:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘Displacement [1]’ [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2223:26: note: at offset 56 into object ‘myDisplacement’ of size 128
 2223 |             Displacement myDisplacement;
      |                          ^~~~~~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘Displacement::Displacement()’ at /<<PKGBUILDDIR>>/include/Utils.h:544:8,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2223:19:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘Displacement [1]’ [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2223:26: note: at offset 56 into object ‘myDisplacement’ of size 128
 2223 |             Displacement myDisplacement;
      |                          ^~~~~~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::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 /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2224:22:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72
 2224 |             Rotation myRotation;
      |                      ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::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 /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2224:22:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72
 2224 |             Rotation myRotation;
      |                      ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::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 /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2224:22:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72
 2224 |             Rotation myRotation;
      |                      ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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_<P>& SimTK::Rotation_<P>::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 /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2225:52:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72
 2224 |             Rotation myRotation;
      |                      ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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_<P>& SimTK::Rotation_<P>::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 /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2225:52:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72
 2224 |             Rotation myRotation;
      |                      ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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_<P>& SimTK::Rotation_<P>::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 /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2225:52:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72
 2224 |             Rotation myRotation;
      |                      ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘Displacement::Displacement()’ at /<<PKGBUILDDIR>>/include/Utils.h:544:8,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2207:30:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘Displacement [1]’ [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2207:30: note: at offset 56 into object ‘myDisplacement’ of size 128
 2207 |                 Displacement myDisplacement;
      |                              ^~~~~~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘Displacement::Displacement()’ at /<<PKGBUILDDIR>>/include/Utils.h:544:8,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2207:30:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘Displacement [1]’ [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2207:30: note: at offset 56 into object ‘myDisplacement’ of size 128
 2207 |                 Displacement myDisplacement;
      |                              ^~~~~~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘Displacement::Displacement()’ at /<<PKGBUILDDIR>>/include/Utils.h:544:8,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2207:30:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘Displacement [1]’ [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2207:30: note: at offset 56 into object ‘myDisplacement’ of size 128
 2207 |                 Displacement myDisplacement;
      |                              ^~~~~~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::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 /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2209:26:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72
 2209 |                 Rotation myRotation;
      |                          ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::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 /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2209:26:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72
 2209 |                 Rotation myRotation;
      |                          ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::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 /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2209:26:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72
 2209 |                 Rotation myRotation;
      |                          ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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_<P>& SimTK::Rotation_<P>::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 /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2210:56:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72
 2209 |                 Rotation myRotation;
      |                          ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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_<P>& SimTK::Rotation_<P>::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 /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2210:56:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72
 2209 |                 Rotation myRotation;
      |                          ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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_<P>& SimTK::Rotation_<P>::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 /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2210:56:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72
 2209 |                 Rotation myRotation;
      |                          ^~~~~~~~~~
[ 50%] Building CXX object CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/BaseInteractionParameterReader.cpp.o -MF CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o.d -o CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o -c /<<PKGBUILDDIR>>/src/BaseInteractionParameterReader.cpp
In file included from /<<PKGBUILDDIR>>/include/BaseInteractionParameterReader.h:22,
                 from /<<PKGBUILDDIR>>/src/BaseInteractionParameterReader.cpp:18:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 53%] Building CXX object CMakeFiles/MMB.dir/src/TetherForce.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/TetherForce.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/TetherForce.h:19,
                 from /<<PKGBUILDDIR>>/src/TetherForce.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 56%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClassTwoTransformForces.h:17,
                 from /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:10:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’:
/<<PKGBUILDDIR>>/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.
      |                ^~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:280:16: warning: variable ‘scrubberPeriod’ set but not used [-Wunused-but-set-variable]
  280 |         double scrubberPeriod;
      |                ^~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93,
                 from /usr/include/simbody/SimTKcommon/Simmatrix.h:37,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/Simbody.h:38,
                 from /usr/include/molmodel/SimTKmolmodel.h:47,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClassTwoTransformForces.h:16:
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::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::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’ at /<<PKGBUILDDIR>>/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_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72
  116 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::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::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’ at /<<PKGBUILDDIR>>/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_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72
  116 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::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::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’ at /<<PKGBUILDDIR>>/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_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72
  116 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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_<P>& SimTK::Rotation_<P>::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::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’ at /<<PKGBUILDDIR>>/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_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72
  116 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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_<P>& SimTK::Rotation_<P>::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::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’ at /<<PKGBUILDDIR>>/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_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72
  116 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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_<P>& SimTK::Rotation_<P>::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::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’ at /<<PKGBUILDDIR>>/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_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72
  116 |             Rotation rotation2;
      |                      ^~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:254:29: warning: ‘myFrcScalar’ may be used uninitialized [-Wmaybe-uninitialized]
  254 |                 myFrcScalar *= myParameterReader.twoTransformForceMultiplier;
      |                 ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:167:20: note: ‘myFrcScalar’ was declared here
  167 |             double myFrcScalar;
      |                    ^~~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::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 /<<PKGBUILDDIR>>/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_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72
  319 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::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 /<<PKGBUILDDIR>>/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_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72
  319 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::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<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>::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_<P>::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 /<<PKGBUILDDIR>>/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_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72
  319 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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_<P>& SimTK::Rotation_<P>::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 /<<PKGBUILDDIR>>/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_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72
  319 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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_<P>& SimTK::Rotation_<P>::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 /<<PKGBUILDDIR>>/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_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72
  319 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::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_<P>& SimTK::Rotation_<P>::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 /<<PKGBUILDDIR>>/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_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72
  319 |             Rotation rotation2;
      |                      ^~~~~~~~~
[ 59%] Building CXX object CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o -MF CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o.d -o CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o -c /<<PKGBUILDDIR>>/src/WaterDroplet.cpp
In file included from /<<PKGBUILDDIR>>/include/WaterDroplet.h:16,
                 from /<<PKGBUILDDIR>>/src/WaterDroplet.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/WaterDroplet.h:17:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 62%] Building CXX object CMakeFiles/MMB.dir/src/DensityMap.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/DensityMap.cpp
In file included from /<<PKGBUILDDIR>>/src/DensityMap.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp: In member function ‘void DensityMap::resizeVectorOfAmplitudeAndRandomPhases()’:
/<<PKGBUILDDIR>>/src/DensityMap.cpp:177:62: warning: comparison of integer expressions of different signedness: ‘std::vector<std::vector<std::vector<AmplitudeFrequencyAndRandomPhases> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  177 |         if (vectorOfAmplitudeFrequencyAndRandomPhases.size() != (unitCellParameters.calcMaxFrequencyDoublingsZ()+1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:181:78: warning: comparison of integer expressions of different signedness: ‘std::vector<std::vector<AmplitudeFrequencyAndRandomPhases> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  181 |                 if (vectorOfAmplitudeFrequencyAndRandomPhases[zIndex].size() != (unitCellParameters.calcMaxFrequencyDoublingsY()+1) ) {
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:185:90: warning: comparison of integer expressions of different signedness: ‘std::vector<AmplitudeFrequencyAndRandomPhases>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  185 |                     if (vectorOfAmplitudeFrequencyAndRandomPhases[zIndex][yIndex].size() != (unitCellParameters.calcMaxFrequencyDoublingsX()+1 )) {
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp: In member function ‘void DensityMap::densityAutocorrelation(bool, bool) const’:
/<<PKGBUILDDIR>>/src/DensityMap.cpp:209:12: warning: unused variable ‘ySquared’ [-Wunused-variable]
  209 |     double ySquared = 0.;
      |            ^~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:210:12: warning: unused variable ‘zSquared’ [-Wunused-variable]
  210 |     double zSquared = 0.;
      |            ^~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp: In member function ‘void DensityMap::populateNoiseMap()’:
/<<PKGBUILDDIR>>/src/DensityMap.cpp:307:12: warning: unused variable ‘groundFrequencyX’ [-Wunused-variable]
  307 |     double groundFrequencyX = 1/unitCellParameters.getNa()/unitCellParameters.geta()/2;
      |            ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:308:12: warning: unused variable ‘groundFrequencyY’ [-Wunused-variable]
  308 |     double groundFrequencyY = 1/unitCellParameters.getNb()/unitCellParameters.getb()/2;
      |            ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:309:12: warning: unused variable ‘groundFrequencyZ’ [-Wunused-variable]
  309 |     double groundFrequencyZ = 1/unitCellParameters.getNc()/unitCellParameters.getc()/2;
      |            ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:311:12: warning: unused variable ‘maxFrequencyX’ [-Wunused-variable]
  311 |     double maxFrequencyX = 1/unitCellParameters.geta()/2;
      |            ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:312:12: warning: unused variable ‘maxFrequencyY’ [-Wunused-variable]
  312 |     double maxFrequencyY = 1/unitCellParameters.getb()/2;
      |            ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:313:12: warning: unused variable ‘maxFrequencyZ’ [-Wunused-variable]
  313 |     double maxFrequencyZ = 1/unitCellParameters.getc()/2;
      |            ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:318:12: warning: variable ‘signalToNoiseRatio’ set but not used [-Wunused-but-set-variable]
  318 |     double signalToNoiseRatio = 0.;
      |            ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/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.
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp: In member function ‘void DensityMap::loadParametersAndDensity_CCP4MAP()’:
/<<PKGBUILDDIR>>/src/DensityMap.cpp:543:13: warning: unused variable ‘newU’ [-Wunused-variable]
  543 |         int newU, newV, newW;
      |             ^~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:543:19: warning: unused variable ‘newV’ [-Wunused-variable]
  543 |         int newU, newV, newW;
      |                   ^~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:543:25: warning: unused variable ‘newW’ [-Wunused-variable]
  543 |         int newU, newV, newW;
      |                         ^~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:507:9: warning: unused variable ‘xGridInds’ [-Wunused-variable]
  507 |     int xGridInds                                     = xDimInds;
      |         ^~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:508:9: warning: unused variable ‘yGridInds’ [-Wunused-variable]
  508 |     int yGridInds                                     = yDimInds;
      |         ^~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:509:9: warning: unused variable ‘zGridInds’ [-Wunused-variable]
  509 |     int zGridInds                                     = zDimInds;
      |         ^~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp: In member function ‘void DensityMap::writeDensityMapXplor(SimTK::String, bool, bool)’:
/<<PKGBUILDDIR>>/src/DensityMap.cpp:689:13: warning: unused variable ‘densitiesPerLine’ [-Wunused-variable]
  689 |         int densitiesPerLine = 6;
      |             ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 65%] Building CXX object CMakeFiles/MMB.dir/src/DensityForce.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/DensityForce.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/DensityForce.h:20,
                 from /<<PKGBUILDDIR>>/src/DensityForce.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 68%] Building CXX object CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/ElectrostaticPotentialGridForce.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/ElectrostaticPotentialGridForce.h:19,
                 from /<<PKGBUILDDIR>>/src/ElectrostaticPotentialGridForce.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 71%] Building CXX object CMakeFiles/MMB.dir/src/MMBLogger.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/PeriodicPdbAndEnergyWriter.h:13,
                 from /<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:18:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp: In member function ‘virtual void SimTK::PeriodicPdbAndEnergyWriter::handleEvent(SimTK::State&, SimTK::Real, bool&) const’:
/<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:201:30: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  201 |         if(myEnergies.size() > myParameterReader.convergenceTimeout) {
      |            ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:202:20: warning: unused variable ‘lastEnergy’ [-Wunused-variable]
  202 |             double lastEnergy = myEnergies.back();
      |                    ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:49:9: warning: unused variable ‘compoundNumber’ [-Wunused-variable]
   49 |     int compoundNumber                                = 1;
      |         ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:50:9: warning: unused variable ‘requiredPrecision’ [-Wunused-variable]
   50 |     int requiredPrecision                             = 12;
      |         ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 78%] Building CXX object CMakeFiles/MMB.dir/src/CifOutput.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/CifOutput.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20,
                 from /<<PKGBUILDDIR>>/include/CifOutput.h:5,
                 from /<<PKGBUILDDIR>>/src/CifOutput.cpp:1:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::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 /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/PeriodicPdbAndEnergyWriter.h:13,
                 from /<<PKGBUILDDIR>>/include/CifOutput.h:12:
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 81%] Building CXX object CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/NTC_PARAMETER_READER.cpp
In file included from /<<PKGBUILDDIR>>/include/NtC_Class_Container.h:14,
                 from /<<PKGBUILDDIR>>/src/NTC_PARAMETER_READER.cpp:16:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/NTC_FORCE_CLASS.h:4,
                 from /<<PKGBUILDDIR>>/src/NTC_PARAMETER_READER.cpp:17:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 87%] Building CXX object CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/NtCClassContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20,
                 from /<<PKGBUILDDIR>>/src/NtCClassContainer.cpp:13:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 90%] Building CXX object CMakeFiles/MMB.dir/src/NtCForces.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/NtCForces.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/NtCForces.h:13,
                 from /<<PKGBUILDDIR>>/src/NtCForces.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 93%] Linking CXX shared library libMMB.so
/usr/bin/cmake -E cmake_link_script CMakeFiles/MMB.dir/link.txt --verbose=1
/usr/bin/x86_64-linux-gnu-g++ -fPIC -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -Wl,-z,relro -shared -Wl,-soname,libMMB.so.4.0 -o libMMB.so.4.0 CMakeFiles/MMB.dir/src/Utils.cpp.o CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o CMakeFiles/MMB.dir/src/DensityContainer.cpp.o CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o CMakeFiles/MMB.dir/src/ContactContainer.cpp.o CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o CMakeFiles/MMB.dir/src/Repel.cpp.o CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o CMakeFiles/MMB.dir/src/Spiral.cpp.o CMakeFiles/MMB.dir/src/ParameterReader.cpp.o CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o CMakeFiles/MMB.dir/src/TetherForce.cpp.o CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o CMakeFiles/MMB.dir/src/DensityMap.cpp.o CMakeFiles/MMB.dir/src/DensityForce.cpp.o CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o CMakeFiles/MMB.dir/src/MMBLogger.cpp.o CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o CMakeFiles/MMB.dir/src/CifOutput.cpp.o CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o CMakeFiles/MMB.dir/src/NtCForces.cpp.o   -L/<<PKGBUILDDIR>>/SYSTEM  -Wl,-rpath,/<<PKGBUILDDIR>>/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.4.0 libMMB.so.4.0 libMMB.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles/MMB_EXEC.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make  -f CMakeFiles/MMB_EXEC.dir/build.make CMakeFiles/MMB_EXEC.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 /<<PKGBUILDDIR>>/src/RNABuilder.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/src/RNABuilder.cpp:22:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[100%] Linking CXX executable MMB
/usr/bin/cmake -E cmake_link_script CMakeFiles/MMB_EXEC.dir/link.txt --verbose=1
/usr/bin/x86_64-linux-gnu-g++ -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -Wl,-z,relro CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o -o MMB   -L/<<PKGBUILDDIR>>/SYSTEM  -Wl,-rpath,/<<PKGBUILDDIR>>/SYSTEM:/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu: libMMB.so.4.0 /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 '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[100%] Built target MMB_EXEC
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/CMakeFiles 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>/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=/<<BUILDDIR>>/macromoleculebuilder-4.0.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
make  -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/AddBackboneOxygenForces.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/AddNASTForces.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/AtomSpringContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/BaseInteractionParameterReader.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/BasePairContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/BiopolymerClass.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/BiopolymerClassTwoTransformForces.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/CalcTransformCorrection.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/CenterOfMass.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/CifOutput.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/Constexpr.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/ConstraintContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/ContactContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/DensityContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/DensityForce.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/DensityMap.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/DisplacementContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/ElectrostaticPotentialGridForce.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/ExportMacros.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/ExtraMath.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/GeometricCenter.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/HarmonicVelocityRescalingThermostat.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/Impossible.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/KBBackboneTorsionForce.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/Lepton.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/LigandDroplet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/Ligands.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/Ligands.sam.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/MMBLogger.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/MobilizerContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/MoleculeContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/MonoAtoms.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/Mutation.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/NTC_FORCE_CLASS.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/NTC_PARAMETER_READER.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/NtCBackboneTorsionForce.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/NtCForces.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/NtCInteractionParameterReader.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/NtC_Class_Container.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/ParameterReader.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/ParameterReader_wrapper.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/PeriodicParameterReaderUpdater.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/PeriodicPdbAndCOMWriter.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/PeriodicPdbAndEnergySingleFrameWriter.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/PeriodicPdbAndEnergyWriter.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/PeriodicPdbSingleFrameWriter.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/PeriodicScrubber.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/ProgressWriter.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/RandomizeRNACoordinates.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/Repel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/ResidueStretchContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/RigidifyFormedHelices.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/SetChiMobility.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/SetSingleBondMobility.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/Spiral.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/StackingForceSubsystem.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/Sterics.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/TetherForce.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/Threading.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/UnitCellParameters.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/Utils.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/WadleyKeatingDuartePyleTorsionForce.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/Water.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/WaterDroplet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/superimposer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/MMB_config.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libMMB.so.4.0
-- Set non-toolchain portion of runtime path of "/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libMMB.so.4.0" to ""
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libMMB.so
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/MMB/parameters.csv
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/MMB
-- Set non-toolchain portion of runtime path of "/<<PKGBUILDDIR>>/debian/tmp/usr/bin/MMB" to ""
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/mmb/MmbConfigVersion.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/mmb/MmbTargets.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/mmb/MmbTargets-release.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/mmb.pc
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
   dh_install -a
   dh_installdocs -a
   dh_installchangelogs -a
   debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
a2x -d manpage -f manpage -D debian/tmp debian/MMB.1.asciidoc
dh_installman
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_lintian -a
   dh_perl -a
   dh_link -a
   dh_strip_nondeterminism -a
   dh_compress -a
   dh_fixperms -a
   dh_missing -a
   dh_dwz -a
   dh_strip -a
   dh_makeshlibs -a
   dh_shlibdeps -a
   dh_installdeb -a
   dh_gencontrol -a
   dh_md5sums -a
   dh_builddeb -a
dpkg-deb: building package 'libmmb-dev' in '../libmmb-dev_4.0.0+dfsg-3.1_amd64.deb'.
dpkg-deb: building package 'libmmb4.0t64' in '../libmmb4.0t64_4.0.0+dfsg-3.1_amd64.deb'.
dpkg-deb: building package 'libmmb4.0t64-dbgsym' in '../libmmb4.0t64-dbgsym_4.0.0+dfsg-3.1_amd64.deb'.
dpkg-deb: building package 'mmb' in '../mmb_4.0.0+dfsg-3.1_amd64.deb'.
dpkg-deb: building package 'mmb-dbgsym' in '../mmb-dbgsym_4.0.0+dfsg-3.1_amd64.deb'.
 dpkg-genbuildinfo --build=any -O../macromoleculebuilder_4.0.0+dfsg-3.1_amd64.buildinfo
 dpkg-genchanges --build=any -O../macromoleculebuilder_4.0.0+dfsg-3.1_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 2024-04-24T09:12:30Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


macromoleculebuilder_4.0.0+dfsg-3.1_amd64.changes:
--------------------------------------------------

Format: 1.8
Date: Thu, 29 Feb 2024 10:59:56 +0000
Source: macromoleculebuilder
Binary: libmmb-dev libmmb4.0t64 libmmb4.0t64-dbgsym mmb mmb-dbgsym
Built-For-Profiles: cross nocheck
Architecture: amd64
Version: 4.0.0+dfsg-3.1
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Changed-By: Graham Inggs <ginggs@debian.org>
Description:
 libmmb-dev - development files of MacroMoleculeBuilder
 libmmb4.0t64 - shared library of MacroMoleculeBuilder
 mmb        - model the structure and dynamics of macromolecules
Closes: 1062681
Changes:
 macromoleculebuilder (4.0.0+dfsg-3.1) unstable; urgency=medium
 .
   * Non-maintainer upload.
   * Rename libraries for 64-bit time_t transition.  Closes: #1062681
Checksums-Sha1:
 3462dc521a38163924604513d23ababb093e0997 76468 libmmb-dev_4.0.0+dfsg-3.1_amd64.deb
 302dcf1a0c7deb270cef275a552e3565f40bc0b1 25294188 libmmb4.0t64-dbgsym_4.0.0+dfsg-3.1_amd64.deb
 0fa08ff88209174070033746bcffeb786076ff5a 1153268 libmmb4.0t64_4.0.0+dfsg-3.1_amd64.deb
 d0f87f8c156683704af86922aec9fa8936f7e8cb 10634 macromoleculebuilder_4.0.0+dfsg-3.1_amd64.buildinfo
 04f8bb56c70b8424ccf6e15d2aab2ac38d26c6cf 1649432 mmb-dbgsym_4.0.0+dfsg-3.1_amd64.deb
 aa1f98b6f9c99d70396ca4a20a2d406c9f05b550 30920 mmb_4.0.0+dfsg-3.1_amd64.deb
Checksums-Sha256:
 afcde5c6dbdc06225e704e6b541e299f7f34789fd1c21e6e7b3c9dbcacead39e 76468 libmmb-dev_4.0.0+dfsg-3.1_amd64.deb
 19d07d9b33770a1280724beb2584dc2a8458c28816cb826792447dcd089beb91 25294188 libmmb4.0t64-dbgsym_4.0.0+dfsg-3.1_amd64.deb
 5138b77e687348c88b88310a8e1b6041166db2b08cbe8c4158d81628b9a6ed8f 1153268 libmmb4.0t64_4.0.0+dfsg-3.1_amd64.deb
 ada5bb286af055dd0c2eb23a131113b1214f4759190686f6079057b678351d37 10634 macromoleculebuilder_4.0.0+dfsg-3.1_amd64.buildinfo
 76c5d7076a9bbda0483373b0883e69582ca23ce592d8a7a8f48b202323614e36 1649432 mmb-dbgsym_4.0.0+dfsg-3.1_amd64.deb
 33dc2348b5e416406b8cbe43a754d0ef94cb6107eb87fb983a4c059d370e2f5f 30920 mmb_4.0.0+dfsg-3.1_amd64.deb
Files:
 2e4dacf1fb31580be2a1fd3cce2fdc78 76468 libdevel optional libmmb-dev_4.0.0+dfsg-3.1_amd64.deb
 63427c837cacb06821c7e6b2a78fcb55 25294188 debug optional libmmb4.0t64-dbgsym_4.0.0+dfsg-3.1_amd64.deb
 7306646351150df7a12a89dc49dfa45b 1153268 libs optional libmmb4.0t64_4.0.0+dfsg-3.1_amd64.deb
 c53e33585bbac9a447bff7f06011dbc4 10634 science optional macromoleculebuilder_4.0.0+dfsg-3.1_amd64.buildinfo
 f3404b8cc9bea4c1727dcc44fab46203 1649432 debug optional mmb-dbgsym_4.0.0+dfsg-3.1_amd64.deb
 be36f9cf90780c65075a5d4480044038 30920 science optional mmb_4.0.0+dfsg-3.1_amd64.deb

+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

Format: 1.0
Source: macromoleculebuilder
Binary: libmmb-dev libmmb4.0t64 libmmb4.0t64-dbgsym mmb mmb-dbgsym
Architecture: amd64
Version: 4.0.0+dfsg-3.1
Checksums-Md5:
 2e4dacf1fb31580be2a1fd3cce2fdc78 76468 libmmb-dev_4.0.0+dfsg-3.1_amd64.deb
 63427c837cacb06821c7e6b2a78fcb55 25294188 libmmb4.0t64-dbgsym_4.0.0+dfsg-3.1_amd64.deb
 7306646351150df7a12a89dc49dfa45b 1153268 libmmb4.0t64_4.0.0+dfsg-3.1_amd64.deb
 f3404b8cc9bea4c1727dcc44fab46203 1649432 mmb-dbgsym_4.0.0+dfsg-3.1_amd64.deb
 be36f9cf90780c65075a5d4480044038 30920 mmb_4.0.0+dfsg-3.1_amd64.deb
Checksums-Sha1:
 3462dc521a38163924604513d23ababb093e0997 76468 libmmb-dev_4.0.0+dfsg-3.1_amd64.deb
 302dcf1a0c7deb270cef275a552e3565f40bc0b1 25294188 libmmb4.0t64-dbgsym_4.0.0+dfsg-3.1_amd64.deb
 0fa08ff88209174070033746bcffeb786076ff5a 1153268 libmmb4.0t64_4.0.0+dfsg-3.1_amd64.deb
 04f8bb56c70b8424ccf6e15d2aab2ac38d26c6cf 1649432 mmb-dbgsym_4.0.0+dfsg-3.1_amd64.deb
 aa1f98b6f9c99d70396ca4a20a2d406c9f05b550 30920 mmb_4.0.0+dfsg-3.1_amd64.deb
Checksums-Sha256:
 afcde5c6dbdc06225e704e6b541e299f7f34789fd1c21e6e7b3c9dbcacead39e 76468 libmmb-dev_4.0.0+dfsg-3.1_amd64.deb
 19d07d9b33770a1280724beb2584dc2a8458c28816cb826792447dcd089beb91 25294188 libmmb4.0t64-dbgsym_4.0.0+dfsg-3.1_amd64.deb
 5138b77e687348c88b88310a8e1b6041166db2b08cbe8c4158d81628b9a6ed8f 1153268 libmmb4.0t64_4.0.0+dfsg-3.1_amd64.deb
 76c5d7076a9bbda0483373b0883e69582ca23ce592d8a7a8f48b202323614e36 1649432 mmb-dbgsym_4.0.0+dfsg-3.1_amd64.deb
 33dc2348b5e416406b8cbe43a754d0ef94cb6107eb87fb983a4c059d370e2f5f 30920 mmb_4.0.0+dfsg-3.1_amd64.deb
Build-Origin: Debian
Build-Architecture: arm64
Build-Date: Wed, 24 Apr 2024 09:12:27 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
 merged-usr-via-aliased-dirs
Installed-Build-Depends:
 asciidoc-base (= 10.2.0-2),
 asciidoc-common (= 10.2.0-2),
 autoconf (= 2.71-3),
 automake (= 1:1.16.5-1.3),
 autopoint (= 0.21-14),
 autotools-dev (= 20220109.1),
 base-files (= 13.1),
 base-passwd (= 3.6.3),
 bash (= 5.2.21-2),
 binutils (= 2.42-4),
 binutils-aarch64-linux-gnu (= 2.42-4),
 binutils-common (= 2.42-4),
 bsdextrautils (= 2.40-6),
 bsdutils (= 1:2.40-6),
 build-essential (= 12.10),
 bzip2 (= 1.0.8-5.1),
 cmake (= 3.28.3-1+b1),
 cmake-data (= 3.28.3-1),
 coreutils (= 9.4-3.1),
 cpp (= 4:13.2.0-7),
 cpp-13 (= 13.2.0-23),
 cpp-13-aarch64-linux-gnu (= 13.2.0-23),
 cpp-aarch64-linux-gnu (= 4:13.2.0-7),
 dash (= 0.5.12-6),
 debconf (= 1.5.86),
 debhelper (= 13.15.3),
 debianutils (= 5.17),
 dh-autoreconf (= 20),
 dh-strip-nondeterminism (= 1.13.1-1),
 diffutils (= 1:3.10-1),
 docbook-xml (= 4.5-12),
 docbook-xsl (= 1.79.2+dfsg-7),
 dpkg (= 1.22.6),
 dpkg-dev (= 1.22.6),
 dwz (= 0.15-1+b1),
 file (= 1:5.45-3),
 findutils (= 4.9.0-5),
 freeglut3-dev (= 3.4.0-1+b1),
 g++ (= 4:13.2.0-7),
 g++-13 (= 13.2.0-23),
 g++-13-aarch64-linux-gnu (= 13.2.0-23),
 g++-aarch64-linux-gnu (= 4:13.2.0-7),
 gcc (= 4:13.2.0-7),
 gcc-13 (= 13.2.0-23),
 gcc-13-aarch64-linux-gnu (= 13.2.0-23),
 gcc-13-base (= 13.2.0-23),
 gcc-14-base (= 14-20240330-1),
 gcc-aarch64-linux-gnu (= 4:13.2.0-7),
 gemmi-dev (= 0.6.4+ds-1),
 gettext (= 0.21-14+b1),
 gettext-base (= 0.21-14+b1),
 grep (= 3.11-4),
 groff-base (= 1.23.0-3+b1),
 gzip (= 1.12-1.1),
 hostname (= 3.23+nmu2),
 init-system-helpers (= 1.66),
 intltool-debian (= 0.35.0+20060710.6),
 libacl1 (= 2.3.2-1),
 libarchive-zip-perl (= 1.68-1),
 libarchive13t64 (= 3.7.2-2),
 libasan8 (= 14-20240330-1),
 libatomic1 (= 14-20240330-1),
 libattr1 (= 1:2.5.2-1),
 libaudit-common (= 1:3.1.2-2.1),
 libaudit1 (= 1:3.1.2-2.1),
 libbinutils (= 2.42-4),
 libblas-dev (= 3.12.0-3),
 libblas3 (= 3.12.0-3),
 libblkid1 (= 2.40-6),
 libbrotli1 (= 1.1.0-2+b3),
 libbsd0 (= 0.12.2-1),
 libbz2-1.0 (= 1.0.8-5.1),
 libc-bin (= 2.37-18),
 libc-dev-bin (= 2.37-18),
 libc6 (= 2.37-18),
 libc6-dev (= 2.37-18),
 libcap-ng0 (= 0.8.5-1),
 libcap2 (= 1:2.66-5),
 libcc1-0 (= 14-20240330-1),
 libcom-err2 (= 1.47.0-2.4),
 libcrypt-dev (= 1:4.4.36-4),
 libcrypt1 (= 1:4.4.36-4),
 libctf-nobfd0 (= 2.42-4),
 libctf0 (= 2.42-4),
 libcurl4t64 (= 8.7.1-3),
 libdb5.3t64 (= 5.3.28+dfsg2-7),
 libdebconfclient0 (= 0.271+b3),
 libdebhelper-perl (= 13.15.3),
 libdpkg-perl (= 1.22.6),
 libdrm-amdgpu1 (= 2.4.120-2),
 libdrm-common (= 2.4.120-2),
 libdrm-intel1 (= 2.4.120-2),
 libdrm-nouveau2 (= 2.4.120-2),
 libdrm-radeon1 (= 2.4.120-2),
 libdrm2 (= 2.4.120-2),
 libedit2 (= 3.1-20230828-1),
 libegl-dev (= 1.7.0-1),
 libegl-mesa0 (= 24.0.5-1),
 libegl1 (= 1.7.0-1),
 libelf1t64 (= 0.191-1+b1),
 libexpat1 (= 2.6.2-1),
 libffi8 (= 3.4.6-1),
 libfile-find-rule-perl (= 0.34-3),
 libfile-stripnondeterminism-perl (= 1.13.1-1),
 libgbm1 (= 24.0.5-1),
 libgcc-13-dev (= 13.2.0-23),
 libgcc-s1 (= 14-20240330-1),
 libgcrypt20 (= 1.10.3-2),
 libgdbm-compat4t64 (= 1.23-5.1+b1),
 libgdbm6t64 (= 1.23-5.1+b1),
 libgfortran5 (= 14-20240330-1),
 libgl-dev (= 1.7.0-1),
 libgl1 (= 1.7.0-1),
 libgl1-mesa-dev (= 24.0.5-1),
 libgl1-mesa-dri (= 24.0.5-1),
 libglapi-mesa (= 24.0.5-1),
 libgles-dev (= 1.7.0-1),
 libgles1 (= 1.7.0-1),
 libgles2 (= 1.7.0-1),
 libglu1-mesa (= 9.0.2-1.1),
 libglu1-mesa-dev (= 9.0.2-1.1),
 libglut-dev (= 3.4.0-1+b1),
 libglut3.12 (= 3.4.0-1+b1),
 libglvnd-core-dev (= 1.7.0-1),
 libglvnd-dev (= 1.7.0-1),
 libglvnd0 (= 1.7.0-1),
 libglx-dev (= 1.7.0-1),
 libglx-mesa0 (= 24.0.5-1),
 libglx0 (= 1.7.0-1),
 libgmp10 (= 2:6.3.0+dfsg-2+b1),
 libgnutls30t64 (= 3.8.5-2),
 libgomp1 (= 14-20240330-1),
 libgpg-error0 (= 1.47-3),
 libgprofng0 (= 2.42-4),
 libgssapi-krb5-2 (= 1.20.1-6+b1),
 libhogweed6t64 (= 3.9.1-2.2),
 libhwasan0 (= 14-20240330-1),
 libice-dev (= 2:1.0.10-1),
 libice6 (= 2:1.0.10-1),
 libicu72 (= 72.1-4+b1),
 libidn2-0 (= 2.3.7-2),
 libisl23 (= 0.26-3+b2),
 libitm1 (= 14-20240330-1),
 libjansson4 (= 2.14-2+b2),
 libjsoncpp25 (= 1.9.5-6+b2),
 libk5crypto3 (= 1.20.1-6+b1),
 libkeyutils1 (= 1.6.3-3),
 libkrb5-3 (= 1.20.1-6+b1),
 libkrb5support0 (= 1.20.1-6+b1),
 liblapack-dev (= 3.12.0-3),
 liblapack3 (= 3.12.0-3),
 libldap-2.5-0 (= 2.5.16+dfsg-2),
 libllvm17t64 (= 1:17.0.6-9+b2),
 liblsan0 (= 14-20240330-1),
 liblz4-1 (= 1.9.4-2),
 liblzma5 (= 5.6.1+really5.4.5-1),
 libmagic-mgc (= 1:5.45-3),
 libmagic1t64 (= 1:5.45-3),
 libmd0 (= 1.1.0-2),
 libmount1 (= 2.40-6),
 libmpc3 (= 1.3.1-1+b2),
 libmpfr6 (= 4.2.1-1+b1),
 libncursesw6 (= 6.4+20240414-1),
 libnettle8t64 (= 3.9.1-2.2),
 libnghttp2-14 (= 1.61.0-1+b1),
 libnumber-compare-perl (= 0.03-3),
 libopengl-dev (= 1.7.0-1),
 libopengl0 (= 1.7.0-1),
 libopenmm-dev (= 8.0.0+dfsg-6.1),
 libopenmm8.0t64 (= 8.0.0+dfsg-6.1),
 libp11-kit0 (= 0.25.3-4),
 libpam-modules (= 1.5.3-7),
 libpam-modules-bin (= 1.5.3-7),
 libpam-runtime (= 1.5.3-7),
 libpam0g (= 1.5.3-7),
 libpciaccess0 (= 0.17-3),
 libpcre2-8-0 (= 10.42-4+b1),
 libperl5.38t64 (= 5.38.2-3.2+b2),
 libpipeline1 (= 1.5.7-2),
 libproc2-0 (= 2:4.0.4-4),
 libpsl5t64 (= 0.21.2-1.1),
 libpthread-stubs0-dev (= 0.4-1),
 libpython3-stdlib (= 3.11.8-1),
 libpython3.11-minimal (= 3.11.9-1),
 libpython3.11-stdlib (= 3.11.9-1),
 libquadmath0 (= 14-20240330-1),
 libreadline8t64 (= 8.2-4),
 librhash0 (= 1.4.3-3+b1),
 librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b4),
 libsasl2-2 (= 2.1.28+dfsg1-6),
 libsasl2-modules-db (= 2.1.28+dfsg1-6),
 libseccomp2 (= 2.5.5-1),
 libselinux1 (= 3.5-2+b2),
 libsensors-config (= 1:3.6.0-9),
 libsensors5 (= 1:3.6.0-9),
 libseqan2-dev (= 2.4.0+dfsg-16),
 libsframe1 (= 2.42-4),
 libsimbody-dev (= 3.7+dfsg-3),
 libsimbody3.7 (= 3.7+dfsg-3),
 libsimtkmolmodel-dev (= 3.1.0-4.1+b1),
 libsimtkmolmodel-plugins (= 3.1.0-4.1+b1),
 libsimtkmolmodel3.1t64 (= 3.1.0-4.1+b1),
 libsm-dev (= 2:1.2.3-1),
 libsm6 (= 2:1.2.3-1),
 libsmartcols1 (= 2.40-6),
 libsqlite3-0 (= 3.45.3-1),
 libssh2-1t64 (= 1.11.0-4.1+b2),
 libssl3t64 (= 3.2.1-3),
 libstb-dev (= 0.0~git20230129.5736b15+ds-1.2),
 libstb0t64 (= 0.0~git20230129.5736b15+ds-1.2),
 libstdc++-13-dev (= 13.2.0-23),
 libstdc++6 (= 14-20240330-1),
 libsub-override-perl (= 0.10-1),
 libsystemd0 (= 255.4-1+b1),
 libtasn1-6 (= 4.19.0-3+b2),
 libtext-glob-perl (= 0.11-3),
 libtinfo6 (= 6.4+20240414-1),
 libtool (= 2.4.7-7),
 libtsan2 (= 14-20240330-1),
 libubsan1 (= 14-20240330-1),
 libuchardet0 (= 0.0.8-1+b1),
 libudev1 (= 255.4-1+b1),
 libunistring5 (= 1.2-1),
 libuuid1 (= 2.40-6),
 libuv1t64 (= 1.48.0-1.1),
 libvulkan1 (= 1.3.280.0-1),
 libwayland-client0 (= 1.22.0-2.1+b1),
 libwayland-server0 (= 1.22.0-2.1+b1),
 libx11-6 (= 2:1.8.7-1),
 libx11-data (= 2:1.8.7-1),
 libx11-dev (= 2:1.8.7-1),
 libx11-xcb1 (= 2:1.8.7-1),
 libxau-dev (= 1:1.0.9-1),
 libxau6 (= 1:1.0.9-1),
 libxcb-dri2-0 (= 1.17.0-1),
 libxcb-dri3-0 (= 1.17.0-1),
 libxcb-glx0 (= 1.17.0-1),
 libxcb-present0 (= 1.17.0-1),
 libxcb-randr0 (= 1.17.0-1),
 libxcb-shm0 (= 1.17.0-1),
 libxcb-sync1 (= 1.17.0-1),
 libxcb-xfixes0 (= 1.17.0-1),
 libxcb1 (= 1.17.0-1),
 libxcb1-dev (= 1.17.0-1),
 libxdmcp-dev (= 1:1.1.2-3),
 libxdmcp6 (= 1:1.1.2-3),
 libxext-dev (= 2:1.3.4-1+b1),
 libxext6 (= 2:1.3.4-1+b1),
 libxfixes-dev (= 1:6.0.0-2),
 libxfixes3 (= 1:6.0.0-2),
 libxi-dev (= 2:1.8.1-1),
 libxi6 (= 2:1.8.1-1),
 libxml2 (= 2.9.14+dfsg-1.3+b2),
 libxml2-utils (= 2.9.14+dfsg-1.3+b2),
 libxmu-dev (= 2:1.1.3-3+b2),
 libxmu-headers (= 2:1.1.3-3),
 libxmu6 (= 2:1.1.3-3+b2),
 libxshmfence1 (= 1.3-1),
 libxslt1.1 (= 1.1.35-1),
 libxt-dev (= 1:1.2.1-1.2),
 libxt6t64 (= 1:1.2.1-1.2),
 libxxf86vm1 (= 1:1.1.4-1+b2),
 libz3-4 (= 4.8.12-3.1+b2),
 libzstd1 (= 1.5.5+dfsg2-2),
 linux-libc-dev (= 6.7.9-2),
 login (= 1:4.13+dfsg1-4),
 m4 (= 1.4.19-4),
 make (= 4.3-4.1),
 man-db (= 2.12.1-1),
 mawk (= 1.3.4.20240123-1),
 media-types (= 10.1.0),
 ncurses-base (= 6.4+20240414-1),
 ncurses-bin (= 6.4+20240414-1),
 netbase (= 6.4),
 patch (= 2.7.6-7),
 perl (= 5.38.2-3.2+b2),
 perl-base (= 5.38.2-3.2+b2),
 perl-modules-5.38 (= 5.38.2-3.2),
 po-debconf (= 1.0.21+nmu1),
 procps (= 2:4.0.4-4),
 python3 (= 3.11.8-1),
 python3-minimal (= 3.11.8-1),
 python3.11 (= 3.11.9-1),
 python3.11-minimal (= 3.11.9-1),
 readline-common (= 8.2-4),
 rpcsvc-proto (= 1.4.3-1),
 sed (= 4.9-2),
 sensible-utils (= 0.0.22),
 sgml-base (= 1.31),
 sgml-data (= 2.0.11+nmu1),
 sysvinit-utils (= 3.09-1),
 tao-pegtl-dev (= 3.2.7-1),
 tar (= 1.35+dfsg-3),
 tzdata (= 2024a-3),
 usrmerge (= 39),
 util-linux (= 2.40-6),
 x11-common (= 1:7.7+23),
 x11proto-dev (= 2024.1-1),
 xml-core (= 0.19),
 xorg-sgml-doctools (= 1:1.11-1.1),
 xsltproc (= 1.1.35-1),
 xtrans-dev (= 1.4.0-1),
 xz-utils (= 5.6.1+really5.4.5-1),
 zlib1g (= 1:1.3.dfsg-3.1),
 zlib1g-dev (= 1:1.3.dfsg-3.1)
Environment:
 DEB_BUILD_OPTIONS="nocheck parallel=1"
 DEB_BUILD_PROFILES="cross nocheck"
 LANG="en_GB.UTF-8"
 LC_ALL="C.UTF-8"
 LC_COLLATE="C.UTF-8"
 SOURCE_DATE_EPOCH="1709204396"


+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


libmmb-dev_4.0.0+dfsg-3.1_amd64.deb
-----------------------------------

 new Debian package, version 2.0.
 size 76468 bytes: control archive=2904 bytes.
     781 bytes,    20 lines      control
    5109 bytes,    72 lines      md5sums
 Package: libmmb-dev
 Source: macromoleculebuilder
 Version: 4.0.0+dfsg-3.1
 Architecture: amd64
 Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
 Installed-Size: 559
 Depends: libmmb4.0t64 (= 4.0.0+dfsg-3.1)
 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 2024-02-29 10:59 ./
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/include/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/include/MMB/
-rw-r--r-- root/root      8108 2022-11-29 12:01 ./usr/include/MMB/AddBackboneOxygenForces.h
-rw-r--r-- root/root      6293 2022-11-29 12:01 ./usr/include/MMB/AddNASTForces.h
-rw-r--r-- root/root      5724 2022-11-29 12:01 ./usr/include/MMB/AtomSpringContainer.h
-rw-r--r-- root/root      3559 2022-11-29 12:01 ./usr/include/MMB/BaseInteractionParameterReader.h
-rw-r--r-- root/root      3477 2022-11-29 12:01 ./usr/include/MMB/BasePairContainer.h
-rw-r--r-- root/root     42905 2022-11-29 12:01 ./usr/include/MMB/BiopolymerClass.h
-rw-r--r-- root/root      2644 2022-11-29 12:01 ./usr/include/MMB/BiopolymerClassTwoTransformForces.h
-rw-r--r-- root/root     19309 2022-11-29 12:01 ./usr/include/MMB/CalcTransformCorrection.h
-rw-r--r-- root/root      3188 2022-11-29 12:01 ./usr/include/MMB/CenterOfMass.h
-rw-r--r-- root/root      1328 2022-11-29 12:01 ./usr/include/MMB/CifOutput.h
-rw-r--r-- root/root       188 2022-11-29 12:01 ./usr/include/MMB/Constexpr.h
-rw-r--r-- root/root      3848 2022-11-29 12:01 ./usr/include/MMB/ConstraintContainer.h
-rw-r--r-- root/root      3295 2022-11-29 12:01 ./usr/include/MMB/ContactContainer.h
-rw-r--r-- root/root      1793 2022-11-29 12:01 ./usr/include/MMB/DensityContainer.h
-rw-r--r-- root/root      2105 2022-11-29 12:01 ./usr/include/MMB/DensityForce.h
-rw-r--r-- root/root      7794 2022-11-29 12:01 ./usr/include/MMB/DensityMap.h
-rw-r--r-- root/root      1912 2022-11-29 12:01 ./usr/include/MMB/DisplacementContainer.h
-rw-r--r-- root/root      2165 2022-11-29 12:01 ./usr/include/MMB/ElectrostaticPotentialGridForce.h
-rw-r--r-- root/root      3001 2022-11-29 12:01 ./usr/include/MMB/ExportMacros.h
-rw-r--r-- root/root       752 2022-11-29 12:01 ./usr/include/MMB/ExtraMath.h
-rw-r--r-- root/root      1756 2022-11-29 12:01 ./usr/include/MMB/GeometricCenter.h
-rw-r--r-- root/root      4613 2022-11-29 12:01 ./usr/include/MMB/HarmonicVelocityRescalingThermostat.h
-rw-r--r-- root/root       227 2022-11-29 12:01 ./usr/include/MMB/Impossible.h
-rw-r--r-- root/root      4871 2022-11-29 12:01 ./usr/include/MMB/KBBackboneTorsionForce.h
-rw-r--r-- root/root       312 2022-11-29 12:01 ./usr/include/MMB/Lepton.h
-rw-r--r-- root/root      8211 2022-11-29 12:01 ./usr/include/MMB/LigandDroplet.h
-rw-r--r-- root/root     16881 2022-11-29 12:01 ./usr/include/MMB/Ligands.h
-rw-r--r-- root/root     16712 2022-11-29 12:01 ./usr/include/MMB/Ligands.sam.h
-rw-r--r-- root/root      3129 2022-11-29 12:01 ./usr/include/MMB/MMBLogger.h
-rw-r--r-- root/root        91 2024-02-29 10:59 ./usr/include/MMB/MMB_config.h
-rw-r--r-- root/root      5172 2022-11-29 12:01 ./usr/include/MMB/MobilizerContainer.h
-rw-r--r-- root/root      3821 2022-11-29 12:01 ./usr/include/MMB/MoleculeContainer.h
-rw-r--r-- root/root      4156 2022-11-29 12:01 ./usr/include/MMB/MonoAtoms.h
-rw-r--r-- root/root      7486 2022-11-29 12:01 ./usr/include/MMB/Mutation.h
-rw-r--r-- root/root       328 2022-11-29 12:01 ./usr/include/MMB/NTC_FORCE_CLASS.h
-rw-r--r-- root/root      4598 2022-11-29 12:01 ./usr/include/MMB/NTC_PARAMETER_READER.h
-rw-r--r-- root/root      4871 2022-11-29 12:01 ./usr/include/MMB/NtCBackboneTorsionForce.h
-rw-r--r-- root/root      1747 2022-11-29 12:01 ./usr/include/MMB/NtCForces.h
-rw-r--r-- root/root      4568 2022-11-29 12:01 ./usr/include/MMB/NtCInteractionParameterReader.h
-rw-r--r-- root/root      2181 2022-11-29 12:01 ./usr/include/MMB/NtC_Class_Container.h
-rw-r--r-- root/root     15506 2022-11-29 12:01 ./usr/include/MMB/ParameterReader.h
-rw-r--r-- root/root     56249 2022-11-29 12:01 ./usr/include/MMB/ParameterReader_wrapper.h
-rw-r--r-- root/root      5300 2022-11-29 12:01 ./usr/include/MMB/PeriodicParameterReaderUpdater.h
-rw-r--r-- root/root      5408 2022-11-29 12:01 ./usr/include/MMB/PeriodicPdbAndCOMWriter.h
-rw-r--r-- root/root      3151 2022-11-29 12:01 ./usr/include/MMB/PeriodicPdbAndEnergySingleFrameWriter.h
-rw-r--r-- root/root      2002 2022-11-29 12:01 ./usr/include/MMB/PeriodicPdbAndEnergyWriter.h
-rw-r--r-- root/root      4985 2022-11-29 12:01 ./usr/include/MMB/PeriodicPdbSingleFrameWriter.h
-rw-r--r-- root/root      4299 2022-11-29 12:01 ./usr/include/MMB/PeriodicScrubber.h
-rw-r--r-- root/root      1615 2022-11-29 12:01 ./usr/include/MMB/ProgressWriter.h
-rw-r--r-- root/root      8487 2022-11-29 12:01 ./usr/include/MMB/RandomizeRNACoordinates.h
-rw-r--r-- root/root      8587 2022-11-29 12:01 ./usr/include/MMB/Repel.h
-rw-r--r-- root/root     23919 2022-11-29 12:01 ./usr/include/MMB/ResidueStretchContainer.h
-rw-r--r-- root/root     12884 2022-11-29 12:01 ./usr/include/MMB/RigidifyFormedHelices.h
-rw-r--r-- root/root      7179 2022-11-29 12:01 ./usr/include/MMB/SetChiMobility.h
-rw-r--r-- root/root      3252 2022-11-29 12:01 ./usr/include/MMB/SetSingleBondMobility.h
-rw-r--r-- root/root      3132 2022-11-29 12:01 ./usr/include/MMB/Spiral.h
-rw-r--r-- root/root      2359 2022-11-29 12:01 ./usr/include/MMB/StackingForceSubsystem.h
-rw-r--r-- root/root     15674 2022-11-29 12:01 ./usr/include/MMB/Sterics.h
-rw-r--r-- root/root      1958 2022-11-29 12:01 ./usr/include/MMB/TetherForce.h
-rw-r--r-- root/root     12675 2022-11-29 12:01 ./usr/include/MMB/Threading.h
-rw-r--r-- root/root      5366 2022-11-29 12:01 ./usr/include/MMB/UnitCellParameters.h
-rw-r--r-- root/root     63474 2022-11-29 12:01 ./usr/include/MMB/Utils.h
-rw-r--r-- root/root     12299 2022-11-29 12:01 ./usr/include/MMB/WadleyKeatingDuartePyleTorsionForce.h
-rw-r--r-- root/root      2817 2022-11-29 12:01 ./usr/include/MMB/Water.h
-rw-r--r-- root/root      3544 2022-11-29 12:01 ./usr/include/MMB/WaterDroplet.h
-rw-r--r-- root/root       845 2022-11-29 12:01 ./usr/include/MMB/superimposer.h
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/lib/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/lib/x86_64-linux-gnu/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/lib/x86_64-linux-gnu/cmake/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/lib/x86_64-linux-gnu/cmake/mmb/
-rw-r--r-- root/root      2756 2024-02-29 10:59 ./usr/lib/x86_64-linux-gnu/cmake/mmb/MmbConfigVersion.cmake
-rw-r--r-- root/root       818 2024-02-29 10:59 ./usr/lib/x86_64-linux-gnu/cmake/mmb/MmbTargets-release.cmake
-rw-r--r-- root/root      4452 2024-02-29 10:59 ./usr/lib/x86_64-linux-gnu/cmake/mmb/MmbTargets.cmake
lrwxrwxrwx root/root         0 2024-02-29 10:59 ./usr/lib/x86_64-linux-gnu/libMMB.so -> libMMB.so.4.0
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/lib/x86_64-linux-gnu/pkgconfig/
-rw-r--r-- root/root       194 2024-02-29 10:59 ./usr/lib/x86_64-linux-gnu/pkgconfig/mmb.pc
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/share/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/share/doc/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/share/doc/libmmb-dev/
-rw-r--r-- root/root      1277 2024-02-29 10:59 ./usr/share/doc/libmmb-dev/changelog.Debian.gz
-rw-r--r-- root/root      1550 2023-06-23 05:37 ./usr/share/doc/libmmb-dev/copyright


libmmb4.0t64-dbgsym_4.0.0+dfsg-3.1_amd64.deb
--------------------------------------------

 new Debian package, version 2.0.
 size 25294188 bytes: control archive=564 bytes.
     413 bytes,    13 lines      control
     106 bytes,     1 lines      md5sums
 Package: libmmb4.0t64-dbgsym
 Source: macromoleculebuilder
 Version: 4.0.0+dfsg-3.1
 Auto-Built-Package: debug-symbols
 Architecture: amd64
 Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
 Installed-Size: 26880
 Depends: libmmb4.0t64 (= 4.0.0+dfsg-3.1)
 Section: debug
 Priority: optional
 Multi-Arch: same
 Description: debug symbols for libmmb4.0t64
 Build-Ids: 570143f3a0e0d43e3e0e846ddb9df6051a497722

drwxr-xr-x root/root         0 2024-02-29 10:59 ./
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/lib/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/lib/debug/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/lib/debug/.build-id/57/
-rw-r--r-- root/root  27514792 2024-02-29 10:59 ./usr/lib/debug/.build-id/57/0143f3a0e0d43e3e0e846ddb9df6051a497722.debug
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/share/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/share/doc/
lrwxrwxrwx root/root         0 2024-02-29 10:59 ./usr/share/doc/libmmb4.0t64-dbgsym -> libmmb4.0t64


libmmb4.0t64_4.0.0+dfsg-3.1_amd64.deb
-------------------------------------

 new Debian package, version 2.0.
 size 1153268 bytes: control archive=1084 bytes.
     947 bytes,    21 lines      control
     300 bytes,     4 lines      md5sums
      40 bytes,     1 lines      shlibs
      68 bytes,     2 lines      triggers
 Package: libmmb4.0t64
 Source: macromoleculebuilder
 Version: 4.0.0+dfsg-3.1
 Architecture: amd64
 Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
 Installed-Size: 4565
 Depends: libc6 (>= 2.33), libgcc-s1 (>= 3.0), libopenmm8.0t64 (>= 8.0.0+dfsg), libsimbody3.7 (>= 3.7+dfsg), libsimtkmolmodel3.1t64 (>= 3.1.0), libstdc++6 (>= 13.1), zlib1g (>= 1:1.2.6)
 Breaks: libmmb4.0 (<< 4.0.0+dfsg-3.1)
 Replaces: libmmb4.0
 Provides: libmmb4.0 (= 4.0.0+dfsg-3.1)
 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 2024-02-29 10:59 ./
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/lib/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/lib/x86_64-linux-gnu/
-rw-r--r-- root/root   4656680 2024-02-29 10:59 ./usr/lib/x86_64-linux-gnu/libMMB.so.4.0
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/share/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/share/doc/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/share/doc/libmmb4.0t64/
-rw-r--r-- root/root      1277 2024-02-29 10:59 ./usr/share/doc/libmmb4.0t64/changelog.Debian.gz
-rw-r--r-- root/root      1550 2023-06-23 05:37 ./usr/share/doc/libmmb4.0t64/copyright
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/share/lintian/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/share/lintian/overrides/
-rw-r--r-- root/root        58 2024-02-29 10:59 ./usr/share/lintian/overrides/libmmb4.0t64


mmb-dbgsym_4.0.0+dfsg-3.1_amd64.deb
-----------------------------------

 new Debian package, version 2.0.
 size 1649432 bytes: control archive=544 bytes.
     368 bytes,    12 lines      control
     106 bytes,     1 lines      md5sums
 Package: mmb-dbgsym
 Source: macromoleculebuilder
 Version: 4.0.0+dfsg-3.1
 Auto-Built-Package: debug-symbols
 Architecture: amd64
 Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
 Installed-Size: 1667
 Depends: mmb (= 4.0.0+dfsg-3.1)
 Section: debug
 Priority: optional
 Description: debug symbols for mmb
 Build-Ids: 4e6a9af65214b4a20e70589a943cb0a46a855341

drwxr-xr-x root/root         0 2024-02-29 10:59 ./
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/lib/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/lib/debug/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/lib/debug/.build-id/4e/
-rw-r--r-- root/root   1696248 2024-02-29 10:59 ./usr/lib/debug/.build-id/4e/6a9af65214b4a20e70589a943cb0a46a855341.debug
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/share/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/share/doc/
lrwxrwxrwx root/root         0 2024-02-29 10:59 ./usr/share/doc/mmb-dbgsym -> mmb


mmb_4.0.0+dfsg-3.1_amd64.deb
----------------------------

 new Debian package, version 2.0.
 size 30920 bytes: control archive=892 bytes.
     780 bytes,    15 lines      control
     242 bytes,     4 lines      md5sums
 Package: mmb
 Source: macromoleculebuilder
 Version: 4.0.0+dfsg-3.1
 Architecture: amd64
 Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
 Installed-Size: 118
 Depends: mmb-common, libc6 (>= 2.34), libgcc-s1 (>= 3.0), libmmb4.0t64 (>= 4.0.0+dfsg), libsimbody3.7 (>= 3.7+dfsg), libsimtkmolmodel3.1t64 (>= 3.1.0), libstdc++6 (>= 13.1)
 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 2024-02-29 10:59 ./
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/bin/
-rwxr-xr-x root/root    105632 2024-02-29 10:59 ./usr/bin/MMB
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/share/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/share/doc/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/share/doc/mmb/
-rw-r--r-- root/root      1277 2024-02-29 10:59 ./usr/share/doc/mmb/changelog.Debian.gz
-rw-r--r-- root/root      1550 2023-06-23 05:37 ./usr/share/doc/mmb/copyright
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/share/man/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/share/man/man1/
-rw-r--r-- root/root       788 2024-02-29 10:59 ./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 '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-lintian-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [615 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [1524 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [1604 B]
Fetched 3743 B in 0s (204 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:
  ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl
  libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl
  libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl
  libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl
  libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl
  libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl
  libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl
  libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl
  libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl
  libemail-address-xs-perl libencode-locale-perl libexception-class-perl
  libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl
  libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl
  libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl
  libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl
  libimport-into-perl libio-html-perl libio-interactive-perl
  libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl
  libiterator-perl libiterator-util-perl libjson-maybexs-perl
  liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl
  liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2
  libmarkdown2 libmldbm-perl libmodule-implementation-perl
  libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl
  libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl
  libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl
  libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl
  libparams-util-perl libpath-tiny-perl libperlio-gzip-perl
  libperlio-utf8-strict-perl libproc-processtable-perl
  libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl
  libsereal-encoder-perl libsort-versions-perl libstrictures-perl
  libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl
  libsub-install-perl libsub-name-perl libsub-quote-perl
  libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl
  libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl
  libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl
  liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl
  libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2
  libyaml-libyaml-perl lintian lzop openssl patchutils perl-openssl-defaults
  plzip t1utils unzip
Suggested packages:
  isoquery libxml-parser-perl libdata-dump-perl libcrypt-ssleay-perl
  libscalar-number-perl libbareword-filehandles-perl libindirect-perl
  libmultidimensional-perl libbusiness-isbn-perl libregexp-ipv6-perl
  libauthen-ntlm-perl binutils-multiarch libtext-template-perl zip
Recommended packages:
  gnupg libcgi-fast-perl 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
The following NEW packages will be installed:
  ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl
  libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl
  libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl
  libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl
  libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl
  libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl
  libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl
  libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl
  libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl
  libemail-address-xs-perl libencode-locale-perl libexception-class-perl
  libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl
  libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl
  libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl
  libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl
  libimport-into-perl libio-html-perl libio-interactive-perl
  libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl
  libiterator-perl libiterator-util-perl libjson-maybexs-perl
  liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl
  liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2
  libmarkdown2 libmldbm-perl libmodule-implementation-perl
  libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl
  libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl
  libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl
  libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl
  libparams-util-perl libpath-tiny-perl libperlio-gzip-perl
  libperlio-utf8-strict-perl libproc-processtable-perl
  libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl
  libsereal-encoder-perl libsort-versions-perl libstrictures-perl
  libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl
  libsub-install-perl libsub-name-perl libsub-quote-perl
  libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl
  libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl
  libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl
  liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl
  libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2
  libyaml-libyaml-perl lintian lzop openssl patchutils perl-openssl-defaults
  plzip sbuild-build-depends-lintian-dummy:amd64 t1utils unzip
0 upgraded, 122 newly installed, 0 to remove and 0 not upgraded.
Need to get 12.3 MB of archives.
After this operation, 50.9 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [844 B]
Get:2 http://mirror.einval.org/debian unstable/main arm64 openssl arm64 3.2.1-3 [1324 kB]
Get:3 http://mirror.einval.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB]
Get:4 http://mirror.einval.org/debian unstable/main arm64 diffstat arm64 1.66-1 [31.6 kB]
Get:5 http://mirror.einval.org/debian unstable/main arm64 libassuan0 arm64 2.5.6-1 [47.3 kB]
Get:6 http://mirror.einval.org/debian unstable/main arm64 gpgconf arm64 2.2.40-3 [558 kB]
Get:7 http://mirror.einval.org/debian unstable/main arm64 gpg arm64 2.2.40-3 [903 kB]
Get:8 http://mirror.einval.org/debian unstable/main arm64 iso-codes all 4.16.0-1 [2936 kB]
Get:9 http://mirror.einval.org/debian unstable/main arm64 libaliased-perl all 0.34-3 [13.5 kB]
Get:10 http://mirror.einval.org/debian unstable/main arm64 libapt-pkg-perl arm64 0.1.40+b5 [63.8 kB]
Get:11 http://mirror.einval.org/debian unstable/main arm64 libb-hooks-op-check-perl arm64 0.22-3+b1 [10.6 kB]
Get:12 http://mirror.einval.org/debian unstable/main arm64 libdynaloader-functions-perl all 0.003-3 [12.7 kB]
Get:13 http://mirror.einval.org/debian unstable/main arm64 libdevel-callchecker-perl arm64 0.008-2+b2 [15.2 kB]
Get:14 http://mirror.einval.org/debian unstable/main arm64 libparams-classify-perl arm64 0.015-2+b3 [22.3 kB]
Get:15 http://mirror.einval.org/debian unstable/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get:16 http://mirror.einval.org/debian unstable/main arm64 libtry-tiny-perl all 0.31-2 [22.6 kB]
Get:17 http://mirror.einval.org/debian unstable/main arm64 libmodule-implementation-perl all 0.09-2 [12.6 kB]
Get:18 http://mirror.einval.org/debian unstable/main arm64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B]
Get:19 http://mirror.einval.org/debian unstable/main arm64 libvariable-magic-perl arm64 0.64-1 [43.5 kB]
Get:20 http://mirror.einval.org/debian unstable/main arm64 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB]
Get:21 http://mirror.einval.org/debian unstable/main arm64 libberkeleydb-perl arm64 0.64-2+b3 [120 kB]
Get:22 http://mirror.einval.org/debian unstable/main arm64 libcapture-tiny-perl all 0.48-2 [24.6 kB]
Get:23 http://mirror.einval.org/debian unstable/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB]
Get:24 http://mirror.einval.org/debian unstable/main arm64 liburi-perl all 5.28-1 [98.6 kB]
Get:25 http://mirror.einval.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.82-1 [96.9 kB]
Get:26 http://mirror.einval.org/debian unstable/main arm64 libcgi-pm-perl all 4.64-1 [217 kB]
Get:27 http://mirror.einval.org/debian unstable/main arm64 libclass-data-inheritable-perl all 0.08-3 [8588 B]
Get:28 http://mirror.einval.org/debian unstable/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB]
Get:29 http://mirror.einval.org/debian unstable/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b3 [35.2 kB]
Get:30 http://mirror.einval.org/debian unstable/main arm64 libclone-perl arm64 0.46-1+b2 [13.6 kB]
Get:31 http://mirror.einval.org/debian unstable/main arm64 libconfig-tiny-perl all 2.30-1 [18.9 kB]
Get:32 http://mirror.einval.org/debian unstable/main arm64 libparams-util-perl arm64 1.102-3 [23.4 kB]
Get:33 http://mirror.einval.org/debian unstable/main arm64 libsub-install-perl all 0.929-1 [10.5 kB]
Get:34 http://mirror.einval.org/debian unstable/main arm64 libdata-optlist-perl all 0.114-1 [10.6 kB]
Get:35 http://mirror.einval.org/debian unstable/main arm64 libsub-exporter-perl all 0.990-1 [50.6 kB]
Get:36 http://mirror.einval.org/debian unstable/main arm64 libconst-fast-perl all 0.014-2 [8792 B]
Get:37 http://mirror.einval.org/debian unstable/main arm64 libcpanel-json-xs-perl arm64 4.37-1+b2 [127 kB]
Get:38 http://mirror.einval.org/debian unstable/main arm64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB]
Get:39 http://mirror.einval.org/debian unstable/main arm64 libexception-class-perl all 1.45-1 [34.6 kB]
Get:40 http://mirror.einval.org/debian unstable/main arm64 libiterator-perl all 0.03+ds1-2 [18.8 kB]
Get:41 http://mirror.einval.org/debian unstable/main arm64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB]
Get:42 http://mirror.einval.org/debian unstable/main arm64 libdata-dpath-perl all 0.59-1 [43.6 kB]
Get:43 http://mirror.einval.org/debian unstable/main arm64 libdata-messagepack-perl arm64 1.02-1+b3 [31.2 kB]
Get:44 http://mirror.einval.org/debian unstable/main arm64 libnet-domain-tld-perl all 1.75-3 [31.9 kB]
Get:45 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB]
Get:46 http://mirror.einval.org/debian unstable/main arm64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB]
Get:47 http://mirror.einval.org/debian unstable/main arm64 libnet-netmask-perl all 2.0002-2 [28.6 kB]
Get:48 http://mirror.einval.org/debian unstable/main arm64 libnetaddr-ip-perl arm64 4.079+dfsg-2+b3 [97.6 kB]
Get:49 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-ip-perl all 0.31-1 [20.6 kB]
Get:50 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-uri-perl all 0.07-3 [11.0 kB]
Get:51 http://mirror.einval.org/debian unstable/main arm64 libdevel-size-perl arm64 0.83-2+b3 [24.1 kB]
Get:52 http://mirror.einval.org/debian unstable/main arm64 libemail-address-xs-perl arm64 1.05-1+b3 [28.3 kB]
Get:53 http://mirror.einval.org/debian unstable/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB]
Get:54 http://mirror.einval.org/debian unstable/main arm64 libipc-system-simple-perl all 1.30-2 [26.8 kB]
Get:55 http://mirror.einval.org/debian unstable/main arm64 libfile-basedir-perl all 0.09-2 [15.1 kB]
Get:56 http://mirror.einval.org/debian unstable/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB]
Get:57 http://mirror.einval.org/debian unstable/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB]
Get:58 http://mirror.einval.org/debian unstable/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB]
Get:59 http://mirror.einval.org/debian unstable/main arm64 libfont-ttf-perl all 1.06-2 [318 kB]
Get:60 http://mirror.einval.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB]
Get:61 http://mirror.einval.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB]
Get:62 http://mirror.einval.org/debian unstable/main arm64 libhttp-message-perl all 6.45-1 [82.0 kB]
Get:63 http://mirror.einval.org/debian unstable/main arm64 libhtml-form-perl all 6.11-1 [33.1 kB]
Get:64 http://mirror.einval.org/debian unstable/main arm64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB]
Get:65 http://mirror.einval.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB]
Get:66 http://mirror.einval.org/debian unstable/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB]
Get:67 http://mirror.einval.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB]
Get:68 http://mirror.einval.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b2 [6712 B]
Get:69 http://mirror.einval.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.94-1+b1 [328 kB]
Get:70 http://mirror.einval.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.085-1 [218 kB]
Get:71 http://mirror.einval.org/debian unstable/main arm64 libnet-http-perl all 6.23-1 [23.9 kB]
Get:72 http://mirror.einval.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB]
Get:73 http://mirror.einval.org/debian unstable/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB]
Get:74 http://mirror.einval.org/debian unstable/main arm64 libwww-perl all 6.77-1 [183 kB]
Get:75 http://mirror.einval.org/debian unstable/main arm64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB]
Get:76 http://mirror.einval.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB]
Get:77 http://mirror.einval.org/debian unstable/main arm64 libio-interactive-perl all 1.025-1 [11.4 kB]
Get:78 http://mirror.einval.org/debian unstable/main arm64 libipc-run3-perl all 0.049-1 [31.5 kB]
Get:79 http://mirror.einval.org/debian unstable/main arm64 libjson-maybexs-perl all 1.004005-1 [12.9 kB]
Get:80 http://mirror.einval.org/debian unstable/main arm64 liblist-compare-perl all 0.55-2 [65.7 kB]
Get:81 http://mirror.einval.org/debian unstable/main arm64 liblist-someutils-perl all 0.59-1 [37.1 kB]
Get:82 http://mirror.einval.org/debian unstable/main arm64 liblist-utilsby-perl all 0.12-2 [15.5 kB]
Get:83 http://mirror.einval.org/debian unstable/main arm64 liblz1 arm64 1.14-1 [37.7 kB]
Get:84 http://mirror.einval.org/debian unstable/main arm64 liblzo2-2 arm64 2.10-2+b1 [49.2 kB]
Get:85 http://mirror.einval.org/debian unstable/main arm64 libmarkdown2 arm64 2.2.7-2+b1 [33.2 kB]
Get:86 http://mirror.einval.org/debian unstable/main arm64 libmldbm-perl all 2.05-4 [16.8 kB]
Get:87 http://mirror.einval.org/debian unstable/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB]
Get:88 http://mirror.einval.org/debian unstable/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB]
Get:89 http://mirror.einval.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB]
Get:90 http://mirror.einval.org/debian unstable/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB]
Get:91 http://mirror.einval.org/debian unstable/main arm64 libmoox-aliases-perl all 0.001006-2 [7156 B]
Get:92 http://mirror.einval.org/debian unstable/main arm64 libmouse-perl arm64 2.5.10-1+b5 [141 kB]
Get:93 http://mirror.einval.org/debian unstable/main arm64 libpackage-stash-perl all 0.40-1 [22.0 kB]
Get:94 http://mirror.einval.org/debian unstable/main arm64 libsub-identify-perl arm64 0.14-3+b2 [11.2 kB]
Get:95 http://mirror.einval.org/debian unstable/main arm64 libsub-name-perl arm64 0.27-1+b2 [12.3 kB]
Get:96 http://mirror.einval.org/debian unstable/main arm64 libnamespace-clean-perl all 0.27-2 [17.8 kB]
Get:97 http://mirror.einval.org/debian unstable/main arm64 libpath-tiny-perl all 0.144-1 [56.4 kB]
Get:98 http://mirror.einval.org/debian unstable/main arm64 libperlio-gzip-perl arm64 0.20-1+b3 [17.4 kB]
Get:99 http://mirror.einval.org/debian unstable/main arm64 libperlio-utf8-strict-perl arm64 0.010-1+b2 [11.4 kB]
Get:100 http://mirror.einval.org/debian unstable/main arm64 libproc-processtable-perl arm64 0.636-1+b2 [41.6 kB]
Get:101 http://mirror.einval.org/debian unstable/main arm64 libregexp-wildcards-perl all 1.05-3 [14.1 kB]
Get:102 http://mirror.einval.org/debian unstable/main arm64 libsereal-decoder-perl arm64 5.004+ds-1+b2 [95.4 kB]
Get:103 http://mirror.einval.org/debian unstable/main arm64 libsereal-encoder-perl arm64 5.004+ds-1+b2 [97.6 kB]
Get:104 http://mirror.einval.org/debian unstable/main arm64 libsort-versions-perl all 1.62-3 [8928 B]
Get:105 http://mirror.einval.org/debian unstable/main arm64 libxs-parse-keyword-perl arm64 0.39-1+b2 [56.3 kB]
Get:106 http://mirror.einval.org/debian unstable/main arm64 libsyntax-keyword-try-perl arm64 0.29-2 [26.6 kB]
Get:107 http://mirror.einval.org/debian unstable/main arm64 libterm-readkey-perl arm64 2.38-2+b3 [24.4 kB]
Get:108 http://mirror.einval.org/debian unstable/main arm64 libtext-levenshteinxs-perl arm64 0.03-5+b3 [8680 B]
Get:109 http://mirror.einval.org/debian unstable/main arm64 libtext-markdown-discount-perl arm64 0.16-1+b2 [13.1 kB]
Get:110 http://mirror.einval.org/debian unstable/main arm64 libtext-xslate-perl arm64 3.5.9-2 [171 kB]
Get:111 http://mirror.einval.org/debian unstable/main arm64 libtime-duration-perl all 1.21-2 [13.1 kB]
Get:112 http://mirror.einval.org/debian unstable/main arm64 libtime-moment-perl arm64 0.44-2+b3 [72.2 kB]
Get:113 http://mirror.einval.org/debian unstable/main arm64 libunicode-utf8-perl arm64 0.62-2+b2 [19.9 kB]
Get:114 http://mirror.einval.org/debian unstable/main arm64 libwww-mechanize-perl all 2.18-1 [114 kB]
Get:115 http://mirror.einval.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-1 [50.4 kB]
Get:116 http://mirror.einval.org/debian unstable/main arm64 libyaml-libyaml-perl arm64 0.89+ds-1+b1 [33.2 kB]
Get:117 http://mirror.einval.org/debian unstable/main arm64 plzip arm64 1.11-1 [58.8 kB]
Get:118 http://mirror.einval.org/debian unstable/main arm64 lzop arm64 1.04-2 [82.8 kB]
Get:119 http://mirror.einval.org/debian unstable/main arm64 patchutils arm64 0.4.2-1 [73.5 kB]
Get:120 http://mirror.einval.org/debian unstable/main arm64 t1utils arm64 1.41-4 [59.8 kB]
Get:121 http://mirror.einval.org/debian unstable/main arm64 unzip arm64 6.0-28 [157 kB]
Get:122 http://mirror.einval.org/debian unstable/main arm64 lintian all 2.117.0 [1052 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 12.3 MB in 0s (50.3 MB/s)
Selecting previously unselected package openssl.
(Reading database ... 27285 files and directories currently installed.)
Preparing to unpack .../000-openssl_3.2.1-3_arm64.deb ...
Unpacking openssl (3.2.1-3) ...
Selecting previously unselected package ca-certificates.
Preparing to unpack .../001-ca-certificates_20240203_all.deb ...
Unpacking ca-certificates (20240203) ...
Selecting previously unselected package diffstat.
Preparing to unpack .../002-diffstat_1.66-1_arm64.deb ...
Unpacking diffstat (1.66-1) ...
Selecting previously unselected package libassuan0:arm64.
Preparing to unpack .../003-libassuan0_2.5.6-1_arm64.deb ...
Unpacking libassuan0:arm64 (2.5.6-1) ...
Selecting previously unselected package gpgconf.
Preparing to unpack .../004-gpgconf_2.2.40-3_arm64.deb ...
Unpacking gpgconf (2.2.40-3) ...
Selecting previously unselected package gpg.
Preparing to unpack .../005-gpg_2.2.40-3_arm64.deb ...
Unpacking gpg (2.2.40-3) ...
Selecting previously unselected package iso-codes.
Preparing to unpack .../006-iso-codes_4.16.0-1_all.deb ...
Unpacking iso-codes (4.16.0-1) ...
Selecting previously unselected package libaliased-perl.
Preparing to unpack .../007-libaliased-perl_0.34-3_all.deb ...
Unpacking libaliased-perl (0.34-3) ...
Selecting previously unselected package libapt-pkg-perl.
Preparing to unpack .../008-libapt-pkg-perl_0.1.40+b5_arm64.deb ...
Unpacking libapt-pkg-perl (0.1.40+b5) ...
Selecting previously unselected package libb-hooks-op-check-perl:arm64.
Preparing to unpack .../009-libb-hooks-op-check-perl_0.22-3+b1_arm64.deb ...
Unpacking libb-hooks-op-check-perl:arm64 (0.22-3+b1) ...
Selecting previously unselected package libdynaloader-functions-perl.
Preparing to unpack .../010-libdynaloader-functions-perl_0.003-3_all.deb ...
Unpacking libdynaloader-functions-perl (0.003-3) ...
Selecting previously unselected package libdevel-callchecker-perl:arm64.
Preparing to unpack .../011-libdevel-callchecker-perl_0.008-2+b2_arm64.deb ...
Unpacking libdevel-callchecker-perl:arm64 (0.008-2+b2) ...
Selecting previously unselected package libparams-classify-perl:arm64.
Preparing to unpack .../012-libparams-classify-perl_0.015-2+b3_arm64.deb ...
Unpacking libparams-classify-perl:arm64 (0.015-2+b3) ...
Selecting previously unselected package libmodule-runtime-perl.
Preparing to unpack .../013-libmodule-runtime-perl_0.016-2_all.deb ...
Unpacking libmodule-runtime-perl (0.016-2) ...
Selecting previously unselected package libtry-tiny-perl.
Preparing to unpack .../014-libtry-tiny-perl_0.31-2_all.deb ...
Unpacking libtry-tiny-perl (0.31-2) ...
Selecting previously unselected package libmodule-implementation-perl.
Preparing to unpack .../015-libmodule-implementation-perl_0.09-2_all.deb ...
Unpacking libmodule-implementation-perl (0.09-2) ...
Selecting previously unselected package libsub-exporter-progressive-perl.
Preparing to unpack .../016-libsub-exporter-progressive-perl_0.001013-3_all.deb ...
Unpacking libsub-exporter-progressive-perl (0.001013-3) ...
Selecting previously unselected package libvariable-magic-perl.
Preparing to unpack .../017-libvariable-magic-perl_0.64-1_arm64.deb ...
Unpacking libvariable-magic-perl (0.64-1) ...
Selecting previously unselected package libb-hooks-endofscope-perl.
Preparing to unpack .../018-libb-hooks-endofscope-perl_0.28-1_all.deb ...
Unpacking libb-hooks-endofscope-perl (0.28-1) ...
Selecting previously unselected package libberkeleydb-perl:arm64.
Preparing to unpack .../019-libberkeleydb-perl_0.64-2+b3_arm64.deb ...
Unpacking libberkeleydb-perl:arm64 (0.64-2+b3) ...
Selecting previously unselected package libcapture-tiny-perl.
Preparing to unpack .../020-libcapture-tiny-perl_0.48-2_all.deb ...
Unpacking libcapture-tiny-perl (0.48-2) ...
Selecting previously unselected package libhtml-tagset-perl.
Preparing to unpack .../021-libhtml-tagset-perl_3.24-1_all.deb ...
Unpacking libhtml-tagset-perl (3.24-1) ...
Selecting previously unselected package liburi-perl.
Preparing to unpack .../022-liburi-perl_5.28-1_all.deb ...
Unpacking liburi-perl (5.28-1) ...
Selecting previously unselected package libhtml-parser-perl:arm64.
Preparing to unpack .../023-libhtml-parser-perl_3.82-1_arm64.deb ...
Unpacking libhtml-parser-perl:arm64 (3.82-1) ...
Selecting previously unselected package libcgi-pm-perl.
Preparing to unpack .../024-libcgi-pm-perl_4.64-1_all.deb ...
Unpacking libcgi-pm-perl (4.64-1) ...
Selecting previously unselected package libclass-data-inheritable-perl.
Preparing to unpack .../025-libclass-data-inheritable-perl_0.08-3_all.deb ...
Unpacking libclass-data-inheritable-perl (0.08-3) ...
Selecting previously unselected package libclass-method-modifiers-perl.
Preparing to unpack .../026-libclass-method-modifiers-perl_2.15-1_all.deb ...
Unpacking libclass-method-modifiers-perl (2.15-1) ...
Selecting previously unselected package libclass-xsaccessor-perl.
Preparing to unpack .../027-libclass-xsaccessor-perl_1.19-4+b3_arm64.deb ...
Unpacking libclass-xsaccessor-perl (1.19-4+b3) ...
Selecting previously unselected package libclone-perl:arm64.
Preparing to unpack .../028-libclone-perl_0.46-1+b2_arm64.deb ...
Unpacking libclone-perl:arm64 (0.46-1+b2) ...
Selecting previously unselected package libconfig-tiny-perl.
Preparing to unpack .../029-libconfig-tiny-perl_2.30-1_all.deb ...
Unpacking libconfig-tiny-perl (2.30-1) ...
Selecting previously unselected package libparams-util-perl.
Preparing to unpack .../030-libparams-util-perl_1.102-3_arm64.deb ...
Unpacking libparams-util-perl (1.102-3) ...
Selecting previously unselected package libsub-install-perl.
Preparing to unpack .../031-libsub-install-perl_0.929-1_all.deb ...
Unpacking libsub-install-perl (0.929-1) ...
Selecting previously unselected package libdata-optlist-perl.
Preparing to unpack .../032-libdata-optlist-perl_0.114-1_all.deb ...
Unpacking libdata-optlist-perl (0.114-1) ...
Selecting previously unselected package libsub-exporter-perl.
Preparing to unpack .../033-libsub-exporter-perl_0.990-1_all.deb ...
Unpacking libsub-exporter-perl (0.990-1) ...
Selecting previously unselected package libconst-fast-perl.
Preparing to unpack .../034-libconst-fast-perl_0.014-2_all.deb ...
Unpacking libconst-fast-perl (0.014-2) ...
Selecting previously unselected package libcpanel-json-xs-perl:arm64.
Preparing to unpack .../035-libcpanel-json-xs-perl_4.37-1+b2_arm64.deb ...
Unpacking libcpanel-json-xs-perl:arm64 (4.37-1+b2) ...
Selecting previously unselected package libdevel-stacktrace-perl.
Preparing to unpack .../036-libdevel-stacktrace-perl_2.0500-1_all.deb ...
Unpacking libdevel-stacktrace-perl (2.0500-1) ...
Selecting previously unselected package libexception-class-perl.
Preparing to unpack .../037-libexception-class-perl_1.45-1_all.deb ...
Unpacking libexception-class-perl (1.45-1) ...
Selecting previously unselected package libiterator-perl.
Preparing to unpack .../038-libiterator-perl_0.03+ds1-2_all.deb ...
Unpacking libiterator-perl (0.03+ds1-2) ...
Selecting previously unselected package libiterator-util-perl.
Preparing to unpack .../039-libiterator-util-perl_0.02+ds1-2_all.deb ...
Unpacking libiterator-util-perl (0.02+ds1-2) ...
Selecting previously unselected package libdata-dpath-perl.
Preparing to unpack .../040-libdata-dpath-perl_0.59-1_all.deb ...
Unpacking libdata-dpath-perl (0.59-1) ...
Selecting previously unselected package libdata-messagepack-perl.
Preparing to unpack .../041-libdata-messagepack-perl_1.02-1+b3_arm64.deb ...
Unpacking libdata-messagepack-perl (1.02-1+b3) ...
Selecting previously unselected package libnet-domain-tld-perl.
Preparing to unpack .../042-libnet-domain-tld-perl_1.75-3_all.deb ...
Unpacking libnet-domain-tld-perl (1.75-3) ...
Selecting previously unselected package libdata-validate-domain-perl.
Preparing to unpack .../043-libdata-validate-domain-perl_0.10-1.1_all.deb ...
Unpacking libdata-validate-domain-perl (0.10-1.1) ...
Selecting previously unselected package libnet-ipv6addr-perl.
Preparing to unpack .../044-libnet-ipv6addr-perl_1.02-1_all.deb ...
Unpacking libnet-ipv6addr-perl (1.02-1) ...
Selecting previously unselected package libnet-netmask-perl.
Preparing to unpack .../045-libnet-netmask-perl_2.0002-2_all.deb ...
Unpacking libnet-netmask-perl (2.0002-2) ...
Selecting previously unselected package libnetaddr-ip-perl.
Preparing to unpack .../046-libnetaddr-ip-perl_4.079+dfsg-2+b3_arm64.deb ...
Unpacking libnetaddr-ip-perl (4.079+dfsg-2+b3) ...
Selecting previously unselected package libdata-validate-ip-perl.
Preparing to unpack .../047-libdata-validate-ip-perl_0.31-1_all.deb ...
Unpacking libdata-validate-ip-perl (0.31-1) ...
Selecting previously unselected package libdata-validate-uri-perl.
Preparing to unpack .../048-libdata-validate-uri-perl_0.07-3_all.deb ...
Unpacking libdata-validate-uri-perl (0.07-3) ...
Selecting previously unselected package libdevel-size-perl.
Preparing to unpack .../049-libdevel-size-perl_0.83-2+b3_arm64.deb ...
Unpacking libdevel-size-perl (0.83-2+b3) ...
Selecting previously unselected package libemail-address-xs-perl.
Preparing to unpack .../050-libemail-address-xs-perl_1.05-1+b3_arm64.deb ...
Unpacking libemail-address-xs-perl (1.05-1+b3) ...
Selecting previously unselected package libencode-locale-perl.
Preparing to unpack .../051-libencode-locale-perl_1.05-3_all.deb ...
Unpacking libencode-locale-perl (1.05-3) ...
Selecting previously unselected package libipc-system-simple-perl.
Preparing to unpack .../052-libipc-system-simple-perl_1.30-2_all.deb ...
Unpacking libipc-system-simple-perl (1.30-2) ...
Selecting previously unselected package libfile-basedir-perl.
Preparing to unpack .../053-libfile-basedir-perl_0.09-2_all.deb ...
Unpacking libfile-basedir-perl (0.09-2) ...
Selecting previously unselected package libtimedate-perl.
Preparing to unpack .../054-libtimedate-perl_2.3300-2_all.deb ...
Unpacking libtimedate-perl (2.3300-2) ...
Selecting previously unselected package libhttp-date-perl.
Preparing to unpack .../055-libhttp-date-perl_6.06-1_all.deb ...
Unpacking libhttp-date-perl (6.06-1) ...
Selecting previously unselected package libfile-listing-perl.
Preparing to unpack .../056-libfile-listing-perl_6.16-1_all.deb ...
Unpacking libfile-listing-perl (6.16-1) ...
Selecting previously unselected package libfont-ttf-perl.
Preparing to unpack .../057-libfont-ttf-perl_1.06-2_all.deb ...
Unpacking libfont-ttf-perl (1.06-2) ...
Selecting previously unselected package libio-html-perl.
Preparing to unpack .../058-libio-html-perl_1.004-3_all.deb ...
Unpacking libio-html-perl (1.004-3) ...
Selecting previously unselected package liblwp-mediatypes-perl.
Preparing to unpack .../059-liblwp-mediatypes-perl_6.04-2_all.deb ...
Unpacking liblwp-mediatypes-perl (6.04-2) ...
Selecting previously unselected package libhttp-message-perl.
Preparing to unpack .../060-libhttp-message-perl_6.45-1_all.deb ...
Unpacking libhttp-message-perl (6.45-1) ...
Selecting previously unselected package libhtml-form-perl.
Preparing to unpack .../061-libhtml-form-perl_6.11-1_all.deb ...
Unpacking libhtml-form-perl (6.11-1) ...
Selecting previously unselected package libhtml-html5-entities-perl.
Preparing to unpack .../062-libhtml-html5-entities-perl_0.004-3_all.deb ...
Unpacking libhtml-html5-entities-perl (0.004-3) ...
Selecting previously unselected package libhtml-tree-perl.
Preparing to unpack .../063-libhtml-tree-perl_5.07-3_all.deb ...
Unpacking libhtml-tree-perl (5.07-3) ...
Selecting previously unselected package libhttp-cookies-perl.
Preparing to unpack .../064-libhttp-cookies-perl_6.11-1_all.deb ...
Unpacking libhttp-cookies-perl (6.11-1) ...
Selecting previously unselected package libhttp-negotiate-perl.
Preparing to unpack .../065-libhttp-negotiate-perl_6.01-2_all.deb ...
Unpacking libhttp-negotiate-perl (6.01-2) ...
Selecting previously unselected package perl-openssl-defaults:arm64.
Preparing to unpack .../066-perl-openssl-defaults_7+b2_arm64.deb ...
Unpacking perl-openssl-defaults:arm64 (7+b2) ...
Selecting previously unselected package libnet-ssleay-perl:arm64.
Preparing to unpack .../067-libnet-ssleay-perl_1.94-1+b1_arm64.deb ...
Unpacking libnet-ssleay-perl:arm64 (1.94-1+b1) ...
Selecting previously unselected package libio-socket-ssl-perl.
Preparing to unpack .../068-libio-socket-ssl-perl_2.085-1_all.deb ...
Unpacking libio-socket-ssl-perl (2.085-1) ...
Selecting previously unselected package libnet-http-perl.
Preparing to unpack .../069-libnet-http-perl_6.23-1_all.deb ...
Unpacking libnet-http-perl (6.23-1) ...
Selecting previously unselected package liblwp-protocol-https-perl.
Preparing to unpack .../070-liblwp-protocol-https-perl_6.14-1_all.deb ...
Unpacking liblwp-protocol-https-perl (6.14-1) ...
Selecting previously unselected package libwww-robotrules-perl.
Preparing to unpack .../071-libwww-robotrules-perl_6.02-1_all.deb ...
Unpacking libwww-robotrules-perl (6.02-1) ...
Selecting previously unselected package libwww-perl.
Preparing to unpack .../072-libwww-perl_6.77-1_all.deb ...
Unpacking libwww-perl (6.77-1) ...
Selecting previously unselected package libhtml-tokeparser-simple-perl.
Preparing to unpack .../073-libhtml-tokeparser-simple-perl_3.16-4_all.deb ...
Unpacking libhtml-tokeparser-simple-perl (3.16-4) ...
Selecting previously unselected package libimport-into-perl.
Preparing to unpack .../074-libimport-into-perl_1.002005-2_all.deb ...
Unpacking libimport-into-perl (1.002005-2) ...
Selecting previously unselected package libio-interactive-perl.
Preparing to unpack .../075-libio-interactive-perl_1.025-1_all.deb ...
Unpacking libio-interactive-perl (1.025-1) ...
Selecting previously unselected package libipc-run3-perl.
Preparing to unpack .../076-libipc-run3-perl_0.049-1_all.deb ...
Unpacking libipc-run3-perl (0.049-1) ...
Selecting previously unselected package libjson-maybexs-perl.
Preparing to unpack .../077-libjson-maybexs-perl_1.004005-1_all.deb ...
Unpacking libjson-maybexs-perl (1.004005-1) ...
Selecting previously unselected package liblist-compare-perl.
Preparing to unpack .../078-liblist-compare-perl_0.55-2_all.deb ...
Unpacking liblist-compare-perl (0.55-2) ...
Selecting previously unselected package liblist-someutils-perl.
Preparing to unpack .../079-liblist-someutils-perl_0.59-1_all.deb ...
Unpacking liblist-someutils-perl (0.59-1) ...
Selecting previously unselected package liblist-utilsby-perl.
Preparing to unpack .../080-liblist-utilsby-perl_0.12-2_all.deb ...
Unpacking liblist-utilsby-perl (0.12-2) ...
Selecting previously unselected package liblz1:arm64.
Preparing to unpack .../081-liblz1_1.14-1_arm64.deb ...
Unpacking liblz1:arm64 (1.14-1) ...
Selecting previously unselected package liblzo2-2:arm64.
Preparing to unpack .../082-liblzo2-2_2.10-2+b1_arm64.deb ...
Unpacking liblzo2-2:arm64 (2.10-2+b1) ...
Selecting previously unselected package libmarkdown2:arm64.
Preparing to unpack .../083-libmarkdown2_2.2.7-2+b1_arm64.deb ...
Unpacking libmarkdown2:arm64 (2.2.7-2+b1) ...
Selecting previously unselected package libmldbm-perl.
Preparing to unpack .../084-libmldbm-perl_2.05-4_all.deb ...
Unpacking libmldbm-perl (2.05-4) ...
Selecting previously unselected package librole-tiny-perl.
Preparing to unpack .../085-librole-tiny-perl_2.002004-1_all.deb ...
Unpacking librole-tiny-perl (2.002004-1) ...
Selecting previously unselected package libsub-quote-perl.
Preparing to unpack .../086-libsub-quote-perl_2.006008-1_all.deb ...
Unpacking libsub-quote-perl (2.006008-1) ...
Selecting previously unselected package libmoo-perl.
Preparing to unpack .../087-libmoo-perl_2.005005-1_all.deb ...
Unpacking libmoo-perl (2.005005-1) ...
Selecting previously unselected package libstrictures-perl.
Preparing to unpack .../088-libstrictures-perl_2.000006-1_all.deb ...
Unpacking libstrictures-perl (2.000006-1) ...
Selecting previously unselected package libmoox-aliases-perl.
Preparing to unpack .../089-libmoox-aliases-perl_0.001006-2_all.deb ...
Unpacking libmoox-aliases-perl (0.001006-2) ...
Selecting previously unselected package libmouse-perl.
Preparing to unpack .../090-libmouse-perl_2.5.10-1+b5_arm64.deb ...
Unpacking libmouse-perl (2.5.10-1+b5) ...
Selecting previously unselected package libpackage-stash-perl.
Preparing to unpack .../091-libpackage-stash-perl_0.40-1_all.deb ...
Unpacking libpackage-stash-perl (0.40-1) ...
Selecting previously unselected package libsub-identify-perl.
Preparing to unpack .../092-libsub-identify-perl_0.14-3+b2_arm64.deb ...
Unpacking libsub-identify-perl (0.14-3+b2) ...
Selecting previously unselected package libsub-name-perl:arm64.
Preparing to unpack .../093-libsub-name-perl_0.27-1+b2_arm64.deb ...
Unpacking libsub-name-perl:arm64 (0.27-1+b2) ...
Selecting previously unselected package libnamespace-clean-perl.
Preparing to unpack .../094-libnamespace-clean-perl_0.27-2_all.deb ...
Unpacking libnamespace-clean-perl (0.27-2) ...
Selecting previously unselected package libpath-tiny-perl.
Preparing to unpack .../095-libpath-tiny-perl_0.144-1_all.deb ...
Unpacking libpath-tiny-perl (0.144-1) ...
Selecting previously unselected package libperlio-gzip-perl.
Preparing to unpack .../096-libperlio-gzip-perl_0.20-1+b3_arm64.deb ...
Unpacking libperlio-gzip-perl (0.20-1+b3) ...
Selecting previously unselected package libperlio-utf8-strict-perl.
Preparing to unpack .../097-libperlio-utf8-strict-perl_0.010-1+b2_arm64.deb ...
Unpacking libperlio-utf8-strict-perl (0.010-1+b2) ...
Selecting previously unselected package libproc-processtable-perl:arm64.
Preparing to unpack .../098-libproc-processtable-perl_0.636-1+b2_arm64.deb ...
Unpacking libproc-processtable-perl:arm64 (0.636-1+b2) ...
Selecting previously unselected package libregexp-wildcards-perl.
Preparing to unpack .../099-libregexp-wildcards-perl_1.05-3_all.deb ...
Unpacking libregexp-wildcards-perl (1.05-3) ...
Selecting previously unselected package libsereal-decoder-perl.
Preparing to unpack .../100-libsereal-decoder-perl_5.004+ds-1+b2_arm64.deb ...
Unpacking libsereal-decoder-perl (5.004+ds-1+b2) ...
Selecting previously unselected package libsereal-encoder-perl.
Preparing to unpack .../101-libsereal-encoder-perl_5.004+ds-1+b2_arm64.deb ...
Unpacking libsereal-encoder-perl (5.004+ds-1+b2) ...
Selecting previously unselected package libsort-versions-perl.
Preparing to unpack .../102-libsort-versions-perl_1.62-3_all.deb ...
Unpacking libsort-versions-perl (1.62-3) ...
Selecting previously unselected package libxs-parse-keyword-perl.
Preparing to unpack .../103-libxs-parse-keyword-perl_0.39-1+b2_arm64.deb ...
Unpacking libxs-parse-keyword-perl (0.39-1+b2) ...
Selecting previously unselected package libsyntax-keyword-try-perl.
Preparing to unpack .../104-libsyntax-keyword-try-perl_0.29-2_arm64.deb ...
Unpacking libsyntax-keyword-try-perl (0.29-2) ...
Selecting previously unselected package libterm-readkey-perl.
Preparing to unpack .../105-libterm-readkey-perl_2.38-2+b3_arm64.deb ...
Unpacking libterm-readkey-perl (2.38-2+b3) ...
Selecting previously unselected package libtext-levenshteinxs-perl.
Preparing to unpack .../106-libtext-levenshteinxs-perl_0.03-5+b3_arm64.deb ...
Unpacking libtext-levenshteinxs-perl (0.03-5+b3) ...
Selecting previously unselected package libtext-markdown-discount-perl.
Preparing to unpack .../107-libtext-markdown-discount-perl_0.16-1+b2_arm64.deb ...
Unpacking libtext-markdown-discount-perl (0.16-1+b2) ...
Selecting previously unselected package libtext-xslate-perl:arm64.
Preparing to unpack .../108-libtext-xslate-perl_3.5.9-2_arm64.deb ...
Unpacking libtext-xslate-perl:arm64 (3.5.9-2) ...
Selecting previously unselected package libtime-duration-perl.
Preparing to unpack .../109-libtime-duration-perl_1.21-2_all.deb ...
Unpacking libtime-duration-perl (1.21-2) ...
Selecting previously unselected package libtime-moment-perl.
Preparing to unpack .../110-libtime-moment-perl_0.44-2+b3_arm64.deb ...
Unpacking libtime-moment-perl (0.44-2+b3) ...
Selecting previously unselected package libunicode-utf8-perl.
Preparing to unpack .../111-libunicode-utf8-perl_0.62-2+b2_arm64.deb ...
Unpacking libunicode-utf8-perl (0.62-2+b2) ...
Selecting previously unselected package libwww-mechanize-perl.
Preparing to unpack .../112-libwww-mechanize-perl_2.18-1_all.deb ...
Unpacking libwww-mechanize-perl (2.18-1) ...
Selecting previously unselected package libyaml-0-2:arm64.
Preparing to unpack .../113-libyaml-0-2_0.2.5-1_arm64.deb ...
Unpacking libyaml-0-2:arm64 (0.2.5-1) ...
Selecting previously unselected package libyaml-libyaml-perl.
Preparing to unpack .../114-libyaml-libyaml-perl_0.89+ds-1+b1_arm64.deb ...
Unpacking libyaml-libyaml-perl (0.89+ds-1+b1) ...
Selecting previously unselected package plzip.
Preparing to unpack .../115-plzip_1.11-1_arm64.deb ...
Unpacking plzip (1.11-1) ...
Selecting previously unselected package lzop.
Preparing to unpack .../116-lzop_1.04-2_arm64.deb ...
Unpacking lzop (1.04-2) ...
Selecting previously unselected package patchutils.
Preparing to unpack .../117-patchutils_0.4.2-1_arm64.deb ...
Unpacking patchutils (0.4.2-1) ...
Selecting previously unselected package t1utils.
Preparing to unpack .../118-t1utils_1.41-4_arm64.deb ...
Unpacking t1utils (1.41-4) ...
Selecting previously unselected package unzip.
Preparing to unpack .../119-unzip_6.0-28_arm64.deb ...
Unpacking unzip (6.0-28) ...
Selecting previously unselected package lintian.
Preparing to unpack .../120-lintian_2.117.0_all.deb ...
Unpacking lintian (2.117.0) ...
Selecting previously unselected package sbuild-build-depends-lintian-dummy:amd64.
Preparing to unpack .../121-sbuild-build-depends-lintian-dummy_0.invalid.0_amd64.deb ...
Unpacking sbuild-build-depends-lintian-dummy:amd64 (0.invalid.0) ...
Setting up libapt-pkg-perl (0.1.40+b5) ...
Setting up liblz1:arm64 (1.14-1) ...
Setting up libberkeleydb-perl:arm64 (0.64-2+b3) ...
Setting up plzip (1.11-1) ...
update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode
update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode
update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode
Setting up libunicode-utf8-perl (0.62-2+b2) ...
Setting up libmouse-perl (2.5.10-1+b5) ...
Setting up libdata-messagepack-perl (1.02-1+b3) ...
Setting up libdynaloader-functions-perl (0.003-3) ...
Setting up libclass-method-modifiers-perl (2.15-1) ...
Setting up liblist-compare-perl (0.55-2) ...
Setting up libclone-perl:arm64 (0.46-1+b2) ...
Setting up libyaml-0-2:arm64 (0.2.5-1) ...
Setting up libsub-identify-perl (0.14-3+b2) ...
Setting up libcpanel-json-xs-perl:arm64 (4.37-1+b2) ...
Setting up libhtml-tagset-perl (3.24-1) ...
Setting up libdevel-size-perl (0.83-2+b3) ...
Setting up unzip (6.0-28) ...
Setting up liblwp-mediatypes-perl (6.04-2) ...
Setting up libyaml-libyaml-perl (0.89+ds-1+b1) ...
Setting up libio-interactive-perl (1.025-1) ...
Setting up libtry-tiny-perl (0.31-2) ...
Setting up perl-openssl-defaults:arm64 (7+b2) ...
Setting up libmldbm-perl (2.05-4) ...
Setting up liblzo2-2:arm64 (2.10-2+b1) ...
Setting up libtime-moment-perl (0.44-2+b3) ...
Setting up libencode-locale-perl (1.05-3) ...
Setting up libassuan0:arm64 (2.5.6-1) ...
Setting up libconfig-tiny-perl (2.30-1) ...
Setting up libsereal-encoder-perl (5.004+ds-1+b2) ...
Setting up liblist-utilsby-perl (0.12-2) ...
Setting up libnet-netmask-perl (2.0002-2) ...
Setting up libsub-install-perl (0.929-1) ...
Setting up patchutils (0.4.2-1) ...
Setting up libjson-maybexs-perl (1.004005-1) ...
Setting up libnetaddr-ip-perl (4.079+dfsg-2+b3) ...
Setting up libclass-data-inheritable-perl (0.08-3) ...
Setting up libxs-parse-keyword-perl (0.39-1+b2) ...
Setting up libipc-system-simple-perl (1.30-2) ...
Setting up libnet-domain-tld-perl (1.75-3) ...
Setting up libperlio-utf8-strict-perl (0.010-1+b2) ...
Setting up t1utils (1.41-4) ...
Setting up diffstat (1.66-1) ...
Setting up libvariable-magic-perl (0.64-1) ...
Setting up libio-html-perl (1.004-3) ...
Setting up libb-hooks-op-check-perl:arm64 (0.22-3+b1) ...
Setting up libparams-util-perl (1.102-3) ...
Setting up libtime-duration-perl (1.21-2) ...
Setting up libtext-xslate-perl:arm64 (3.5.9-2) ...
Setting up libsub-exporter-progressive-perl (0.001013-3) ...
Setting up libcapture-tiny-perl (0.48-2) ...
Setting up libtimedate-perl (2.3300-2) ...
Setting up libsub-name-perl:arm64 (0.27-1+b2) ...
Setting up libsyntax-keyword-try-perl (0.29-2) ...
Setting up libdata-validate-domain-perl (0.10-1.1) ...
Setting up libproc-processtable-perl:arm64 (0.636-1+b2) ...
Setting up libpath-tiny-perl (0.144-1) ...
Setting up lzop (1.04-2) ...
Setting up gpgconf (2.2.40-3) ...
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 libaliased-perl (0.34-3) ...
Setting up libstrictures-perl (2.000006-1) ...
Setting up libsub-quote-perl (2.006008-1) ...
Setting up libdevel-stacktrace-perl (2.0500-1) ...
Setting up libclass-xsaccessor-perl (1.19-4+b3) ...
Setting up libsort-versions-perl (1.62-3) ...
Setting up libterm-readkey-perl (2.38-2+b3) ...
Setting up libfont-ttf-perl (1.06-2) ...
Setting up openssl (3.2.1-3) ...
Setting up libtext-levenshteinxs-perl (0.03-5+b3) ...
Setting up libperlio-gzip-perl (0.20-1+b3) ...
Setting up libhtml-html5-entities-perl (0.004-3) ...
Setting up libsereal-decoder-perl (5.004+ds-1+b2) ...
Setting up libmarkdown2:arm64 (2.2.7-2+b1) ...
Setting up liburi-perl (5.28-1) ...
Setting up iso-codes (4.16.0-1) ...
Setting up libnet-ipv6addr-perl (1.02-1) ...
Setting up gpg (2.2.40-3) ...
Setting up libdata-validate-ip-perl (0.31-1) ...
Setting up libemail-address-xs-perl (1.05-1+b3) ...
Setting up libnet-ssleay-perl:arm64 (1.94-1+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 libnet-http-perl (6.23-1) ...
Setting up libtext-markdown-discount-perl (0.16-1+b2) ...
Setting up libexception-class-perl (1.45-1) ...
Setting up libdevel-callchecker-perl:arm64 (0.008-2+b2) ...
Setting up ca-certificates (20240203) ...
Updating certificates in /etc/ssl/certs...
146 added, 0 removed; done.
Setting up libdata-validate-uri-perl (0.07-3) ...
Setting up libdata-optlist-perl (0.114-1) ...
Setting up libwww-robotrules-perl (6.02-1) ...
Setting up libhtml-parser-perl:arm64 (3.82-1) ...
Setting up libio-socket-ssl-perl (2.085-1) ...
Setting up libsub-exporter-perl (0.990-1) ...
Setting up libhttp-message-perl (6.45-1) ...
Setting up libhtml-form-perl (6.11-1) ...
Setting up libiterator-perl (0.03+ds1-2) ...
Setting up libhttp-negotiate-perl (6.01-2) ...
Setting up libiterator-util-perl (0.02+ds1-2) ...
Setting up libhttp-cookies-perl (6.11-1) ...
Setting up libhtml-tree-perl (5.07-3) ...
Setting up libparams-classify-perl:arm64 (0.015-2+b3) ...
Setting up libcgi-pm-perl (4.64-1) ...
Setting up libmodule-runtime-perl (0.016-2) ...
Setting up libconst-fast-perl (0.014-2) ...
Setting up libdata-dpath-perl (0.59-1) ...
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 (0.28-1) ...
Setting up libnamespace-clean-perl (0.27-2) ...
Setting up libwww-perl (6.77-1) ...
Setting up libhtml-tokeparser-simple-perl (3.16-4) ...
Setting up libwww-mechanize-perl (2.18-1) ...
Setting up liblwp-protocol-https-perl (6.14-1) ...
Processing triggers for libc-bin (2.37-18) ...
Processing triggers for man-db (2.12.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Processing triggers for sgml-base (1.31) ...
Setting up lintian (2.117.0) ...
Setting up sbuild-build-depends-lintian-dummy:amd64 (0.invalid.0) ...
Processing triggers for ca-certificates (20240203) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Running lintian...

I: Lintian run was successful.

+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: arm64
Build Profiles: cross nocheck
Build Type: any
Build-Space: 666452
Build-Time: 2307
Distribution: unstable
Foreign Architectures: amd64
Host Architecture: amd64
Install-Time: 93
Job: macromoleculebuilder_4.0.0+dfsg-3.1
Lintian: pass
Machine Architecture: arm64
Package: macromoleculebuilder
Package-Time: 2450
Source-Version: 4.0.0+dfsg-3.1
Space: 666452
Status: successful
Version: 4.0.0+dfsg-3.1
--------------------------------------------------------------------------------
Finished at 2024-04-24T09:12:30Z
Build needed 00:40:50, 666452k disk space