sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley

+==============================================================================+
| macromoleculebuilder 4.0.0+dfsg-3.1 (armhf)  Thu, 04 Apr 2024 11:32:54 +0000 |
+==============================================================================+

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

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-d000b6dc-ffd1-4725-b905-7fbdcb38dd3a' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-e2cl23/resolver-ey5S4q' with '<<RESOLVERDIR>>'

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

Get:1 http://localhost:3142/debian sid InRelease [198 kB]
Get:2 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB]
Get:3 http://localhost:3142/debian sid/main amd64 Packages.diff/Index [63.6 kB]
Get:4 http://localhost:3142/debian sid/main Sources T-2024-04-04-0804.50-F-2024-04-04-0220.16.pdiff [24.7 kB]
Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2024-04-04-0804.50-F-2024-04-04-0220.16.pdiff [26.1 kB]
Get:4 http://localhost:3142/debian sid/main Sources T-2024-04-04-0804.50-F-2024-04-04-0220.16.pdiff [24.7 kB]
Get:6 http://localhost:3142/debian sid/main armhf Packages [9462 kB]
Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2024-04-04-0804.50-F-2024-04-04-0220.16.pdiff [26.1 kB]
Fetched 9839 kB in 3s (3546 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

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


Check APT
---------

Checking available source versions...

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

Reading package lists...
NOTICE: 'macromoleculebuilder' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/debichem-team/macromoleculebuilder.git
Please use:
git clone https://salsa.debian.org/debichem-team/macromoleculebuilder.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 2575 kB of source archives.
Get:1 http://localhost:3142/debian sid/main macromoleculebuilder 4.0.0+dfsg-3.1 (dsc) [2450 B]
Get:2 http://localhost:3142/debian sid/main macromoleculebuilder 4.0.0+dfsg-3.1 (tar) [2567 kB]
Get:3 http://localhost:3142/debian sid/main macromoleculebuilder 4.0.0+dfsg-3.1 (diff) [5704 B]
Fetched 2575 kB in 0s (32.1 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-e2cl23/macromoleculebuilder-4.0.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-e2cl23' 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:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf
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:amd64, fakeroot:amd64, crossbuild-essential-armhf:amd64, libc-dev:armhf, libstdc++-dev:armhf
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 (0 B/s)
Reading package lists...
Reading package lists...

Install main build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
Execute external solver...
The following package was automatically installed and is no longer required:
  mount
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
  asciidoc-base asciidoc-common autoconf automake autopoint autotools-dev
  binutils-arm-linux-gnueabihf bsdextrautils cmake cmake-data
  cpp-13-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config
  crossbuild-essential-armhf debhelper dh-autoreconf dh-strip-nondeterminism
  docbook-xml docbook-xsl dpkg-cross dwz fakeroot file freeglut3-dev:armhf
  g++-13-arm-linux-gnueabihf g++-arm-linux-gnueabihf
  gcc-13-arm-linux-gnueabihf gcc-13-arm-linux-gnueabihf-base gcc-13-base:armhf
  gcc-13-cross-base gcc-14-base:armhf gcc-14-cross-base
  gcc-arm-linux-gnueabihf gemmi-dev:armhf gettext gettext-base groff-base
  intltool-debian libarchive-zip-perl libarchive13t64 libasan8:armhf
  libasan8-armhf-cross libatomic1:armhf libatomic1-armhf-cross
  libblas-dev:armhf libblas3:armhf libbrotli1 libbsd0 libbsd0:armhf
  libc6:armhf libc6-armhf-cross libc6-dev:armhf libc6-dev-armhf-cross
  libcom-err2 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:armhf
  libcrypt1:armhf libcurl4t64 libdebhelper-perl libdebian-dpkgcross-perl
  libdrm-amdgpu1:armhf libdrm-common libdrm-nouveau2:armhf
  libdrm-radeon1:armhf libdrm2:armhf libedit2:armhf libegl-dev:armhf
  libegl-mesa0:armhf libegl1:armhf libelf1t64 libelf1t64:armhf libexpat1
  libexpat1:armhf libfakeroot libffi8:armhf libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libgbm1:armhf
  libgcc-13-dev:armhf libgcc-13-dev-armhf-cross libgcc-s1:armhf
  libgcc-s1-armhf-cross libgfortran5:armhf libgl-dev:armhf libgl1:armhf
  libgl1-mesa-dev:armhf libgl1-mesa-dri:armhf libglapi-mesa:armhf
  libgles-dev:armhf libgles1:armhf libgles2:armhf libglu1-mesa:armhf
  libglu1-mesa-dev:armhf libglut-dev:armhf libglut3.12:armhf
  libglvnd-core-dev:armhf libglvnd-dev:armhf libglvnd0:armhf libglx-dev:armhf
  libglx-mesa0:armhf libglx0:armhf libgomp1:armhf libgomp1-armhf-cross
  libgssapi-krb5-2 libice-dev:armhf libice6:armhf libicu72 libicu72:armhf
  libio-string-perl libjsoncpp25 libk5crypto3 libkeyutils1 libkrb5-3
  libkrb5support0 liblapack-dev:armhf liblapack3:armhf libldap-2.5-0
  libllvm17t64:armhf liblocale-gettext-perl liblzma5:armhf libmagic-mgc
  libmagic1t64 libmd0:armhf libncursesw6 libnghttp2-14 libopengl-dev:armhf
  libopengl0:armhf libopenmm-dev:armhf libopenmm8.0t64:armhf libpipeline1
  libproc2-0 libpsl5t64 libpthread-stubs0-dev libpthread-stubs0-dev:armhf
  libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8t64
  librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config
  libsensors5:armhf libseqan2-dev libsimbody-dev:armhf libsimbody3.7:armhf
  libsimtkmolmodel-dev:armhf libsimtkmolmodel-plugins:armhf
  libsimtkmolmodel3.1t64:armhf libsm-dev:armhf libsm6:armhf libsqlite3-0
  libssh2-1t64 libstb-dev:armhf libstb0t64:armhf libstdc++-13-dev:armhf
  libstdc++-13-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross
  libsub-override-perl libtinfo6:armhf libtool libubsan1:armhf
  libubsan1-armhf-cross libuchardet0 libuuid1:armhf libuv1t64 libvulkan1:armhf
  libwayland-client0:armhf libwayland-server0:armhf libx11-6 libx11-6:armhf
  libx11-data libx11-dev libx11-dev:armhf libx11-xcb1:armhf libxau-dev
  libxau-dev:armhf libxau6 libxau6:armhf libxcb-dri2-0:armhf
  libxcb-dri3-0:armhf libxcb-glx0:armhf libxcb-present0:armhf
  libxcb-randr0:armhf libxcb-shm0:armhf libxcb-sync1:armhf
  libxcb-xfixes0:armhf libxcb1 libxcb1:armhf libxcb1-dev libxcb1-dev:armhf
  libxdmcp-dev libxdmcp-dev:armhf libxdmcp6 libxdmcp6:armhf libxext-dev:armhf
  libxext6:armhf libxfixes-dev:armhf libxfixes3:armhf libxi-dev:armhf
  libxi6:armhf libxml-libxml-perl libxml-namespacesupport-perl
  libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2
  libxml2:armhf libxml2-utils libxmu-dev:armhf libxmu-headers libxmu6:armhf
  libxshmfence1:armhf libxslt1.1 libxt-dev:armhf libxt6t64:armhf
  libxxf86vm1:armhf libyaml-perl libz3-4:armhf libzstd1:armhf 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 ucf x11-common x11proto-dev xml-core xorg-sgml-doctools
  xsltproc xtrans-dev zlib1g:armhf zlib1g-dev:armhf
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-arm-linux-gnueabihf gcc-doc gettext-doc
  libasprintf-dev libgettextpo-dev groff lrzip liblapack-doc:armhf
  glibc-doc:armhf libc-l10n:armhf locales:armhf libnss-nis:armhf
  libnss-nisplus:armhf manpages-dev:armhf krb5-doc krb5-user libice-doc:armhf
  lm-sensors lm-sensors:armhf libsm-doc:armhf libstdc++-13-doc:armhf
  libtool-doc gfortran | fortran95-compiler gcj-jdk libx11-doc
  libx11-doc:armhf libxcb-doc libxcb-doc:armhf libxext-doc:armhf
  libxt-doc:armhf 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:armhf ca-certificates
  libarchive-cpio-perl krb5-locales libldap-common libgpm2 publicsuffix
  libsasl2-modules libltdl-dev uuid-runtime:armhf mesa-vulkan-drivers:armhf
  | vulkan-icd:armhf 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-arm-linux-gnueabihf bsdextrautils cmake cmake-data
  cpp-13-arm-linux-gnueabihf cpp-arm-linux-gnueabihf cross-config
  crossbuild-essential-armhf debhelper dh-autoreconf dh-strip-nondeterminism
  docbook-xml docbook-xsl dpkg-cross dwz fakeroot file freeglut3-dev:armhf
  g++-13-arm-linux-gnueabihf g++-arm-linux-gnueabihf
  gcc-13-arm-linux-gnueabihf gcc-13-arm-linux-gnueabihf-base gcc-13-base:armhf
  gcc-13-cross-base gcc-14-base:armhf gcc-14-cross-base
  gcc-arm-linux-gnueabihf gemmi-dev:armhf gettext gettext-base groff-base
  intltool-debian libarchive-zip-perl libarchive13t64 libasan8:armhf
  libasan8-armhf-cross libatomic1:armhf libatomic1-armhf-cross
  libblas-dev:armhf libblas3:armhf libbrotli1 libbsd0 libbsd0:armhf
  libc6:armhf libc6-armhf-cross libc6-dev:armhf libc6-dev-armhf-cross
  libcom-err2 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:armhf
  libcrypt1:armhf libcurl4t64 libdebhelper-perl libdebian-dpkgcross-perl
  libdrm-amdgpu1:armhf libdrm-common libdrm-nouveau2:armhf
  libdrm-radeon1:armhf libdrm2:armhf libedit2:armhf libegl-dev:armhf
  libegl-mesa0:armhf libegl1:armhf libelf1t64 libelf1t64:armhf libexpat1
  libexpat1:armhf libfakeroot libffi8:armhf libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libgbm1:armhf
  libgcc-13-dev:armhf libgcc-13-dev-armhf-cross libgcc-s1:armhf
  libgcc-s1-armhf-cross libgfortran5:armhf libgl-dev:armhf libgl1:armhf
  libgl1-mesa-dev:armhf libgl1-mesa-dri:armhf libglapi-mesa:armhf
  libgles-dev:armhf libgles1:armhf libgles2:armhf libglu1-mesa:armhf
  libglu1-mesa-dev:armhf libglut-dev:armhf libglut3.12:armhf
  libglvnd-core-dev:armhf libglvnd-dev:armhf libglvnd0:armhf libglx-dev:armhf
  libglx-mesa0:armhf libglx0:armhf libgomp1:armhf libgomp1-armhf-cross
  libgssapi-krb5-2 libice-dev:armhf libice6:armhf libicu72 libicu72:armhf
  libio-string-perl libjsoncpp25 libk5crypto3 libkeyutils1 libkrb5-3
  libkrb5support0 liblapack-dev:armhf liblapack3:armhf libldap-2.5-0
  libllvm17t64:armhf liblocale-gettext-perl liblzma5:armhf libmagic-mgc
  libmagic1t64 libmd0:armhf libncursesw6 libnghttp2-14 libopengl-dev:armhf
  libopengl0:armhf libopenmm-dev:armhf libopenmm8.0t64:armhf libpipeline1
  libproc2-0 libpsl5t64 libpthread-stubs0-dev libpthread-stubs0-dev:armhf
  libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8t64
  librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config
  libsensors5:armhf libseqan2-dev libsimbody-dev:armhf libsimbody3.7:armhf
  libsimtkmolmodel-dev:armhf libsimtkmolmodel-plugins:armhf
  libsimtkmolmodel3.1t64:armhf libsm-dev:armhf libsm6:armhf libsqlite3-0
  libssh2-1t64 libstb-dev:armhf libstb0t64:armhf libstdc++-13-dev:armhf
  libstdc++-13-dev-armhf-cross libstdc++6:armhf libstdc++6-armhf-cross
  libsub-override-perl libtinfo6:armhf libtool libubsan1:armhf
  libubsan1-armhf-cross libuchardet0 libuuid1:armhf libuv1t64 libvulkan1:armhf
  libwayland-client0:armhf libwayland-server0:armhf libx11-6 libx11-6:armhf
  libx11-data libx11-dev libx11-dev:armhf libx11-xcb1:armhf libxau-dev
  libxau-dev:armhf libxau6 libxau6:armhf libxcb-dri2-0:armhf
  libxcb-dri3-0:armhf libxcb-glx0:armhf libxcb-present0:armhf
  libxcb-randr0:armhf libxcb-shm0:armhf libxcb-sync1:armhf
  libxcb-xfixes0:armhf libxcb1 libxcb1:armhf libxcb1-dev libxcb1-dev:armhf
  libxdmcp-dev libxdmcp-dev:armhf libxdmcp6 libxdmcp6:armhf libxext-dev:armhf
  libxext6:armhf libxfixes-dev:armhf libxfixes3:armhf libxi-dev:armhf
  libxi6:armhf libxml-libxml-perl libxml-namespacesupport-perl
  libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2
  libxml2:armhf libxml2-utils libxmu-dev:armhf libxmu-headers libxmu6:armhf
  libxshmfence1:armhf libxslt1.1 libxt-dev:armhf libxt6t64:armhf
  libxxf86vm1:armhf libyaml-perl libz3-4:armhf libzstd1:armhf m4 man-db
  media-types netbase po-debconf procps python3 python3-minimal python3.11
  python3.11-minimal readline-common sbuild-build-depends-main-dummy:armhf
  sensible-utils sgml-base sgml-data tao-pegtl-dev ucf x11-common x11proto-dev
  xml-core xorg-sgml-doctools xsltproc xtrans-dev zlib1g:armhf
  zlib1g-dev:armhf
0 upgraded, 249 newly installed, 0 to remove and 0 not upgraded.
Need to get 179 MB of archives.
After this operation, 709 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1032 B]
Get:2 http://localhost:3142/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-7 [15.0 kB]
Get:3 http://localhost:3142/debian sid/main amd64 libpython3.11-minimal amd64 3.11.8-3+b2 [817 kB]
Get:4 http://localhost:3142/debian sid/main amd64 libexpat1 amd64 2.6.2-1 [103 kB]
Get:5 http://localhost:3142/debian sid/main amd64 python3.11-minimal amd64 3.11.8-3+b2 [1879 kB]
Get:6 http://localhost:3142/debian sid/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB]
Get:7 http://localhost:3142/debian sid/main amd64 media-types all 10.1.0 [26.9 kB]
Get:8 http://localhost:3142/debian sid/main amd64 netbase all 6.4 [12.8 kB]
Get:9 http://localhost:3142/debian sid/main amd64 libncursesw6 amd64 6.4+20240113-1 [135 kB]
Get:10 http://localhost:3142/debian sid/main amd64 readline-common all 8.2-4 [69.3 kB]
Get:11 http://localhost:3142/debian sid/main amd64 libreadline8t64 amd64 8.2-4 [167 kB]
Get:12 http://localhost:3142/debian sid/main amd64 libsqlite3-0 amd64 3.45.2-1 [895 kB]
Get:13 http://localhost:3142/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.8-3+b2 [1792 kB]
Get:14 http://localhost:3142/debian sid/main amd64 python3.11 amd64 3.11.8-3+b2 [597 kB]
Get:15 http://localhost:3142/debian sid/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B]
Get:16 http://localhost:3142/debian sid/main amd64 python3 amd64 3.11.8-1 [27.4 kB]
Get:17 http://localhost:3142/debian sid/main amd64 sgml-base all 1.31 [15.4 kB]
Get:18 http://localhost:3142/debian sid/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB]
Get:19 http://localhost:3142/debian sid/main amd64 procps amd64 2:4.0.4-4 [880 kB]
Get:20 http://localhost:3142/debian sid/main amd64 sensible-utils all 0.0.22 [22.4 kB]
Get:21 http://localhost:3142/debian sid/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB]
Get:22 http://localhost:3142/debian sid/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB]
Get:23 http://localhost:3142/debian sid/main amd64 file amd64 1:5.45-3 [42.9 kB]
Get:24 http://localhost:3142/debian sid/main amd64 gettext-base amd64 0.21-14+b1 [161 kB]
Get:25 http://localhost:3142/debian sid/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB]
Get:26 http://localhost:3142/debian sid/main amd64 groff-base amd64 1.23.0-3+b1 [1180 kB]
Get:27 http://localhost:3142/debian sid/main amd64 bsdextrautils amd64 2.39.3-11 [89.8 kB]
Get:28 http://localhost:3142/debian sid/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB]
Get:29 http://localhost:3142/debian sid/main amd64 man-db amd64 2.12.0-4 [1409 kB]
Get:30 http://localhost:3142/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB]
Get:31 http://localhost:3142/debian sid/main amd64 asciidoc-common all 10.2.0-2 [104 kB]
Get:32 http://localhost:3142/debian sid/main amd64 xml-core all 0.19 [20.1 kB]
Get:33 http://localhost:3142/debian sid/main amd64 docbook-xsl all 1.79.2+dfsg-7 [1221 kB]
Get:34 http://localhost:3142/debian sid/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB]
Get:35 http://localhost:3142/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB]
Get:36 http://localhost:3142/debian sid/main amd64 libxml2-utils amd64 2.9.14+dfsg-1.3+b2 [98.9 kB]
Get:37 http://localhost:3142/debian sid/main amd64 libxslt1.1 amd64 1.1.35-1 [242 kB]
Get:38 http://localhost:3142/debian sid/main amd64 xsltproc amd64 1.1.35-1 [126 kB]
Get:39 http://localhost:3142/debian sid/main amd64 asciidoc-base all 10.2.0-2 [85.3 kB]
Get:40 http://localhost:3142/debian sid/main amd64 m4 amd64 1.4.19-4 [287 kB]
Get:41 http://localhost:3142/debian sid/main amd64 autoconf all 2.71-3 [332 kB]
Get:42 http://localhost:3142/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get:43 http://localhost:3142/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get:44 http://localhost:3142/debian sid/main amd64 autopoint all 0.21-14 [496 kB]
Get:45 http://localhost:3142/debian sid/main amd64 binutils-arm-linux-gnueabihf amd64 2.42-4 [3216 kB]
Get:46 http://localhost:3142/debian sid/main amd64 libarchive13t64 amd64 3.7.2-2 [346 kB]
Get:47 http://localhost:3142/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB]
Get:48 http://localhost:3142/debian sid/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB]
Get:49 http://localhost:3142/debian sid/main amd64 libcom-err2 amd64 1.47.0-2.4 [20.2 kB]
Get:50 http://localhost:3142/debian sid/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB]
Get:51 http://localhost:3142/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B]
Get:52 http://localhost:3142/debian sid/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB]
Get:53 http://localhost:3142/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB]
Get:54 http://localhost:3142/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB]
Get:55 http://localhost:3142/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB]
Get:56 http://localhost:3142/debian sid/main amd64 libldap-2.5-0 amd64 2.5.16+dfsg-2 [185 kB]
Get:57 http://localhost:3142/debian sid/main amd64 libnghttp2-14 amd64 1.60.0-1 [75.3 kB]
Get:58 http://localhost:3142/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB]
Get:59 http://localhost:3142/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b3 [58.5 kB]
Get:60 http://localhost:3142/debian sid/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b1 [215 kB]
Get:61 http://localhost:3142/debian sid/main amd64 libcurl4t64 amd64 8.7.1-2 [440 kB]
Get:62 http://localhost:3142/debian sid/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB]
Get:63 http://localhost:3142/debian sid/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB]
Get:64 http://localhost:3142/debian sid/main amd64 libuv1t64 amd64 1.48.0-1.1 [147 kB]
Get:65 http://localhost:3142/debian sid/main amd64 cmake-data all 3.28.3-1 [2128 kB]
Get:66 http://localhost:3142/debian sid/main amd64 cmake amd64 3.28.3-1+b1 [10.5 MB]
Get:67 http://localhost:3142/debian sid/main amd64 gcc-13-arm-linux-gnueabihf-base amd64 13.2.0-12cross1 [42.6 kB]
Get:68 http://localhost:3142/debian sid/main amd64 cpp-13-arm-linux-gnueabihf amd64 13.2.0-12cross1 [9286 kB]
Get:69 http://localhost:3142/debian sid/main amd64 cpp-arm-linux-gnueabihf amd64 4:13.2.0-7 [4732 B]
Get:70 http://localhost:3142/debian sid/main amd64 cross-config all 2.6.20 [16.3 kB]
Get:71 http://localhost:3142/debian sid/main amd64 gcc-13-cross-base all 13.2.0-12cross1 [38.1 kB]
Get:72 http://localhost:3142/debian sid/main amd64 gcc-14-cross-base all 14-20240127-1cross1 [37.9 kB]
Get:73 http://localhost:3142/debian sid/main amd64 libc6-armhf-cross all 2.37-12cross1 [868 kB]
Get:74 http://localhost:3142/debian sid/main amd64 libgcc-s1-armhf-cross all 14-20240127-1cross1 [36.9 kB]
Get:75 http://localhost:3142/debian sid/main amd64 libgomp1-armhf-cross all 14-20240127-1cross1 [108 kB]
Get:76 http://localhost:3142/debian sid/main amd64 libatomic1-armhf-cross all 14-20240127-1cross1 [6768 B]
Get:77 http://localhost:3142/debian sid/main amd64 libasan8-armhf-cross all 14-20240127-1cross1 [2567 kB]
Get:78 http://localhost:3142/debian sid/main amd64 libstdc++6-armhf-cross all 14-20240127-1cross1 [560 kB]
Get:79 http://localhost:3142/debian sid/main amd64 libubsan1-armhf-cross all 14-20240127-1cross1 [1036 kB]
Get:80 http://localhost:3142/debian sid/main amd64 libgcc-13-dev-armhf-cross all 13.2.0-12cross1 [783 kB]
Get:81 http://localhost:3142/debian sid/main amd64 gcc-13-arm-linux-gnueabihf amd64 13.2.0-12cross1 [17.8 MB]
Get:82 http://localhost:3142/debian sid/main amd64 gcc-arm-linux-gnueabihf amd64 4:13.2.0-7 [1452 B]
Get:83 http://localhost:3142/debian sid/main amd64 libc6-dev-armhf-cross all 2.37-12cross1 [1265 kB]
Get:84 http://localhost:3142/debian sid/main amd64 libstdc++-13-dev-armhf-cross all 13.2.0-12cross1 [2216 kB]
Get:85 http://localhost:3142/debian sid/main amd64 g++-13-arm-linux-gnueabihf amd64 13.2.0-12cross1 [10.2 MB]
Get:86 http://localhost:3142/debian sid/main amd64 g++-arm-linux-gnueabihf amd64 4:13.2.0-7 [1204 B]
Get:87 http://localhost:3142/debian sid/main amd64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB]
Get:88 http://localhost:3142/debian sid/main amd64 libio-string-perl all 1.08-4 [12.1 kB]
Get:89 http://localhost:3142/debian sid/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB]
Get:90 http://localhost:3142/debian sid/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB]
Get:91 http://localhost:3142/debian sid/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB]
Get:92 http://localhost:3142/debian sid/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b3 [313 kB]
Get:93 http://localhost:3142/debian sid/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB]
Get:94 http://localhost:3142/debian sid/main amd64 libyaml-perl all 1.31-1 [64.8 kB]
Get:95 http://localhost:3142/debian sid/main amd64 libconfig-auto-perl all 0.44-2 [19.2 kB]
Get:96 http://localhost:3142/debian sid/main amd64 libfile-which-perl all 1.27-2 [15.1 kB]
Get:97 http://localhost:3142/debian sid/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB]
Get:98 http://localhost:3142/debian sid/main amd64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB]
Get:99 http://localhost:3142/debian sid/main amd64 dpkg-cross all 2.6.20 [25.8 kB]
Get:100 http://localhost:3142/debian sid/main amd64 crossbuild-essential-armhf all 12.10 [3484 B]
Get:101 http://localhost:3142/debian sid/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB]
Get:102 http://localhost:3142/debian sid/main amd64 libtool all 2.4.7-7 [517 kB]
Get:103 http://localhost:3142/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB]
Get:104 http://localhost:3142/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:105 http://localhost:3142/debian sid/main amd64 libsub-override-perl all 0.10-1 [10.6 kB]
Get:106 http://localhost:3142/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:107 http://localhost:3142/debian sid/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:108 http://localhost:3142/debian sid/main amd64 libelf1t64 amd64 0.191-1 [189 kB]
Get:109 http://localhost:3142/debian sid/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get:110 http://localhost:3142/debian sid/main amd64 gettext amd64 0.21-14+b1 [1301 kB]
Get:111 http://localhost:3142/debian sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:112 http://localhost:3142/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:113 http://localhost:3142/debian sid/main amd64 debhelper all 13.15.3 [901 kB]
Get:114 http://localhost:3142/debian sid/main amd64 sgml-data all 2.0.11+nmu1 [179 kB]
Get:115 http://localhost:3142/debian sid/main amd64 docbook-xml all 4.5-12 [85.2 kB]
Get:116 http://localhost:3142/debian sid/main amd64 libfakeroot amd64 1.34-1 [28.9 kB]
Get:117 http://localhost:3142/debian sid/main amd64 fakeroot amd64 1.34-1 [74.0 kB]
Get:118 http://localhost:3142/debian sid/main armhf gcc-14-base armhf 14-20240330-1 [43.2 kB]
Get:119 http://localhost:3142/debian sid/main armhf libgcc-s1 armhf 14-20240330-1 [36.8 kB]
Get:120 http://localhost:3142/debian sid/main armhf libc6 armhf 2.37-15.1 [2132 kB]
Get:121 http://localhost:3142/debian sid/main armhf libglvnd0 armhf 1.7.0-1 [52.3 kB]
Get:122 http://localhost:3142/debian sid/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB]
Get:123 http://localhost:3142/debian sid/main armhf libmd0 armhf 1.1.0-2 [31.8 kB]
Get:124 http://localhost:3142/debian sid/main armhf libbsd0 armhf 0.12.2-1 [127 kB]
Get:125 http://localhost:3142/debian sid/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB]
Get:126 http://localhost:3142/debian sid/main armhf libxcb1 armhf 1.15-1 [140 kB]
Get:127 http://localhost:3142/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB]
Get:128 http://localhost:3142/debian sid/main armhf libx11-6 armhf 2:1.8.7-1 [735 kB]
Get:129 http://localhost:3142/debian sid/main amd64 libdrm-common all 2.4.120-2 [7688 B]
Get:130 http://localhost:3142/debian sid/main armhf libdrm2 armhf 2.4.120-2 [33.8 kB]
Get:131 http://localhost:3142/debian sid/main armhf libexpat1 armhf 2.6.2-1 [83.5 kB]
Get:132 http://localhost:3142/debian sid/main armhf libglapi-mesa armhf 24.0.4-1 [43.4 kB]
Get:133 http://localhost:3142/debian sid/main armhf libx11-xcb1 armhf 2:1.8.7-1 [231 kB]
Get:134 http://localhost:3142/debian sid/main armhf libxcb-dri2-0 armhf 1.15-1 [107 kB]
Get:135 http://localhost:3142/debian sid/main armhf libxcb-dri3-0 armhf 1.15-1 [107 kB]
Get:136 http://localhost:3142/debian sid/main armhf libxcb-glx0 armhf 1.15-1 [120 kB]
Get:137 http://localhost:3142/debian sid/main armhf libxcb-present0 armhf 1.15-1 [105 kB]
Get:138 http://localhost:3142/debian sid/main armhf libxcb-randr0 armhf 1.15-1 [116 kB]
Get:139 http://localhost:3142/debian sid/main armhf libxcb-shm0 armhf 1.15-1 [106 kB]
Get:140 http://localhost:3142/debian sid/main armhf libxcb-sync1 armhf 1.15-1 [108 kB]
Get:141 http://localhost:3142/debian sid/main armhf libxcb-xfixes0 armhf 1.15-1 [110 kB]
Get:142 http://localhost:3142/debian sid/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB]
Get:143 http://localhost:3142/debian sid/main armhf libxfixes3 armhf 1:6.0.0-2 [21.1 kB]
Get:144 http://localhost:3142/debian sid/main armhf libxshmfence1 armhf 1.3-1 [8592 B]
Get:145 http://localhost:3142/debian sid/main armhf libxxf86vm1 armhf 1:1.1.4-1+b2 [20.2 kB]
Get:146 http://localhost:3142/debian sid/main armhf libvulkan1 armhf 1.3.275.0-1 [109 kB]
Get:147 http://localhost:3142/debian sid/main armhf libdrm-amdgpu1 armhf 2.4.120-2 [20.0 kB]
Get:148 http://localhost:3142/debian sid/main armhf libdrm-nouveau2 armhf 2.4.120-2 [16.9 kB]
Get:149 http://localhost:3142/debian sid/main armhf libdrm-radeon1 armhf 2.4.120-2 [19.5 kB]
Get:150 http://localhost:3142/debian sid/main armhf libzstd1 armhf 1.5.5+dfsg2-2 [257 kB]
Get:151 http://localhost:3142/debian sid/main armhf zlib1g armhf 1:1.3.dfsg-3.1 [74.4 kB]
Get:152 http://localhost:3142/debian sid/main armhf libelf1t64 armhf 0.191-1 [183 kB]
Get:153 http://localhost:3142/debian sid/main armhf libtinfo6 armhf 6.4+20240113-1 [327 kB]
Get:154 http://localhost:3142/debian sid/main armhf libedit2 armhf 3.1-20230828-1 [76.8 kB]
Get:155 http://localhost:3142/debian sid/main armhf libffi8 armhf 3.4.6-1 [20.0 kB]
Get:156 http://localhost:3142/debian sid/main armhf libstdc++6 armhf 14-20240330-1 [607 kB]
Get:157 http://localhost:3142/debian sid/main armhf libicu72 armhf 72.1-4+b1 [9070 kB]
Get:158 http://localhost:3142/debian sid/main armhf liblzma5 armhf 5.6.1+really5.4.5-1 [228 kB]
Get:159 http://localhost:3142/debian sid/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB]
Get:160 http://localhost:3142/debian sid/main armhf libz3-4 armhf 4.8.12-3.1+b2 [6324 kB]
Get:161 http://localhost:3142/debian sid/main armhf libllvm17t64 armhf 1:17.0.6-9+b1 [21.6 MB]
Get:162 http://localhost:3142/debian sid/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB]
Get:163 http://localhost:3142/debian sid/main armhf libsensors5 armhf 1:3.6.0-9 [31.9 kB]
Get:164 http://localhost:3142/debian sid/main armhf libgl1-mesa-dri armhf 24.0.4-1 [6473 kB]
Get:165 http://localhost:3142/debian sid/main armhf libglx-mesa0 armhf 24.0.4-1 [130 kB]
Get:166 http://localhost:3142/debian sid/main armhf libglx0 armhf 1.7.0-1 [32.2 kB]
Get:167 http://localhost:3142/debian sid/main armhf libgl1 armhf 1.7.0-1 [90.8 kB]
Get:168 http://localhost:3142/debian sid/main armhf libxi6 armhf 2:1.8.1-1 [73.8 kB]
Get:169 http://localhost:3142/debian sid/main armhf libglut3.12 armhf 3.4.0-1+b1 [125 kB]
Get:170 http://localhost:3142/debian sid/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get:171 http://localhost:3142/debian sid/main amd64 x11proto-dev all 2023.2-1 [598 kB]
Get:172 http://localhost:3142/debian sid/main armhf libxau-dev armhf 1:1.0.9-1 [22.4 kB]
Get:173 http://localhost:3142/debian sid/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.7 kB]
Get:174 http://localhost:3142/debian sid/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB]
Get:175 http://localhost:3142/debian sid/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:176 http://localhost:3142/debian sid/main armhf libxcb1-dev armhf 1.15-1 [179 kB]
Get:177 http://localhost:3142/debian sid/main armhf libx11-dev armhf 2:1.8.7-1 [816 kB]
Get:178 http://localhost:3142/debian sid/main armhf libglx-dev armhf 1.7.0-1 [15.5 kB]
Get:179 http://localhost:3142/debian sid/main armhf libgl-dev armhf 1.7.0-1 [100 kB]
Get:180 http://localhost:3142/debian sid/main armhf libglvnd-core-dev armhf 1.7.0-1 [13.1 kB]
Get:181 http://localhost:3142/debian sid/main armhf libwayland-server0 armhf 1.22.0-2.1+b1 [26.7 kB]
Get:182 http://localhost:3142/debian sid/main armhf libgbm1 armhf 24.0.4-1 [37.3 kB]
Get:183 http://localhost:3142/debian sid/main armhf libwayland-client0 armhf 1.22.0-2.1+b1 [20.4 kB]
Get:184 http://localhost:3142/debian sid/main armhf libegl-mesa0 armhf 24.0.4-1 [98.6 kB]
Get:185 http://localhost:3142/debian sid/main armhf libegl1 armhf 1.7.0-1 [28.7 kB]
Get:186 http://localhost:3142/debian sid/main armhf libegl-dev armhf 1.7.0-1 [19.2 kB]
Get:187 http://localhost:3142/debian sid/main armhf libgles1 armhf 1.7.0-1 [12.0 kB]
Get:188 http://localhost:3142/debian sid/main armhf libgles2 armhf 1.7.0-1 [17.4 kB]
Get:189 http://localhost:3142/debian sid/main armhf libgles-dev armhf 1.7.0-1 [50.5 kB]
Get:190 http://localhost:3142/debian sid/main armhf libopengl0 armhf 1.7.0-1 [31.9 kB]
Get:191 http://localhost:3142/debian sid/main armhf libopengl-dev armhf 1.7.0-1 [5104 B]
Get:192 http://localhost:3142/debian sid/main armhf libglvnd-dev armhf 1.7.0-1 [4868 B]
Get:193 http://localhost:3142/debian sid/main armhf libgl1-mesa-dev armhf 24.0.4-1 [17.0 kB]
Get:194 http://localhost:3142/debian sid/main armhf libglu1-mesa armhf 9.0.2-1.1 [137 kB]
Get:195 http://localhost:3142/debian sid/main armhf libglu1-mesa-dev armhf 9.0.2-1.1 [177 kB]
Get:196 http://localhost:3142/debian sid/main armhf libxext-dev armhf 2:1.3.4-1+b1 [103 kB]
Get:197 http://localhost:3142/debian sid/main amd64 x11-common all 1:7.7+23 [252 kB]
Get:198 http://localhost:3142/debian sid/main armhf libice6 armhf 2:1.0.10-1 [51.9 kB]
Get:199 http://localhost:3142/debian sid/main armhf libuuid1 armhf 2.39.3-11 [29.3 kB]
Get:200 http://localhost:3142/debian sid/main armhf libsm6 armhf 2:1.2.3-1 [33.0 kB]
Get:201 http://localhost:3142/debian sid/main armhf libxt6t64 armhf 1:1.2.1-1.2 [159 kB]
Get:202 http://localhost:3142/debian sid/main armhf libice-dev armhf 2:1.0.10-1 [61.9 kB]
Get:203 http://localhost:3142/debian sid/main armhf libsm-dev armhf 2:1.2.3-1 [36.1 kB]
Get:204 http://localhost:3142/debian sid/main armhf libxt-dev armhf 1:1.2.1-1.2 [385 kB]
Get:205 http://localhost:3142/debian sid/main armhf libglut-dev armhf 3.4.0-1+b1 [153 kB]
Get:206 http://localhost:3142/debian sid/main armhf freeglut3-dev armhf 3.4.0-1+b1 [53.4 kB]
Get:207 http://localhost:3142/debian sid/main armhf gcc-13-base armhf 13.2.0-23 [44.5 kB]
Get:208 http://localhost:3142/debian sid/main armhf gemmi-dev armhf 0.6.4+ds-1 [1071 kB]
Get:209 http://localhost:3142/debian sid/main armhf libasan8 armhf 14-20240330-1 [2578 kB]
Get:210 http://localhost:3142/debian sid/main armhf libatomic1 armhf 14-20240330-1 [7044 B]
Get:211 http://localhost:3142/debian sid/main armhf libblas3 armhf 3.12.0-3 [108 kB]
Get:212 http://localhost:3142/debian sid/main armhf libblas-dev armhf 3.12.0-3 [119 kB]
Get:213 http://localhost:3142/debian sid/main amd64 libbsd0 amd64 0.12.2-1 [131 kB]
Get:214 http://localhost:3142/debian sid/main armhf libcrypt1 armhf 1:4.4.36-4 [96.1 kB]
Get:215 http://localhost:3142/debian sid/main armhf libcrypt-dev armhf 1:4.4.36-4 [125 kB]
Get:216 http://localhost:3142/debian sid/main armhf libc6-dev armhf 2.37-15.1 [1268 kB]
Get:217 http://localhost:3142/debian sid/main armhf libgomp1 armhf 14-20240330-1 [111 kB]
Get:218 http://localhost:3142/debian sid/main armhf libubsan1 armhf 14-20240330-1 [1037 kB]
Get:219 http://localhost:3142/debian sid/main armhf libgcc-13-dev armhf 13.2.0-23 [781 kB]
Get:220 http://localhost:3142/debian sid/main armhf libgfortran5 armhf 14-20240330-1 [264 kB]
Get:221 http://localhost:3142/debian sid/main armhf liblapack3 armhf 3.12.0-3 [1803 kB]
Get:222 http://localhost:3142/debian sid/main armhf liblapack-dev armhf 3.12.0-3 [1903 kB]
Get:223 http://localhost:3142/debian sid/main armhf libopenmm8.0t64 armhf 8.0.0+dfsg-6.1 [857 kB]
Get:224 http://localhost:3142/debian sid/main armhf libopenmm-dev armhf 8.0.0+dfsg-6.1 [320 kB]
Get:225 http://localhost:3142/debian sid/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B]
Get:226 http://localhost:3142/debian sid/main amd64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB]
Get:227 http://localhost:3142/debian sid/main armhf libxfixes-dev armhf 1:6.0.0-2 [23.3 kB]
Get:228 http://localhost:3142/debian sid/main armhf libxi-dev armhf 2:1.8.1-1 [235 kB]
Get:229 http://localhost:3142/debian sid/main armhf libxmu6 armhf 2:1.1.3-3+b1 [51.0 kB]
Get:230 http://localhost:3142/debian sid/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB]
Get:231 http://localhost:3142/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB]
Get:232 http://localhost:3142/debian sid/main amd64 libxcb1 amd64 1.15-1 [144 kB]
Get:233 http://localhost:3142/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB]
Get:234 http://localhost:3142/debian sid/main amd64 libxau-dev amd64 1:1.0.9-1 [22.9 kB]
Get:235 http://localhost:3142/debian sid/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [42.2 kB]
Get:236 http://localhost:3142/debian sid/main amd64 libxcb1-dev amd64 1.15-1 [181 kB]
Get:237 http://localhost:3142/debian sid/main amd64 libx11-dev amd64 2:1.8.7-1 [875 kB]
Get:238 http://localhost:3142/debian sid/main amd64 libxmu-headers all 2:1.1.3-3 [68.5 kB]
Get:239 http://localhost:3142/debian sid/main armhf libxmu-dev armhf 2:1.1.3-3+b1 [57.6 kB]
Get:240 http://localhost:3142/debian sid/main armhf libsimbody3.7 armhf 3.7+dfsg-3 [2674 kB]
Get:241 http://localhost:3142/debian sid/main armhf libsimbody-dev armhf 3.7+dfsg-3 [2727 kB]
Get:242 http://localhost:3142/debian sid/main armhf libsimtkmolmodel3.1t64 armhf 3.1.0-4.1+b1 [600 kB]
Get:243 http://localhost:3142/debian sid/main armhf libsimtkmolmodel-dev armhf 3.1.0-4.1+b1 [1864 kB]
Get:244 http://localhost:3142/debian sid/main armhf libsimtkmolmodel-plugins armhf 3.1.0-4.1+b1 [16.7 kB]
Get:245 http://localhost:3142/debian sid/main armhf libstb0t64 armhf 0.0~git20230129.5736b15+ds-1.2 [178 kB]
Get:246 http://localhost:3142/debian sid/main armhf libstb-dev armhf 0.0~git20230129.5736b15+ds-1.2 [559 kB]
Get:247 http://localhost:3142/debian sid/main armhf libstdc++-13-dev armhf 13.2.0-23 [2263 kB]
Get:248 http://localhost:3142/debian sid/main amd64 tao-pegtl-dev all 3.2.7-1 [69.4 kB]
Get:249 http://localhost:3142/debian sid/main armhf zlib1g-dev armhf 1:1.3.dfsg-3.1 [904 kB]
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invoke-rc.d: could not determine current runlevel
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Setting up docbook-xml (4.5-12) ...
Processing triggers for sgml-base (1.31) ...
Setting up sbuild-build-depends-main-dummy:armhf (0.invalid.0) ...

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

Arch check ok (armhf included in any all)

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

Kernel: Linux 6.1.0-13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.55-1 (2023-09-29) amd64 (x86_64)
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_2.37-15.1 libstdc++-13-dev_13.2.0-23 libstdc++-13-dev-armhf-cross_13.2.0-12cross1 libstdc++6_14-20240330-1 libstdc++6-armhf-cross_14-20240127-1cross1 linux-libc-dev_6.7.9-2
Package versions: adduser_3.137 apt_2.7.14 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 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.42-4 binutils-arm-linux-gnueabihf_2.42-4 binutils-common_2.42-4 binutils-x86-64-linux-gnu_2.42-4 bsdextrautils_2.39.3-11 bsdutils_1:2.39.3-11 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-arm-linux-gnueabihf_13.2.0-12cross1 cpp-13-x86-64-linux-gnu_13.2.0-23 cpp-arm-linux-gnueabihf_4:13.2.0-7 cpp-x86-64-linux-gnu_4:13.2.0-7 cross-config_2.6.20 crossbuild-essential-armhf_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-arm-linux-gnueabihf_13.2.0-12cross1 g++-13-x86-64-linux-gnu_13.2.0-23 g++-arm-linux-gnueabihf_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-arm-linux-gnueabihf_13.2.0-12cross1 gcc-13-arm-linux-gnueabihf-base_13.2.0-12cross1 gcc-13-base_13.2.0-23 gcc-13-cross-base_13.2.0-12cross1 gcc-13-x86-64-linux-gnu_13.2.0-23 gcc-14-base_14-20240330-1 gcc-14-cross-base_14-20240127-1cross1 gcc-arm-linux-gnueabihf_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_2.7.14 libarchive-zip-perl_1.68-1 libarchive13t64_3.7.2-2 libasan8_14-20240330-1 libasan8-armhf-cross_14-20240127-1cross1 libatomic1_14-20240330-1 libatomic1-armhf-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_2.39.3-11 libbrotli1_1.1.0-2+b3 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-5.1 libc-bin_2.37-15.1 libc-dev-bin_2.37-15.1 libc6_2.37-15.1 libc6-armhf-cross_2.37-12cross1 libc6-dev_2.37-15.1 libc6-dev-armhf-cross_2.37-12cross1 libcap-ng0_0.8.4-2 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_8.7.1-2 libdb5.3t64_5.3.28+dfsg2-6 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-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_24.0.4-1 libegl1_1.7.0-1 libelf1t64_0.191-1 libexpat1_2.6.2-1 libfakeroot_1.34-1 libffi8_3.4.6-1 libfile-homedir-perl_1.006-2 libfile-stripnondeterminism-perl_1.13.1-1 libfile-which-perl_1.27-2 libgbm1_24.0.4-1 libgcc-13-dev_13.2.0-23 libgcc-13-dev-armhf-cross_13.2.0-12cross1 libgcc-s1_14-20240330-1 libgcc-s1-armhf-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_24.0.4-1 libgl1-mesa-dri_24.0.4-1 libglapi-mesa_24.0.4-1 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_24.0.4-1 libglx0_1.7.0-1 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.4-2 libgomp1_14-20240330-1 libgomp1-armhf-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 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 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+b1 liblocale-gettext-perl_1.07-7 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_2.39.3-11 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncursesw6_6.4+20240113-1 libnettle8t64_3.9.1-2.2 libnghttp2-14_1.60.0-1 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_1.5.3-6 libpam-modules-bin_1.5.3-6 libpam-runtime_1.5.3-6 libpam0t64_1.5.3-4 libpcre2-8-0_10.42-4+b1 libperl5.38t64_5.38.2-3.2 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_3.11.8-3+b2 libpython3.11-stdlib_3.11.8-3+b2 libquadmath0_14-20240330-1 libreadline8t64_8.2-4 librhash0_1.4.3-3+b1 librtmp1_2.4+20151223.gitfa8646d.1-2+b3 libsasl2-2_2.1.28+dfsg1-6 libsasl2-modules-db_2.1.28+dfsg1-6 libseccomp2_2.5.5-1 libselinux1_3.5-2+b1 libsemanage-common_3.5-1 libsemanage2_3.5-1+b3 libsensors-config_1:3.6.0-9 libsensors5_1:3.6.0-9 libsepol2_3.5-2 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_2.39.3-11 libsqlite3-0_3.45.2-1 libssh2-1t64_1.11.0-4.1+b1 libssl3t64_3.1.5-1.1 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-armhf-cross_13.2.0-12cross1 libstdc++6_14-20240330-1 libstdc++6-armhf-cross_14-20240127-1cross1 libsub-override-perl_0.10-1 libsystemd0_255.4-1+b1 libtasn1-6_4.19.0-3+b2 libtinfo6_6.4+20240113-1 libtool_2.4.7-7 libtsan2_14-20240330-1 libubsan1_14-20240330-1 libubsan1-armhf-cross_14-20240127-1cross1 libuchardet0_0.0.8-1+b1 libudev1_255.4-1+b1 libunistring5_1.2-1 libuuid1_2.39.3-11 libuv1t64_1.48.0-1.1 libvulkan1_1.3.275.0-1 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_1.15-1 libxcb-dri3-0_1.15-1 libxcb-glx0_1.15-1 libxcb-present0_1.15-1 libxcb-randr0_1.15-1 libxcb-shm0_1.15-1 libxcb-sync1_1.15-1 libxcb-xfixes0_1.15-1 libxcb1_1.15-1 libxcb1-dev_1.15-1 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext-dev_2:1.3.4-1+b1 libxext6_2:1.3.4-1+b1 libxfixes-dev_1:6.0.0-2 libxfixes3_1:6.0.0-2 libxi-dev_2:1.8.1-1 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+b1 libxmu-headers_2:1.1.3-3 libxmu6_2:1.1.3-3+b1 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_2.12.0-4 mawk_1.3.4.20240123-1 media-types_10.1.0 mount_2.39.3-11 ncurses-base_6.4+20240113-1 ncurses-bin_6.4+20240113-1 netbase_6.4 passwd_1:4.13+dfsg1-4 patch_2.7.6-7 perl_5.38.2-3.2 perl-base_5.38.2-3.2 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_3.11.8-3+b2 python3.11-minimal_3.11.8-3+b2 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_3.08-7 tao-pegtl-dev_3.2.7-1 tar_1.35+dfsg-3 tzdata_2024a-1 ucf_3.0043+nmu1 usr-is-merged_39 util-linux_2.39.3-11 x11-common_1:7.7+23 x11proto-dev_2023.2-1 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

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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.armhf
DEB_BUILD_OPTIONS=nocheck
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LOGNAME=crossqa
OLDPWD=/home/crossqa
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SBUILD_CONFIG=/tmp/tmp.1mgovCQmVV/sbuild.conf
SCHROOT_ALIAS_NAME=unstable-amd64-sbuild
SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=crossqa
SCHROOT_SESSION_ID=sid-amd64-sbuild-d000b6dc-ffd1-4725-b905-7fbdcb38dd3a
SCHROOT_UID=1000
SCHROOT_USER=crossqa
SHELL=/bin/sh
USER=crossqa
XDG_SESSION_CLASS=user

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

Command: dpkg-buildpackage --sanitize-env -aarmhf -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 arm-linux-gnueabihf does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 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 -O0"
	cd obj-arm-linux-gnueabihf && 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=armv7l -DCMAKE_C_COMPILER=arm-linux-gnueabihf-gcc -DCMAKE_CXX_COMPILER=arm-linux-gnueabihf-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/arm-linux-gnueabihf-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/arm-linux-gnueabihf-pkg-config -DQMAKE_EXECUTABLE=/usr/bin/arm-linux-gnueabihf-qmake -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -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 -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/arm-linux-gnueabihf-g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMM: /usr/include  
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/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 (0.5s)
-- 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


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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/MMB.dir/DependInfo.cmake "--color="
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make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  3%] Building CXX object CMakeFiles/MMB.dir/src/Utils.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /<<PKGBUILDDIR>>/include/Utils.h:22,
                 from /<<PKGBUILDDIR>>/src/Utils.cpp:12:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
/<<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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
In file included from /usr/arm-linux-gnueabihf/include/c++/13/vector:72,
                 from /usr/include/simbody/SimTKcommon/internal/Array.h:39,
                 from /usr/include/simbody/SimTKcommon/basics.h:53,
                 from /usr/include/simbody/SimTKcommon.h:32:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Interface&}; _Tp = Interface; _Alloc = std::allocator<Interface>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<Interface>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interface; _Alloc = std::allocator<Interface>]’,
    inlined from ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, std::vector<SimTK::String>, double, SimTK::String)’ at /<<PKGBUILDDIR>>/src/Utils.cpp:759:30:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Interface*, std::vector<Interface> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const TwoAtomClass&}; _Tp = TwoAtomClass; _Alloc = std::allocator<TwoAtomClass>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<TwoAtomClass>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = TwoAtomClass; _Alloc = std::allocator<TwoAtomClass>]’,
    inlined from ‘std::vector<TwoAtomClass> InterfaceContainer::retrieveCloseContactPairs(std::vector<MMBAtomInfo>&)’ at /<<PKGBUILDDIR>>/src/Utils.cpp:805:59:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TwoAtomClass*, std::vector<TwoAtomClass> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/set:62,
                 from /usr/include/simbody/simmath/internal/Contact.h:30,
                 from /usr/include/simbody/SimTKmath.h:46,
                 from /usr/include/simbody/SimTKsimbody.h:44:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const SimTK::String&&>, std::tuple<>}; _Key = const SimTK::String; _Val = std::pair<const SimTK::String, double>; _KeyOfValue = std::_Select1st<std::pair<const SimTK::String, double> >; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator’ changed in GCC 7.1
 2458 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/map:63,
                 from /usr/include/simbody/simmath/internal/CollisionDetectionAlgorithm.h:32,
                 from /usr/include/simbody/SimTKmath.h:48:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const SimTK::String; _Tp = double; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator’ changed in GCC 7.1
  532 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  533 |                                         std::forward_as_tuple(std::move(__k)),
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  534 |                                         std::tuple<>());
      |                                         ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const SimTK::String; _Tp = double; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]’,
    inlined from ‘myAtoI(std::map<const SimTK::String, double>, const char*)::<lambda()>’ at /<<PKGBUILDDIR>>/src/Utils.cpp:1016:21,
    inlined from ‘constexpr _Res std::__invoke_impl(__invoke_other, _Fn&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Fn = myAtoI(std::map<const SimTK::String, double>, const char*)::<lambda()>&; _Args = {}]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/invoke.h:61:67,
    inlined from ‘constexpr std::enable_if_t<is_invocable_r_v<_Res, _Callable, _Args ...>, _Res> std::__invoke_r(_Callable&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Callable = myAtoI(std::map<const SimTK::String, double>, const char*)::<lambda()>&; _Args = {}]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/invoke.h:116:38,
    inlined from ‘static _Res std::_Function_handler<_Res(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Res = std::__cxx11::basic_ostringstream<char>; _Functor = myAtoI(std::map<const SimTK::String, double>, const char*)::<lambda()>; _ArgTypes = {}]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/std_function.h:291:44:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator’ changed in GCC 7.1
  532 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  533 |                                         std::forward_as_tuple(std::move(__k)),
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  534 |                                         std::tuple<>());
      |                                         ~~~~~~~~~~~~~~~
[  6%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /usr/include/molmodel/molmodel/internal/Compound.h:36,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:16,
                 from /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:14:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20:
/<<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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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();
      |               ^~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
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 ‘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 ‘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 ‘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 ‘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 ‘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/arm-linux-gnueabihf/include/c++/13/memory:69,
                 from /usr/include/simbody/SimTKcommon/internal/ClonePtr.h:29,
                 from /usr/include/simbody/SimTKcommon/basics.h:44,
                 from /usr/include/simbody/SimTKcommon.h:32:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator<MMBAtomInfo*>; _ForwardIterator = MMBAtomInfo*]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘std::move_iterator<MMBAtomInfo*>’ changed in GCC 7.1
  113 |     __do_uninit_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘std::move_iterator<MMBAtomInfo*>’ changed in GCC 7.1
In file included from /usr/arm-linux-gnueabihf/include/c++/13/vector:72,
                 from /usr/include/simbody/SimTKcommon/internal/Array.h:39,
                 from /usr/include/simbody/SimTKcommon/basics.h:53:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AllResiduesWithin&}; _Tp = AllResiduesWithin; _Alloc = std::allocator<AllResiduesWithin>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<AllResiduesWithin>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AllResiduesWithin; _Alloc = std::allocator<AllResiduesWithin>]’,
    inlined from ‘void BiopolymerClass::physicsZone(std::vector<AllResiduesWithin>&, double, SimTK::SimbodyMatterSubsystem&, SimTK::State&)’ at /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:1735:59:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<AllResiduesWithin*, std::vector<AllResiduesWithin> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93,
                 from /usr/include/simbody/SimTKcommon/Simmatrix.h:37:
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;
      |              ^~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  113 |     __do_uninit_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {MMBAtomInfo}; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<MMBAtomInfo>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {MMBAtomInfo}; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’,
    inlined from ‘void BiopolymerClass::initializeAtomInfoVector(SimTK::SimbodyMatterSubsystem&, const std::vector<AtomicPropertyOverrideStruct>&)’ at /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:1163:40:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {MMBAtomInfo}; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’,
    inlined from ‘void BiopolymerClass::initializeAtomInfoVector(SimTK::SimbodyMatterSubsystem&, SimTK::DuMMForceFieldSubsystem&, const std::vector<AtomicPropertyOverrideStruct>&)’ at /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:1189:40:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const MMBAtomInfo&}; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<MMBAtomInfo>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In function ‘void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type ‘std::vector<MMBAtomInfo>::iterator’ changed in GCC 7.1
  751 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<MMBAtomInfo*>; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator<MMBAtomInfo*>; _ForwardIterator = MMBAtomInfo*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = move_iterator<MMBAtomInfo*>; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘_ForwardIterator std::__uninitialized_move_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = MMBAtomInfo*; _ForwardIterator = MMBAtomInfo*; _Allocator = allocator<MMBAtomInfo>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:384:41,
    inlined from ‘void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:766:34:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘std::move_iterator<MMBAtomInfo*>’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:781:34:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<MMBAtomInfo*>; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator<MMBAtomInfo*>; _ForwardIterator = MMBAtomInfo*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = move_iterator<MMBAtomInfo*>; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘_ForwardIterator std::__uninitialized_move_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = MMBAtomInfo*; _ForwardIterator = MMBAtomInfo*; _Allocator = allocator<MMBAtomInfo>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:384:41,
    inlined from ‘void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:786:34:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘std::move_iterator<MMBAtomInfo*>’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:814:38:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >; <template-parameter-2-2> = void; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’,
    inlined from ‘std::vector<MMBAtomInfo> BiopolymerClassContainer::getConcatenatedAtomInfoVector(const SimTK::State&, bool)’ at /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:4286:28:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1483:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
 1483 |           _M_range_insert(begin() + __offset, __first, __last,
      |           ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1484 |                           std::__iterator_category(__first));
      |                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1483:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >; <template-parameter-2-2> = void; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’,
    inlined from ‘std::vector<MMBAtomInfo> BiopolymerClassContainer::getConcatenatedAtomInfoVector(bool)’ at /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:4262:28:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1483:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
 1483 |           _M_range_insert(begin() + __offset, __first, __last,
      |           ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1484 |                           std::__iterator_category(__first));
      |                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1483:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’,
    inlined from ‘void BiopolymerClassContainer::loadCysteineAtomInfoVector(std::vector<MMBAtomInfo>&)’ at /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:4794:49:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[  9%] Building CXX object CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/Simbody.h:38,
                 from /usr/include/molmodel/SimTKmolmodel.h:47,
                 from /<<PKGBUILDDIR>>/include/UnitCellParameters.h:3,
                 from /<<PKGBUILDDIR>>/src/UnitCellParameters.cpp:4:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
[ 12%] Building CXX object CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /<<PKGBUILDDIR>>/include/Utils.h:22,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:12:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
/<<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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  489 |                (bIndex < length(thread.updThreadingPartner(1).sequence)))
      |                 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
/<<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:
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();
      |                                 ^
In file included from /usr/arm-linux-gnueabihf/include/c++/13/vector:72,
                 from /usr/include/simbody/SimTKcommon/internal/Array.h:39,
                 from /usr/include/simbody/SimTKcommon/basics.h:53,
                 from /usr/include/simbody/SimTKcommon.h:32:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AtomSpring&}; _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<AtomSpring>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]’,
    inlined from ‘void AtomSpringContainer::addAtomSpring(const AtomSpring&, BiopolymerClassContainer&)’ at /<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:190:31:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<AtomSpring*, std::vector<AtomSpring> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/memory:69,
                 from /usr/include/simbody/SimTKcommon/internal/ClonePtr.h:29,
                 from /usr/include/simbody/SimTKcommon/basics.h:44:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  113 |     __do_uninit_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1619:35,
    inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:238:44:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:603:31,
    inlined from ‘BiopolymerClass::BiopolymerClass(const BiopolymerClass&)’ at /<<PKGBUILDDIR>>/include/BiopolymerClass.h:147:5:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:603:31,
    inlined from ‘BiopolymerClass::BiopolymerClass(const BiopolymerClass&)’ at /<<PKGBUILDDIR>>/include/BiopolymerClass.h:147:5:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]’,
    inlined from ‘void AtomSpringContainer::add(AtomSpring&)’ at /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:41:102,
    inlined from ‘void AtomSpringContainer::createSpringsFromThreading(BiopolymerClassContainer&)’ at /<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:315:29:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<AtomSpring*, std::vector<AtomSpring> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]’,
    inlined from ‘void AtomSpringContainer::add(AtomSpring&)’ at /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:41:102,
    inlined from ‘void AtomSpringContainer::createSpringsFromThreading(BiopolymerClassContainer&)’ at /<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:316:29:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<AtomSpring*, std::vector<AtomSpring> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]’,
    inlined from ‘void AtomSpringContainer::add(AtomSpring&)’ at /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:41:102,
    inlined from ‘void AtomSpringContainer::createSpringsFromThreading(BiopolymerClassContainer&)’ at /<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:317:29:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<AtomSpring*, std::vector<AtomSpring> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]’,
    inlined from ‘void AtomSpringContainer::add(AtomSpring&)’ at /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:41:102,
    inlined from ‘void AtomSpringContainer::createSpringsFromThreading(BiopolymerClassContainer&)’ at /<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:370:38:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<AtomSpring*, std::vector<AtomSpring> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = ThreadingStruct; _Alloc = std::allocator<ThreadingStruct>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type ‘std::vector<ThreadingStruct>::iterator’ changed in GCC 7.1
  181 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = ThreadingStruct; _Alloc = std::allocator<ThreadingStruct>]’,
    inlined from ‘void AtomSpringContainer::deleteGappedThreading(int)’ at /<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:444:38:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ThreadingStruct*, std::vector<ThreadingStruct> >’ changed in GCC 7.1
 1532 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = ThreadingStruct; _Alloc = std::allocator<ThreadingStruct>]’,
    inlined from ‘void AtomSpringContainer::deleteThreading(int)’ at /<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:263:32:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ThreadingStruct*, std::vector<ThreadingStruct> >’ changed in GCC 7.1
 1532 |       { return _M_erase(begin() + (__position - cbegin())); }
      |                ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ThreadingStruct&}; _Tp = ThreadingStruct; _Alloc = std::allocator<ThreadingStruct>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<ThreadingStruct>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ThreadingStruct; _Alloc = std::allocator<ThreadingStruct>]’,
    inlined from ‘void AtomSpringContainer::addGappedThreading(const ThreadingStruct&, BiopolymerClassContainer&)’ at /<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:426:42:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ThreadingStruct*, std::vector<ThreadingStruct> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ThreadingStruct; _Alloc = std::allocator<ThreadingStruct>]’,
    inlined from ‘void AtomSpringContainer::addThreading(const ThreadingStruct&, BiopolymerClassContainer&)’ at /<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:248:36:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ThreadingStruct*, std::vector<ThreadingStruct> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]’,
    inlined from ‘void AtomSpringContainer::add(AtomSpring&)’ at /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:41:102,
    inlined from ‘void AtomSpringContainer::createSpringsFromGappedThreading(BiopolymerClassContainer&)’ at /<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:535:38:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<AtomSpring*, std::vector<AtomSpring> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 15%] Building CXX object CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /usr/include/molmodel/molmodel/internal/Compound.h:36,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:16,
                 from /<<PKGBUILDDIR>>/include/DisplacementContainer.h:14,
                 from /<<PKGBUILDDIR>>/src/DisplacementContainer.cpp:12:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20:
/<<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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
/<<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/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /<<PKGBUILDDIR>>/include/Utils.h:22,
                 from /<<PKGBUILDDIR>>/src/MobilizerContainer.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
/<<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 ‘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 ‘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 ‘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 ‘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 ‘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)) ||
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
/<<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/arm-linux-gnueabihf/include/c++/13/vector:72,
                 from /usr/include/simbody/SimTKcommon/internal/Array.h:39,
                 from /usr/include/simbody/SimTKcommon/basics.h:53,
                 from /usr/include/simbody/SimTKcommon.h:32:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const MobilizerWithin&}; _Tp = MobilizerWithin; _Alloc = std::allocator<MobilizerWithin>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<MobilizerWithin>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MobilizerWithin; _Alloc = std::allocator<MobilizerWithin>]’,
    inlined from ‘void MobilizerContainer::pushMobilizerWithin(MobilizerWithin, BiopolymerClassContainer&)’ at /<<PKGBUILDDIR>>/src/MobilizerContainer.cpp:287:36:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MobilizerWithin*, std::vector<MobilizerWithin> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MobilizerWithin; _Alloc = std::allocator<MobilizerWithin>]’,
    inlined from ‘void MobilizerContainer::createMobilizersWithin(BiopolymerClassContainer&, SimTK::State&)’ at /<<PKGBUILDDIR>>/src/MobilizerContainer.cpp:268:79:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MobilizerWithin*, std::vector<MobilizerWithin> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/memory:69,
                 from /usr/include/simbody/SimTKcommon/internal/ClonePtr.h:29,
                 from /usr/include/simbody/SimTKcommon/basics.h:44:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  113 |     __do_uninit_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:603:31,
    inlined from ‘BiopolymerClass::BiopolymerClass(const BiopolymerClass&)’ at /<<PKGBUILDDIR>>/include/BiopolymerClass.h:147:5,
    inlined from ‘void MobilizerContainer::addPhiPsiMobility(SimTK::String, BiopolymerClassContainer&)’ at /<<PKGBUILDDIR>>/src/MobilizerContainer.cpp:345:91:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:603:31,
    inlined from ‘BiopolymerClass::BiopolymerClass(const BiopolymerClass&)’ at /<<PKGBUILDDIR>>/include/BiopolymerClass.h:147:5,
    inlined from ‘void MobilizerContainer::addPhiPsiMobility(SimTK::String, BiopolymerClassContainer&)’ at /<<PKGBUILDDIR>>/src/MobilizerContainer.cpp:345:91:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 21%] Building CXX object CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/Simbody.h:38,
                 from /usr/include/molmodel/SimTKmolmodel.h:47,
                 from /<<PKGBUILDDIR>>/include/MoleculeContainer.h:6,
                 from /<<PKGBUILDDIR>>/src/MoleculeContainer.cpp:3:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
In file included from /<<PKGBUILDDIR>>/include/ConstraintContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/MoleculeContainer.h:8:
/<<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 ‘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 ‘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 ‘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 ‘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
      |               ^~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
/<<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/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /usr/include/molmodel/molmodel/internal/Compound.h:36,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:16,
                 from /<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:4,
                 from /<<PKGBUILDDIR>>/include/DensityContainer.h:14,
                 from /<<PKGBUILDDIR>>/src/DensityContainer.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20:
/<<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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
   18 |     if(id < 0 || id >= residueStretchVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
/<<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 ‘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 ‘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/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/Simbody.h:38,
                 from /usr/include/molmodel/SimTKmolmodel.h:47,
                 from /<<PKGBUILDDIR>>/include/BasePairContainer.h:16,
                 from /<<PKGBUILDDIR>>/src/BasePairContainer.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20,
                 from /<<PKGBUILDDIR>>/include/BasePairContainer.h: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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
/<<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/arm-linux-gnueabihf/include/c++/13/vector:72,
                 from /usr/include/simbody/SimTKcommon/internal/Array.h:39,
                 from /usr/include/simbody/SimTKcommon/basics.h:53,
                 from /usr/include/simbody/SimTKcommon.h:32:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BaseInteraction&}; _Tp = BaseInteraction; _Alloc = std::allocator<BaseInteraction>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<BaseInteraction>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BaseInteraction; _Alloc = std::allocator<BaseInteraction>]’,
    inlined from ‘void BasePairContainer::addBasePair(BiopolymerClassContainer&, const LeontisWesthofClass&, BaseInteraction, bool)’ at /<<PKGBUILDDIR>>/src/BasePairContainer.cpp:25:31:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BaseInteraction*, std::vector<BaseInteraction> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_insert_aux(iterator, _Arg&&) [with _Arg = BaseInteraction; _Tp = BaseInteraction; _Alloc = std::allocator<BaseInteraction>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<BaseInteraction>::iterator’ changed in GCC 7.1
  413 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = BaseInteraction; _Alloc = std::allocator<BaseInteraction>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:133:5: note: parameter passing for argument of type ‘std::vector<BaseInteraction>::const_iterator’ changed in GCC 7.1
  133 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:162:28: note: parameter passing for argument of type ‘const __gnu_cxx::__normal_iterator<BaseInteraction*, std::vector<BaseInteraction> >’ changed in GCC 7.1
  162 |               _M_insert_aux(__pos, std::move(__x_copy._M_val()));
      |               ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:170:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BaseInteraction*, std::vector<BaseInteraction> >’ changed in GCC 7.1
  170 |         _M_realloc_insert(begin() + (__position - cbegin()), __x);
      |         ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = BaseInteraction; _Alloc = std::allocator<BaseInteraction>]’,
    inlined from ‘void BasePairContainer::updateBasePair(int, SimTK::String, int, SimTK::String, SimTK::String, int, SimTK::String, SimTK::String, BiopolymerClassContainer&, const LeontisWesthofClass&, bool)’ at /<<PKGBUILDDIR>>/src/BasePairContainer.cpp:63:32:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:162:28: note: parameter passing for argument of type ‘const __gnu_cxx::__normal_iterator<BaseInteraction*, std::vector<BaseInteraction> >’ changed in GCC 7.1
  162 |               _M_insert_aux(__pos, std::move(__x_copy._M_val()));
      |               ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:170:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BaseInteraction*, std::vector<BaseInteraction> >’ changed in GCC 7.1
  170 |         _M_realloc_insert(begin() + (__position - cbegin()), __x);
      |         ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BasePairContainer.cpp: In member function ‘void BasePairContainer::updateBasePair(int, SimTK::String, int, SimTK::String, SimTK::String, int, SimTK::String, SimTK::String, BiopolymerClassContainer&, const LeontisWesthofClass&, bool)’:
/<<PKGBUILDDIR>>/src/BasePairContainer.cpp:69:32: note: parameter passing for argument of type ‘std::vector<BaseInteraction>::const_iterator’ changed in GCC 7.1
   69 |         myBasePairVector.insert(it, original);
      |         ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/memory:69,
                 from /usr/include/simbody/SimTKcommon/internal/ClonePtr.h:29,
                 from /usr/include/simbody/SimTKcommon/basics.h:44:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  113 |     __do_uninit_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:603:31,
    inlined from ‘BiopolymerClass::BiopolymerClass(const BiopolymerClass&)’ at /<<PKGBUILDDIR>>/include/BiopolymerClass.h:147:5:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:603:31,
    inlined from ‘BiopolymerClass::BiopolymerClass(const BiopolymerClass&)’ at /<<PKGBUILDDIR>>/include/BiopolymerClass.h:147:5:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 31%] Building CXX object CMakeFiles/MMB.dir/src/ContactContainer.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /<<PKGBUILDDIR>>/include/Utils.h:22,
                 from /<<PKGBUILDDIR>>/src/ContactContainer.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
/<<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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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).
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
/<<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/arm-linux-gnueabihf/include/c++/13/vector:72,
                 from /usr/include/simbody/SimTKcommon/internal/Array.h:39,
                 from /usr/include/simbody/SimTKcommon/basics.h:53,
                 from /usr/include/simbody/SimTKcommon.h:32:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ContactWithin&}; _Tp = ContactWithin; _Alloc = std::allocator<ContactWithin>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<ContactWithin>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ContactWithin; _Alloc = std::allocator<ContactWithin>]’,
    inlined from ‘void ContactContainer::pushContactWithin(ContactWithin, BiopolymerClassContainer&)’ at /<<PKGBUILDDIR>>/src/ContactContainer.cpp:66:34:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ContactWithin*, std::vector<ContactWithin> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/memory:69,
                 from /usr/include/simbody/SimTKcommon/internal/ClonePtr.h:29,
                 from /usr/include/simbody/SimTKcommon/basics.h:44:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  113 |     __do_uninit_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:603:31,
    inlined from ‘BiopolymerClass::BiopolymerClass(const BiopolymerClass&)’ at /<<PKGBUILDDIR>>/include/BiopolymerClass.h:147:5:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:603:31,
    inlined from ‘BiopolymerClass::BiopolymerClass(const BiopolymerClass&)’ at /<<PKGBUILDDIR>>/include/BiopolymerClass.h:147:5:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, vector<LeontisWesthofBondRow> >; _ForwardIterator = LeontisWesthofBondRow*]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, std::vector<LeontisWesthofBondRow> >’ changed in GCC 7.1
  113 |     __do_uninit_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, std::vector<LeontisWesthofBondRow> >’ changed in GCC 7.1
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, std::vector<LeontisWesthofBondRow> >; _ForwardIterator = LeontisWesthofBondRow*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, vector<LeontisWesthofBondRow> >; _ForwardIterator = LeontisWesthofBondRow*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, vector<LeontisWesthofBondRow> >; _ForwardIterator = LeontisWesthofBondRow*; _Tp = LeontisWesthofBondRow]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = LeontisWesthofBondRow; _Alloc = std::allocator<LeontisWesthofBondRow>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:603:31,
    inlined from ‘LeontisWesthofBondMatrix::LeontisWesthofBondMatrix(const LeontisWesthofBondMatrix&)’ at /<<PKGBUILDDIR>>/include/BaseInteractionParameterReader.h:72:8,
    inlined from ‘LeontisWesthofClass::LeontisWesthofClass(const LeontisWesthofClass&)’ at /<<PKGBUILDDIR>>/include/BaseInteractionParameterReader.h:75:7,
    inlined from ‘void ContactContainer::applyContactsToBiopolymers(BiopolymerClassContainer&, SimTK::GeneralContactSubsystem&, SimTK::GeneralForceSubsystem&, SimTK::SimbodyMatterSubsystem&, LeontisWesthofClass&, double, double)’ at /<<PKGBUILDDIR>>/src/ContactContainer.cpp:246:99:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, std::vector<LeontisWesthofBondRow> >’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 34%] Building CXX object CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /<<PKGBUILDDIR>>/include/Utils.h:22,
                 from /<<PKGBUILDDIR>>/include/ConstraintContainer.h:14,
                 from /<<PKGBUILDDIR>>/src/ConstraintContainer.cpp:10:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
/<<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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  146 |     if(index < 0 || index >= constraintClassVector.size())
      |                     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
/<<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/arm-linux-gnueabihf/include/c++/13/vector:72,
                 from /usr/include/simbody/SimTKcommon/internal/Array.h:39,
                 from /usr/include/simbody/SimTKcommon/basics.h:53,
                 from /usr/include/simbody/SimTKcommon.h:32:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ConstraintClass&}; _Tp = ConstraintClass; _Alloc = std::allocator<ConstraintClass>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<ConstraintClass>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ConstraintClass; _Alloc = std::allocator<ConstraintClass>]’,
    inlined from ‘void ConstraintToGroundContainer::addConstraintClassToVector(ConstraintClass)’ at /<<PKGBUILDDIR>>/src/ConstraintContainer.cpp:75:37:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ConstraintClass*, std::vector<ConstraintClass> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 37%] Building CXX object CMakeFiles/MMB.dir/src/Repel.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/Simbody.h:38,
                 from /usr/include/molmodel/SimTKmolmodel.h:47,
                 from /<<PKGBUILDDIR>>/include/Repel.h:23,
                 from /<<PKGBUILDDIR>>/src/Repel.cpp:12:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
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:
/<<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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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++){
      |           ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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";
      |                 ^~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/vector:65,
                 from /<<PKGBUILDDIR>>/include/Repel.h:18:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Displacement*, vector<Displacement> >; _ForwardIterator = Displacement*]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Displacement*, std::vector<Displacement> >’ changed in GCC 7.1
  113 |     __do_uninit_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Displacement*, std::vector<Displacement> >’ changed in GCC 7.1
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Displacement*, std::vector<Displacement> >; _ForwardIterator = Displacement*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Displacement*, vector<Displacement> >; _ForwardIterator = Displacement*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Displacement*, vector<Displacement> >; _ForwardIterator = Displacement*; _Tp = Displacement]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Displacement; _Alloc = std::allocator<Displacement>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:603:31,
    inlined from ‘std::vector<Displacement> DisplacementContainer::getDisplacementVector()’ at /<<PKGBUILDDIR>>/include/DisplacementContainer.h:31:63,
    inlined from ‘int ConstrainedDynamics::initializeBiopolymersAndCustomMolecules(SimTK::CompoundSystem&)’ at /<<PKGBUILDDIR>>/src/Repel.cpp:390:133:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Displacement*, std::vector<Displacement> >’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Displacement*, std::vector<Displacement> >; _ForwardIterator = Displacement*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Displacement*, vector<Displacement> >; _ForwardIterator = Displacement*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Displacement*, vector<Displacement> >; _ForwardIterator = Displacement*; _Tp = Displacement]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Displacement; _Alloc = std::allocator<Displacement>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:603:31,
    inlined from ‘std::vector<Displacement> DisplacementContainer::getDisplacementVector()’ at /<<PKGBUILDDIR>>/include/DisplacementContainer.h:31:63,
    inlined from ‘void ConstrainedDynamics::initializeBiopolymer(SimTK::String, SimTK::String)’ at /<<PKGBUILDDIR>>/src/Repel.cpp:418:132:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Displacement*, std::vector<Displacement> >’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const WaterDropletAboutResidueStruct*, vector<WaterDropletAboutResidueStruct> >; _ForwardIterator = WaterDropletAboutResidueStruct*]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const WaterDropletAboutResidueStruct*, std::vector<WaterDropletAboutResidueStruct> >’ changed in GCC 7.1
  113 |     __do_uninit_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const WaterDropletAboutResidueStruct*, std::vector<WaterDropletAboutResidueStruct> >’ changed in GCC 7.1
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const WaterDropletAboutResidueStruct*, std::vector<WaterDropletAboutResidueStruct> >; _ForwardIterator = WaterDropletAboutResidueStruct*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const WaterDropletAboutResidueStruct*, vector<WaterDropletAboutResidueStruct> >; _ForwardIterator = WaterDropletAboutResidueStruct*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const WaterDropletAboutResidueStruct*, vector<WaterDropletAboutResidueStruct> >; _ForwardIterator = WaterDropletAboutResidueStruct*; _Tp = WaterDropletAboutResidueStruct]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = WaterDropletAboutResidueStruct; _Alloc = std::allocator<WaterDropletAboutResidueStruct>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:603:31,
    inlined from ‘void ConstrainedDynamics::initializeMoleculesAndBonds(SimTK::CompoundSystem&, SimTK::DuMMForceFieldSubsystem&, SimTK::SimbodyMatterSubsystem&)’ at /<<PKGBUILDDIR>>/src/Repel.cpp:432:140:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const WaterDropletAboutResidueStruct*, std::vector<WaterDropletAboutResidueStruct> >’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, vector<LeontisWesthofBondRow> >; _ForwardIterator = LeontisWesthofBondRow*]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, std::vector<LeontisWesthofBondRow> >’ changed in GCC 7.1
  113 |     __do_uninit_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, std::vector<LeontisWesthofBondRow> >’ changed in GCC 7.1
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, std::vector<LeontisWesthofBondRow> >; _ForwardIterator = LeontisWesthofBondRow*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, vector<LeontisWesthofBondRow> >; _ForwardIterator = LeontisWesthofBondRow*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, vector<LeontisWesthofBondRow> >; _ForwardIterator = LeontisWesthofBondRow*; _Tp = LeontisWesthofBondRow]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = LeontisWesthofBondRow; _Alloc = std::allocator<LeontisWesthofBondRow>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:603:31,
    inlined from ‘LeontisWesthofBondMatrix::LeontisWesthofBondMatrix(const LeontisWesthofBondMatrix&)’ at /<<PKGBUILDDIR>>/include/BaseInteractionParameterReader.h:72:8,
    inlined from ‘LeontisWesthofClass::LeontisWesthofClass(const LeontisWesthofClass&)’ at /<<PKGBUILDDIR>>/include/BaseInteractionParameterReader.h:75:7,
    inlined from ‘void ConstrainedDynamics::initializeCustomForcesConstraints()’ at /<<PKGBUILDDIR>>/src/Repel.cpp:605:36:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, std::vector<LeontisWesthofBondRow> >’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 40%] Building CXX object CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /<<PKGBUILDDIR>>/include/Utils.h:22,
                 from /<<PKGBUILDDIR>>/src/MonoAtoms.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
/<<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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
/<<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/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/Simbody.h:38,
                 from /usr/include/molmodel/SimTKmolmodel.h:47,
                 from /<<PKGBUILDDIR>>/include/Spiral.h:14,
                 from /<<PKGBUILDDIR>>/src/Spiral.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
In file included from /<<PKGBUILDDIR>>/include/Spiral.h: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 ‘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 ‘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 ‘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 ‘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 ‘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
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
/<<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/arm-linux-gnueabihf/include/c++/13/regex:59,
                 from /<<PKGBUILDDIR>>/include/Spiral.h:13:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const frequencyPhaseAmplitude&}; _Tp = frequencyPhaseAmplitude; _Alloc = std::allocator<frequencyPhaseAmplitude>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<frequencyPhaseAmplitude>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/regex:57:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = frequencyPhaseAmplitude; _Alloc = std::allocator<frequencyPhaseAmplitude>]’,
    inlined from ‘void Spiral::parseInput(SimTK::String, double, double, double)’ at /<<PKGBUILDDIR>>/src/Spiral.cpp:449:41:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<frequencyPhaseAmplitude*, std::vector<frequencyPhaseAmplitude> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/regex:55:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const SimTK::String&&>, std::tuple<>}; _Key = const SimTK::String; _Val = std::pair<const SimTK::String, double>; _KeyOfValue = std::_Select1st<std::pair<const SimTK::String, double> >; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator’ changed in GCC 7.1
 2458 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/regex:56:
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const SimTK::String; _Tp = double; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]’,
    inlined from ‘double myAtoF(std::map<const SimTK::String, double>, const char*)’ at /<<PKGBUILDDIR>>/include/Utils.h:180:77:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator’ changed in GCC 7.1
  532 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  533 |                                         std::forward_as_tuple(std::move(__k)),
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  534 |                                         std::tuple<>());
      |                                         ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const SimTK::String; _Tp = double; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]’,
    inlined from ‘myAtoF(std::map<const SimTK::String, double>, const char*)::<lambda()>’ at /<<PKGBUILDDIR>>/include/Utils.h:179:17,
    inlined from ‘constexpr _Res std::__invoke_impl(__invoke_other, _Fn&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Fn = myAtoF(std::map<const SimTK::String, double>, const char*)::<lambda()>&; _Args = {}]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/invoke.h:61:67,
    inlined from ‘constexpr std::enable_if_t<is_invocable_r_v<_Res, _Callable, _Args ...>, _Res> std::__invoke_r(_Callable&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Callable = myAtoF(std::map<const SimTK::String, double>, const char*)::<lambda()>&; _Args = {}]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/invoke.h:116:38,
    inlined from ‘static _Res std::_Function_handler<_Res(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Res = std::__cxx11::basic_ostringstream<char>; _Functor = myAtoF(std::map<const SimTK::String, double>, const char*)::<lambda()>; _ArgTypes = {}]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/std_function.h:291:44:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator’ changed in GCC 7.1
  532 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  533 |                                         std::forward_as_tuple(std::move(__k)),
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  534 |                                         std::tuple<>());
      |                                         ~~~~~~~~~~~~~~~
[ 46%] Building CXX object CMakeFiles/MMB.dir/src/ParameterReader.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /<<PKGBUILDDIR>>/include/Utils.h:22,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/src/ParameterReader.cpp:17:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
/<<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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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))
      |                ^
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
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 ‘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 ‘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 ‘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/arm-linux-gnueabihf/include/c++/13/vector:72,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:18:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const MMBAtomInfo&}; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<MMBAtomInfo>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/vector:66:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AtomSpring&}; _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<AtomSpring>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<AtomSpring*, std::vector<AtomSpring> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]’,
    inlined from ‘void AtomSpringContainer::add(AtomSpring&)’ at /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:41:102,
    inlined from ‘void ParameterReader::addC1pSprings(LeontisWesthofClass)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:153:39:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<AtomSpring*, std::vector<AtomSpring> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AllResiduesWithin&}; _Tp = AllResiduesWithin; _Alloc = std::allocator<AllResiduesWithin>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<AllResiduesWithin>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AllResiduesWithin; _Alloc = std::allocator<AllResiduesWithin>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<AllResiduesWithin*, std::vector<AllResiduesWithin> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AllResiduesWithin; _Alloc = std::allocator<AllResiduesWithin>]’,
    inlined from ‘void ParameterReader::addAllResiduesWithin(SimTK::String, int, double)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:769:45:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<AllResiduesWithin*, std::vector<AllResiduesWithin> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CovalentBondClass&}; _Tp = CovalentBondClass; _Alloc = std::allocator<CovalentBondClass>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<CovalentBondClass>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CovalentBondClass; _Alloc = std::allocator<CovalentBondClass>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<CovalentBondClass*, std::vector<CovalentBondClass> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BasePair&}; _Tp = BasePair; _Alloc = std::allocator<BasePair>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<BasePair>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BasePair; _Alloc = std::allocator<BasePair>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<BasePair*, std::vector<BasePair> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const MobilizerDomainsInterface&}; _Tp = MobilizerDomainsInterface; _Alloc = std::allocator<MobilizerDomainsInterface>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<MobilizerDomainsInterface>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MobilizerDomainsInterface; _Alloc = std::allocator<MobilizerDomainsInterface>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MobilizerDomainsInterface*, std::vector<MobilizerDomainsInterface> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AtomicPropertyOverrideStruct&}; _Tp = AtomicPropertyOverrideStruct; _Alloc = std::allocator<AtomicPropertyOverrideStruct>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<AtomicPropertyOverrideStruct>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomicPropertyOverrideStruct; _Alloc = std::allocator<AtomicPropertyOverrideStruct>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<AtomicPropertyOverrideStruct*, std::vector<AtomicPropertyOverrideStruct> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const WaterDropletAboutResidueStruct&}; _Tp = WaterDropletAboutResidueStruct; _Alloc = std::allocator<WaterDropletAboutResidueStruct>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<WaterDropletAboutResidueStruct>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = WaterDropletAboutResidueStruct; _Alloc = std::allocator<WaterDropletAboutResidueStruct>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<WaterDropletAboutResidueStruct*, std::vector<WaterDropletAboutResidueStruct> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const IncludeIntraChainInterface&}; _Tp = IncludeIntraChainInterface; _Alloc = std::allocator<IncludeIntraChainInterface>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<IncludeIntraChainInterface>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = IncludeIntraChainInterface; _Alloc = std::allocator<IncludeIntraChainInterface>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<IncludeIntraChainInterface*, std::vector<IncludeIntraChainInterface> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/set:62,
                 from /usr/include/simbody/simmath/internal/Contact.h:30,
                 from /usr/include/simbody/SimTKmath.h:46,
                 from /usr/include/simbody/SimTKsimbody.h:44:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const SimTK::String&&>, std::tuple<>}; _Key = const SimTK::String; _Val = std::pair<const SimTK::String, double>; _KeyOfValue = std::_Select1st<std::pair<const SimTK::String, double> >; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator’ changed in GCC 7.1
 2458 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/map:63,
                 from /usr/include/simbody/simmath/internal/CollisionDetectionAlgorithm.h:32,
                 from /usr/include/simbody/SimTKmath.h:48:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const SimTK::String; _Tp = double; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator’ changed in GCC 7.1
  532 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  533 |                                         std::forward_as_tuple(std::move(__k)),
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  534 |                                         std::tuple<>());
      |                                         ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const SimTK::String; _Tp = double; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]’,
    inlined from ‘ParameterReader::initializeFromFileOnly(const char*)::<lambda()>’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:4538:5,
    inlined from ‘constexpr _Res std::__invoke_impl(__invoke_other, _Fn&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Fn = ParameterReader::initializeFromFileOnly(const char*)::<lambda()>&; _Args = {}]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/invoke.h:61:67,
    inlined from ‘constexpr std::enable_if_t<is_invocable_r_v<_Res, _Callable, _Args ...>, _Res> std::__invoke_r(_Callable&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Callable = ParameterReader::initializeFromFileOnly(const char*)::<lambda()>&; _Args = {}]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/invoke.h:116:38,
    inlined from ‘static _Res std::_Function_handler<_Res(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Res = std::__cxx11::basic_ostringstream<char>; _Functor = ParameterReader::initializeFromFileOnly(const char*)::<lambda()>; _ArgTypes = {}]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/std_function.h:291:44:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator’ changed in GCC 7.1
  532 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  533 |                                         std::forward_as_tuple(std::move(__k)),
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  534 |                                         std::tuple<>());
      |                                         ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const SimTK::String; _Tp = double; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]’,
    inlined from ‘myAtoF(std::map<const SimTK::String, double>, const char*)::<lambda()>’ at /<<PKGBUILDDIR>>/include/Utils.h:179:17,
    inlined from ‘constexpr _Res std::__invoke_impl(__invoke_other, _Fn&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Fn = myAtoF(std::map<const SimTK::String, double>, const char*)::<lambda()>&; _Args = {}]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/invoke.h:61:67,
    inlined from ‘constexpr std::enable_if_t<is_invocable_r_v<_Res, _Callable, _Args ...>, _Res> std::__invoke_r(_Callable&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Callable = myAtoF(std::map<const SimTK::String, double>, const char*)::<lambda()>&; _Args = {}]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/invoke.h:116:38,
    inlined from ‘static _Res std::_Function_handler<_Res(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Res = std::__cxx11::basic_ostringstream<char>; _Functor = myAtoF(std::map<const SimTK::String, double>, const char*)::<lambda()>; _ArgTypes = {}]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/std_function.h:291:44:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator’ changed in GCC 7.1
  532 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  533 |                                         std::forward_as_tuple(std::move(__k)),
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  534 |                                         std::tuple<>());
      |                                         ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const SimTK::String; _Tp = double; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]’,
    inlined from ‘ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)::<lambda()>’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:3498:9,
    inlined from ‘constexpr _Res std::__invoke_impl(__invoke_other, _Fn&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Fn = ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)::<lambda()>&; _Args = {}]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/invoke.h:61:67,
    inlined from ‘constexpr std::enable_if_t<is_invocable_r_v<_Res, _Callable, _Args ...>, _Res> std::__invoke_r(_Callable&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Callable = ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)::<lambda()>&; _Args = {}]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/invoke.h:116:38,
    inlined from ‘static _Res std::_Function_handler<_Res(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Res = std::__cxx11::basic_ostringstream<char>; _Functor = ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)::<lambda()>; _ArgTypes = {}]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/std_function.h:291:44:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type ‘std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator’ changed in GCC 7.1
  532 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  533 |                                         std::forward_as_tuple(std::move(__k)),
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  534 |                                         std::tuple<>());
      |                                         ~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/vector:65:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  113 |     __do_uninit_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1619:35,
    inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:238:44:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Displacement&}; _Tp = Displacement; _Alloc = std::allocator<Displacement>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<Displacement>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Displacement; _Alloc = std::allocator<Displacement>]’,
    inlined from ‘void DisplacementContainer::add(Displacement, BiopolymerClassContainer&)’ at /<<PKGBUILDDIR>>/include/DisplacementContainer.h:25:181:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Displacement*, std::vector<Displacement> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93,
                 from /usr/include/simbody/SimTKcommon/Simmatrix.h:37:
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 ‘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/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /<<PKGBUILDDIR>>/src/BaseInteractionParameterReader.cpp:17:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
/<<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/arm-linux-gnueabihf/include/c++/13/vector:72,
                 from /usr/arm-linux-gnueabihf/include/c++/13/functional:64,
                 from /<<PKGBUILDDIR>>/include/MMBLogger.h:6,
                 from /<<PKGBUILDDIR>>/src/BaseInteractionParameterReader.cpp:11:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {LeontisWesthofBondRow}; _Tp = LeontisWesthofBondRow; _Alloc = std::allocator<LeontisWesthofBondRow>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<LeontisWesthofBondRow>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {LeontisWesthofBondRow}; _Tp = LeontisWesthofBondRow; _Alloc = std::allocator<LeontisWesthofBondRow>]’,
    inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = LeontisWesthofBondRow; _Alloc = std::allocator<LeontisWesthofBondRow>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1296:21,
    inlined from ‘void LeontisWesthofClass::initialize(const SimTK::String&)’ at /<<PKGBUILDDIR>>/src/BaseInteractionParameterReader.cpp:215:63:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<LeontisWesthofBondRow*, std::vector<LeontisWesthofBondRow> >’ changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 53%] Building CXX object CMakeFiles/MMB.dir/src/TetherForce.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/Simbody.h:38,
                 from /usr/include/molmodel/SimTKmolmodel.h:47,
                 from /<<PKGBUILDDIR>>/include/TetherForce.h:18,
                 from /<<PKGBUILDDIR>>/src/TetherForce.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/TetherForce.h:19:
/<<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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
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 ‘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 ‘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/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/Simbody.h:38,
                 from /usr/include/molmodel/SimTKmolmodel.h:47,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClassTwoTransformForces.h:16,
                 from /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:10:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClassTwoTransformForces.h: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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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;
      |                ^~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
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 ‘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 ‘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:
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;
      |                      ^~~~~~~~~
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;
      |                    ^~~~~~~~~~~
[ 59%] Building CXX object CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/Simbody.h:38,
                 from /usr/include/molmodel/SimTKmolmodel.h:47,
                 from /<<PKGBUILDDIR>>/include/Water.h:1,
                 from /<<PKGBUILDDIR>>/include/WaterDroplet.h:15,
                 from /<<PKGBUILDDIR>>/src/WaterDroplet.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
In file included from /<<PKGBUILDDIR>>/include/WaterDroplet.h: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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
/<<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/arm-linux-gnueabihf/include/c++/13/vector:72,
                 from /<<PKGBUILDDIR>>/include/WaterDroplet.h:13:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const WaterDroplet&}; _Tp = WaterDroplet; _Alloc = std::allocator<WaterDroplet>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<WaterDroplet>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = WaterDroplet; _Alloc = std::allocator<WaterDroplet>]’,
    inlined from ‘void WaterDropletContainer::add(WaterDroplet&)’ at /<<PKGBUILDDIR>>/src/WaterDroplet.cpp:70:33:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<WaterDroplet*, std::vector<WaterDroplet> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const MMBAtomInfo&}; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<MMBAtomInfo>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]’,
    inlined from ‘void WaterDroplet::addWaterMolecules(SimTK::CompoundSystem&, SimTK::DuMMForceFieldSubsystem&, SimTK::SimbodyMatterSubsystem&, BiopolymerClassContainer&)’ at /<<PKGBUILDDIR>>/src/WaterDroplet.cpp:294:51:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AtomSpring&}; _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<AtomSpring>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]’,
    inlined from ‘void AtomSpringContainer::add(AtomSpring&)’ at /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:41:102,
    inlined from ‘void WaterDroplet::addTethers(AtomSpringContainer&)’ at /<<PKGBUILDDIR>>/src/WaterDroplet.cpp:164:32:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<AtomSpring*, std::vector<AtomSpring> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 62%] Building CXX object CMakeFiles/MMB.dir/src/DensityMap.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /<<PKGBUILDDIR>>/include/Utils.h:22,
                 from /<<PKGBUILDDIR>>/src/DensityMap.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
/<<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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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;
      |             ^~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
/<<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/arm-linux-gnueabihf/include/c++/13/set:62,
                 from /usr/include/simbody/simmath/internal/Contact.h:30,
                 from /usr/include/simbody/SimTKmath.h:46,
                 from /usr/include/simbody/SimTKsimbody.h:44:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_tree.h: In function ‘std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = double; _Val = std::pair<const double, DensityMap::densityAutocorrelation(bool, bool) const::autoCorrelationStruct>; _KeyOfValue = std::_Select1st<std::pair<const double, DensityMap::densityAutocorrelation(bool, bool) const::autoCorrelationStruct> >; _Compare = std::less<double>; _Alloc = std::allocator<std::pair<const double, DensityMap::densityAutocorrelation(bool, bool) const::autoCorrelationStruct> >]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_tree.h:2210:5: note: parameter passing for argument of type ‘std::_Rb_tree<double, std::pair<const double, DensityMap::densityAutocorrelation(bool, bool) const::autoCorrelationStruct>, std::_Select1st<std::pair<const double, DensityMap::densityAutocorrelation(bool, bool) const::autoCorrelationStruct> >, std::less<double>, std::allocator<std::pair<const double, DensityMap::densityAutocorrelation(bool, bool) const::autoCorrelationStruct> > >::const_iterator’ changed in GCC 7.1
 2210 |     _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 65%] Building CXX object CMakeFiles/MMB.dir/src/DensityForce.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/Simbody.h:38,
                 from /usr/include/molmodel/SimTKmolmodel.h:47,
                 from /<<PKGBUILDDIR>>/include/DensityForce.h:19,
                 from /<<PKGBUILDDIR>>/src/DensityForce.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/DensityForce.h:20:
/<<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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
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 ‘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 ‘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/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/Simbody.h:38,
                 from /usr/include/molmodel/SimTKmolmodel.h:47,
                 from /<<PKGBUILDDIR>>/include/ElectrostaticPotentialGridForce.h:18,
                 from /<<PKGBUILDDIR>>/src/ElectrostaticPotentialGridForce.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/ElectrostaticPotentialGridForce.h:19:
/<<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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
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 ‘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 ‘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/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /<<PKGBUILDDIR>>/include/Utils.h:22,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/PeriodicPdbAndEnergyWriter.h:13,
                 from /<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:18:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
/<<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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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;
      |         ^~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
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 ‘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 ‘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/arm-linux-gnueabihf/include/c++/13/vector:72,
                 from /usr/arm-linux-gnueabihf/include/c++/13/functional:64,
                 from /<<PKGBUILDDIR>>/include/MMBLogger.h:6,
                 from /<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:17:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
    inlined from ‘virtual void SimTK::PeriodicPdbAndEnergyWriter::handleEvent(SimTK::State&, SimTK::Real, bool&) const’ at /<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:127:55:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
    inlined from ‘virtual void SimTK::PeriodicPdbAndEnergyWriter::handleEvent(SimTK::State&, SimTK::Real, bool&) const’ at /<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:175:33:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 78%] Building CXX object CMakeFiles/MMB.dir/src/CifOutput.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /usr/include/molmodel/molmodel/internal/Compound.h:36,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:16,
                 from /<<PKGBUILDDIR>>/include/CifOutput.h:5,
                 from /<<PKGBUILDDIR>>/src/CifOutput.cpp:1:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20:
/<<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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
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 ‘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 ‘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/arm-linux-gnueabihf/include/c++/13/memory:69,
                 from /usr/include/simbody/SimTKcommon/internal/ClonePtr.h:29,
                 from /usr/include/simbody/SimTKcommon/basics.h:44,
                 from /usr/include/simbody/SimTKcommon.h:32:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gemmi::Atom*, vector<gemmi::Atom> >; _ForwardIterator = gemmi::Atom*]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gemmi::Atom*, std::vector<gemmi::Atom> >’ changed in GCC 7.1
  113 |     __do_uninit_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gemmi::Atom*, std::vector<gemmi::Atom> >’ changed in GCC 7.1
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gemmi::Atom*, std::vector<gemmi::Atom> >; _ForwardIterator = gemmi::Atom*; bool _TrivialValueTypes = false]’,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gemmi::Atom*, vector<gemmi::Atom> >; _ForwardIterator = gemmi::Atom*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gemmi::Atom*, vector<gemmi::Atom> >; _ForwardIterator = gemmi::Atom*; _Tp = gemmi::Atom]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Atom; _Alloc = std::allocator<gemmi::Atom>]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:603:31,
    inlined from ‘gemmi::Residue::Residue(const gemmi::Residue&)’ at /usr/include/gemmi/model.hpp:176:8,
    inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = gemmi::Residue; _Args = {const gemmi::Residue&}]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_construct.h:119:7,
    inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gemmi::Residue*, vector<gemmi::Residue, allocator<gemmi::Residue> > >; _ForwardIterator = gemmi::Residue*]’ at /usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:120:21:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gemmi::Atom*, std::vector<gemmi::Atom> >’ changed in GCC 7.1
  137 |         { return std::__do_uninit_copy(__first, __last, __result); }
      |                  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 81%] Building CXX object CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /<<PKGBUILDDIR>>/src/NTC_PARAMETER_READER.cpp:15:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
/<<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/arm-linux-gnueabihf/include/c++/13/vector:72,
                 from /usr/arm-linux-gnueabihf/include/c++/13/functional:64,
                 from /<<PKGBUILDDIR>>/include/MMBLogger.h:6,
                 from /<<PKGBUILDDIR>>/src/NTC_PARAMETER_READER.cpp:12:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {NTC_PAR_BondRow}; _Tp = NTC_PAR_BondRow; _Alloc = std::allocator<NTC_PAR_BondRow>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<NTC_PAR_BondRow>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {NTC_PAR_BondRow}; _Tp = NTC_PAR_BondRow; _Alloc = std::allocator<NTC_PAR_BondRow>]’,
    inlined from ‘void NTC_PAR_Class::initialize(const SimTK::String&)’ at /<<PKGBUILDDIR>>/src/NTC_PARAMETER_READER.cpp:133:64:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<NTC_PAR_BondRow*, std::vector<NTC_PAR_BondRow> >’ changed in GCC 7.1
  123 |           _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 87%] Building CXX object CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /usr/include/molmodel/molmodel/internal/Compound.h:36,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:16,
                 from /<<PKGBUILDDIR>>/src/NtCClassContainer.cpp:13:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20:
/<<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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
/<<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/arm-linux-gnueabihf/include/c++/13/vector:72,
                 from /usr/include/simbody/SimTKcommon/internal/Array.h:39,
                 from /usr/include/simbody/SimTKcommon/basics.h:53,
                 from /usr/include/simbody/SimTKcommon.h:32:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const NTC_Classes&}; _Tp = NTC_Classes; _Alloc = std::allocator<NTC_Classes>]’:
/usr/arm-linux-gnueabihf/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<NTC_Classes>::iterator’ changed in GCC 7.1
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/arm-linux-gnueabihf/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = NTC_Classes; _Alloc = std::allocator<NTC_Classes>]’,
    inlined from ‘void NTC_Class_Container::add_NTC_Class(BiopolymerClassContainer&, const NTC_PAR_Class&, NTC_Classes&)’ at /<<PKGBUILDDIR>>/src/NtCClassContainer.cpp:193:37:
/usr/arm-linux-gnueabihf/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<NTC_Classes*, std::vector<NTC_Classes> >’ changed in GCC 7.1
 1289 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 90%] Building CXX object CMakeFiles/MMB.dir/src/NtCForces.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/Simbody.h:38,
                 from /usr/include/molmodel/SimTKmolmodel.h:47,
                 from /<<PKGBUILDDIR>>/include/NtCForces.h:12,
                 from /<<PKGBUILDDIR>>/src/NtCForces.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/NtCForces.h: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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
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 ‘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 ‘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/arm-linux-gnueabihf-g++ -fPIC -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -Wl,-z,relro -shared -Wl,-soname,libMMB.so.4.0 -o libMMB.so.4.0 CMakeFiles/MMB.dir/src/Utils.cpp.o CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o CMakeFiles/MMB.dir/src/DensityContainer.cpp.o CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o CMakeFiles/MMB.dir/src/ContactContainer.cpp.o CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o CMakeFiles/MMB.dir/src/Repel.cpp.o CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o CMakeFiles/MMB.dir/src/Spiral.cpp.o CMakeFiles/MMB.dir/src/ParameterReader.cpp.o CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o CMakeFiles/MMB.dir/src/TetherForce.cpp.o CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o CMakeFiles/MMB.dir/src/DensityMap.cpp.o CMakeFiles/MMB.dir/src/DensityForce.cpp.o CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o CMakeFiles/MMB.dir/src/MMBLogger.cpp.o CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o CMakeFiles/MMB.dir/src/CifOutput.cpp.o CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o CMakeFiles/MMB.dir/src/NtCForces.cpp.o   -L/<<PKGBUILDDIR>>/SYSTEM  -Wl,-rpath,/<<PKGBUILDDIR>>/SYSTEM: /usr/lib/arm-linux-gnueabihf/libSimTKmolmodel.so.3.1 /usr/lib/arm-linux-gnueabihf/libOpenMM.so /usr/lib/arm-linux-gnueabihf/libz.so -lgemmi_cpp /usr/lib/arm-linux-gnueabihf/libSimTKsimbody.so.3.7 /usr/lib/arm-linux-gnueabihf/libSimTKmath.so.3.7 /usr/lib/arm-linux-gnueabihf/libSimTKcommon.so.3.7 /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/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-arm-linux-gnueabihf'
[ 93%] Built target MMB
make  -f CMakeFiles/MMB_EXEC.dir/build.make CMakeFiles/MMB_EXEC.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/MMB_EXEC.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make  -f CMakeFiles/MMB_EXEC.dir/build.make CMakeFiles/MMB_EXEC.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 96%] Building CXX object CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o
/usr/bin/arm-linux-gnueabihf-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf -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 -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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/Simbody.h:38,
                 from /usr/include/molmodel/SimTKmolmodel.h:47,
                 from /<<PKGBUILDDIR>>/src/RNABuilder.cpp:20:
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1169 | approxCompleteEllipticIntegralsKE(double m)
      |                                           ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1177 | approxCompleteEllipticIntegralsKE(float m)
      |                                          ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1186 | approxCompleteEllipticIntegralsKE(int m)
      |                                        ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
      |                                                                  ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function ‘std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)’:
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
      |                                                                  ^
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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
 1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
      |                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of ‘std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]’:
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48:   required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type ‘std::pair<float, float>’ when C++17 is enabled changed to match C++14 in GCC 10.1
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 ‘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 ‘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/arm-linux-gnueabihf-g++ -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-arm-linux-gnueabihf: libMMB.so.4.0 /usr/lib/arm-linux-gnueabihf/libSimTKmolmodel.so.3.1 /usr/lib/arm-linux-gnueabihf/libSimTKsimbody.so.3.7 /usr/lib/arm-linux-gnueabihf/libSimTKmath.so.3.7 /usr/lib/arm-linux-gnueabihf/libSimTKcommon.so.3.7 /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lrt -ldl -lm 
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[100%] Built target MMB_EXEC
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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-arm-linux-gnueabihf && 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-arm-linux-gnueabihf'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
make  -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/libMMB.so.4.0
-- Set non-toolchain portion of runtime path of "/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libMMB.so.4.0" to ""
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/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/arm-linux-gnueabihf/cmake/mmb/MmbConfigVersion.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/mmb/MmbTargets.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/mmb/MmbTargets-release.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/mmb.pc
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
   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
dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libmmb4.0t64/usr/lib/arm-linux-gnueabihf/libMMB.so.4.0 found in none of the libraries
   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_armhf.deb'.
dpkg-deb: building package 'libmmb4.0t64' in '../libmmb4.0t64_4.0.0+dfsg-3.1_armhf.deb'.
dpkg-deb: building package 'libmmb4.0t64-dbgsym' in '../libmmb4.0t64-dbgsym_4.0.0+dfsg-3.1_armhf.deb'.
dpkg-deb: building package 'mmb' in '../mmb_4.0.0+dfsg-3.1_armhf.deb'.
dpkg-deb: building package 'mmb-dbgsym' in '../mmb-dbgsym_4.0.0+dfsg-3.1_armhf.deb'.
 dpkg-genbuildinfo --build=any -O../macromoleculebuilder_4.0.0+dfsg-3.1_armhf.buildinfo
 dpkg-genchanges --build=any -O../macromoleculebuilder_4.0.0+dfsg-3.1_armhf.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 2024-04-04T11:42:10Z

Finished
--------

I: Built successfully

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


macromoleculebuilder_4.0.0+dfsg-3.1_armhf.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: armhf
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
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 6238b3f454ebb3c7f44f7831ef821079 10477 science optional macromoleculebuilder_4.0.0+dfsg-3.1_armhf.buildinfo
 5c1f5ced048a6b4906e3be616bdbe5be 1649400 debug optional mmb-dbgsym_4.0.0+dfsg-3.1_armhf.deb
 772a569f6639ae4018e6d461e7ce6ec1 27308 science optional mmb_4.0.0+dfsg-3.1_armhf.deb

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

Format: 1.0
Source: macromoleculebuilder
Binary: libmmb-dev libmmb4.0t64 libmmb4.0t64-dbgsym mmb mmb-dbgsym
Architecture: armhf
Version: 4.0.0+dfsg-3.1
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Build-Origin: Debian
Build-Architecture: amd64
Build-Date: Thu, 04 Apr 2024 11:42:09 +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),
 base-passwd (= 3.6.3),
 bash (= 5.2.21-2),
 binutils (= 2.42-4),
 binutils-common (= 2.42-4),
 binutils-x86-64-linux-gnu (= 2.42-4),
 bsdextrautils (= 2.39.3-11),
 bsdutils (= 1:2.39.3-11),
 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-x86-64-linux-gnu (= 13.2.0-23),
 cpp-x86-64-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-x86-64-linux-gnu (= 13.2.0-23),
 g++-x86-64-linux-gnu (= 4:13.2.0-7),
 gcc (= 4:13.2.0-7),
 gcc-13 (= 13.2.0-23),
 gcc-13-base (= 13.2.0-23),
 gcc-13-x86-64-linux-gnu (= 13.2.0-23),
 gcc-14-base (= 14-20240330-1),
 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),
 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 (= 2.39.3-11),
 libbrotli1 (= 1.1.0-2+b3),
 libbsd0 (= 0.12.2-1),
 libbz2-1.0 (= 1.0.8-5.1),
 libc-bin (= 2.37-15.1),
 libc-dev-bin (= 2.37-15.1),
 libc6 (= 2.37-15.1),
 libc6-dev (= 2.37-15.1),
 libcap-ng0 (= 0.8.4-2),
 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 (= 8.7.1-2),
 libdb5.3t64 (= 5.3.28+dfsg2-6),
 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-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 (= 24.0.4-1),
 libegl1 (= 1.7.0-1),
 libelf1t64 (= 0.191-1),
 libexpat1 (= 2.6.2-1),
 libffi8 (= 3.4.6-1),
 libfile-stripnondeterminism-perl (= 1.13.1-1),
 libgbm1 (= 24.0.4-1),
 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 (= 24.0.4-1),
 libgl1-mesa-dri (= 24.0.4-1),
 libglapi-mesa (= 24.0.4-1),
 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 (= 24.0.4-1),
 libglx0 (= 1.7.0-1),
 libgmp10 (= 2:6.3.0+dfsg-2+b1),
 libgnutls30t64 (= 3.8.4-2),
 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+b1),
 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 (= 2.39.3-11),
 libmpc3 (= 1.3.1-1+b2),
 libmpfr6 (= 4.2.1-1+b1),
 libncursesw6 (= 6.4+20240113-1),
 libnettle8t64 (= 3.9.1-2.2),
 libnghttp2-14 (= 1.60.0-1),
 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 (= 1.5.3-6),
 libpam-modules-bin (= 1.5.3-6),
 libpam-runtime (= 1.5.3-6),
 libpam0t64 (= 1.5.3-4),
 libpcre2-8-0 (= 10.42-4+b1),
 libperl5.38t64 (= 5.38.2-3.2),
 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 (= 3.11.8-3+b2),
 libpython3.11-stdlib (= 3.11.8-3+b2),
 libquadmath0 (= 14-20240330-1),
 libreadline8t64 (= 8.2-4),
 librhash0 (= 1.4.3-3+b1),
 librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b3),
 libsasl2-2 (= 2.1.28+dfsg1-6),
 libsasl2-modules-db (= 2.1.28+dfsg1-6),
 libseccomp2 (= 2.5.5-1),
 libselinux1 (= 3.5-2+b1),
 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 (= 2.39.3-11),
 libsqlite3-0 (= 3.45.2-1),
 libssh2-1t64 (= 1.11.0-4.1+b1),
 libssl3t64 (= 3.1.5-1.1),
 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),
 libtinfo6 (= 6.4+20240113-1),
 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 (= 2.39.3-11),
 libuv1t64 (= 1.48.0-1.1),
 libvulkan1 (= 1.3.275.0-1),
 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 (= 1.15-1),
 libxcb-dri3-0 (= 1.15-1),
 libxcb-glx0 (= 1.15-1),
 libxcb-present0 (= 1.15-1),
 libxcb-randr0 (= 1.15-1),
 libxcb-shm0 (= 1.15-1),
 libxcb-sync1 (= 1.15-1),
 libxcb-xfixes0 (= 1.15-1),
 libxcb1 (= 1.15-1),
 libxcb1-dev (= 1.15-1),
 libxdmcp-dev (= 1:1.1.2-3),
 libxdmcp6 (= 1:1.1.2-3),
 libxext-dev (= 2:1.3.4-1+b1),
 libxext6 (= 2:1.3.4-1+b1),
 libxfixes-dev (= 1:6.0.0-2),
 libxfixes3 (= 1:6.0.0-2),
 libxi-dev (= 2:1.8.1-1),
 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+b1),
 libxmu-headers (= 2:1.1.3-3),
 libxmu6 (= 2:1.1.3-3+b1),
 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 (= 2.12.0-4),
 mawk (= 1.3.4.20240123-1),
 media-types (= 10.1.0),
 ncurses-base (= 6.4+20240113-1),
 ncurses-bin (= 6.4+20240113-1),
 netbase (= 6.4),
 patch (= 2.7.6-7),
 perl (= 5.38.2-3.2),
 perl-base (= 5.38.2-3.2),
 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 (= 3.11.8-3+b2),
 python3.11-minimal (= 3.11.8-3+b2),
 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 (= 3.08-7),
 tao-pegtl-dev (= 3.2.7-1),
 tar (= 1.35+dfsg-3),
 tzdata (= 2024a-1),
 usr-is-merged (= 39),
 util-linux (= 2.39.3-11),
 x11-common (= 1:7.7+23),
 x11proto-dev (= 2023.2-1),
 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_US.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_armhf.deb
-----------------------------------

 new Debian package, version 2.0.
 size 76468 bytes: control archive=2904 bytes.
     781 bytes,    20 lines      control
    5121 bytes,    72 lines      md5sums
 Package: libmmb-dev
 Source: macromoleculebuilder
 Version: 4.0.0+dfsg-3.1
 Architecture: armhf
 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/arm-linux-gnueabihf/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/lib/arm-linux-gnueabihf/cmake/
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/lib/arm-linux-gnueabihf/cmake/mmb/
-rw-r--r-- root/root      2756 2024-02-29 10:59 ./usr/lib/arm-linux-gnueabihf/cmake/mmb/MmbConfigVersion.cmake
-rw-r--r-- root/root       824 2024-02-29 10:59 ./usr/lib/arm-linux-gnueabihf/cmake/mmb/MmbTargets-release.cmake
-rw-r--r-- root/root      4458 2024-02-29 10:59 ./usr/lib/arm-linux-gnueabihf/cmake/mmb/MmbTargets.cmake
lrwxrwxrwx root/root         0 2024-02-29 10:59 ./usr/lib/arm-linux-gnueabihf/libMMB.so -> libMMB.so.4.0
drwxr-xr-x root/root         0 2024-02-29 10:59 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root       197 2024-02-29 10:59 ./usr/lib/arm-linux-gnueabihf/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_armhf.deb
--------------------------------------------

 new Debian package, version 2.0.
 size 24845232 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: armhf
 Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
 Installed-Size: 26090
 Depends: libmmb4.0t64 (= 4.0.0+dfsg-3.1)
 Section: debug
 Priority: optional
 Multi-Arch: same
 Description: debug symbols for libmmb4.0t64
 Build-Ids: 53487238e0f43fe23a3e09314c0f23663c89e09d

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/53/
-rw-r--r-- root/root  26705052 2024-02-29 10:59 ./usr/lib/debug/.build-id/53/487238e0f43fe23a3e09314c0f23663c89e09d.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_armhf.deb
-------------------------------------

 new Debian package, version 2.0.
 size 983628 bytes: control archive=1076 bytes.
     908 bytes,    20 lines      control
     303 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: armhf
 Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
 Installed-Size: 2865
 Depends: libc6 (>= 2.33), libgcc-s1 (>= 3.5), 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
 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/arm-linux-gnueabihf/
-rw-r--r-- root/root   2915848 2024-02-29 10:59 ./usr/lib/arm-linux-gnueabihf/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_armhf.deb
-----------------------------------

 new Debian package, version 2.0.
 size 1649400 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: armhf
 Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
 Installed-Size: 1660
 Depends: mmb (= 4.0.0+dfsg-3.1)
 Section: debug
 Priority: optional
 Description: debug symbols for mmb
 Build-Ids: f966112cec5e7fc7b269b378d24a26f760cf4447

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/f9/
-rw-r--r-- root/root   1688624 2024-02-29 10:59 ./usr/lib/debug/.build-id/f9/66112cec5e7fc7b269b378d24a26f760cf4447.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_armhf.deb
----------------------------

 new Debian package, version 2.0.
 size 27308 bytes: control archive=888 bytes.
     779 bytes,    15 lines      control
     242 bytes,     4 lines      md5sums
 Package: mmb
 Source: macromoleculebuilder
 Version: 4.0.0+dfsg-3.1
 Architecture: armhf
 Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
 Installed-Size: 77
 Depends: mmb-common, libc6 (>= 2.34), libgcc-s1 (>= 3.5), 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     63556 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:amd64
Filtered Build-Depends: lintian:amd64
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 (0 B/s)
Reading package lists...
Reading package lists...

Install lintian build dependencies (apt-based resolver)
-------------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
Execute external solver...
The following package was automatically installed and is no longer required:
  mount
Use 'apt autoremove' to remove it.
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
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  libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl
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  libipc-run3-perl libipc-system-simple-perl libiterator-perl
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  libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl
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  libtext-levenshteinxs-perl libtext-markdown-discount-perl
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  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
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  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
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  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
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  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-glob-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:armhf t1utils unzip
0 upgraded, 125 newly installed, 0 to remove and 0 not upgraded.
Need to get 12.4 MB of archives.
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Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 B]
Get:2 http://localhost:3142/debian sid/main amd64 openssl amd64 3.1.5-1.1 [1241 kB]
Get:3 http://localhost:3142/debian sid/main amd64 ca-certificates all 20240203 [158 kB]
Get:4 http://localhost:3142/debian sid/main amd64 diffstat amd64 1.66-1 [34.0 kB]
Get:5 http://localhost:3142/debian sid/main amd64 libassuan0 amd64 2.5.6-1 [49.9 kB]
Get:6 http://localhost:3142/debian sid/main amd64 gpgconf amd64 2.2.40-3 [565 kB]
Get:7 http://localhost:3142/debian sid/main amd64 gpg amd64 2.2.40-3 [950 kB]
Get:8 http://localhost:3142/debian sid/main amd64 iso-codes all 4.16.0-1 [2936 kB]
Get:9 http://localhost:3142/debian sid/main amd64 libaliased-perl all 0.34-3 [13.5 kB]
Get:10 http://localhost:3142/debian sid/main amd64 libapt-pkg-perl amd64 0.1.40+b5 [66.9 kB]
Get:11 http://localhost:3142/debian sid/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b1 [10.6 kB]
Get:12 http://localhost:3142/debian sid/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB]
Get:13 http://localhost:3142/debian sid/main amd64 libdevel-callchecker-perl amd64 0.008-2+b2 [15.1 kB]
Get:14 http://localhost:3142/debian sid/main amd64 libparams-classify-perl amd64 0.015-2+b3 [22.4 kB]
Get:15 http://localhost:3142/debian sid/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get:16 http://localhost:3142/debian sid/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB]
Get:17 http://localhost:3142/debian sid/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB]
Get:18 http://localhost:3142/debian sid/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B]
Get:19 http://localhost:3142/debian sid/main amd64 libvariable-magic-perl amd64 0.64-1 [44.7 kB]
Get:20 http://localhost:3142/debian sid/main amd64 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB]
Get:21 http://localhost:3142/debian sid/main amd64 libberkeleydb-perl amd64 0.64-2+b3 [121 kB]
Get:22 http://localhost:3142/debian sid/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB]
Get:23 http://localhost:3142/debian sid/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB]
Get:24 http://localhost:3142/debian sid/main amd64 liburi-perl all 5.28-1 [98.6 kB]
Get:25 http://localhost:3142/debian sid/main amd64 libhtml-parser-perl amd64 3.82-1 [98.9 kB]
Get:26 http://localhost:3142/debian sid/main amd64 libcgi-pm-perl all 4.64-1 [217 kB]
Get:27 http://localhost:3142/debian sid/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B]
Get:28 http://localhost:3142/debian sid/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB]
Get:29 http://localhost:3142/debian sid/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b3 [36.2 kB]
Get:30 http://localhost:3142/debian sid/main amd64 libclone-perl amd64 0.46-1+b2 [13.7 kB]
Get:31 http://localhost:3142/debian sid/main amd64 libconfig-tiny-perl all 2.30-1 [18.9 kB]
Get:32 http://localhost:3142/debian sid/main amd64 libparams-util-perl amd64 1.102-3 [24.0 kB]
Get:33 http://localhost:3142/debian sid/main amd64 libsub-install-perl all 0.929-1 [10.5 kB]
Get:34 http://localhost:3142/debian sid/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB]
Get:35 http://localhost:3142/debian sid/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB]
Get:36 http://localhost:3142/debian sid/main amd64 libconst-fast-perl all 0.014-2 [8792 B]
Get:37 http://localhost:3142/debian sid/main amd64 libcpanel-json-xs-perl amd64 4.37-1+b2 [128 kB]
Get:38 http://localhost:3142/debian sid/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB]
Get:39 http://localhost:3142/debian sid/main amd64 libexception-class-perl all 1.45-1 [34.6 kB]
Get:40 http://localhost:3142/debian sid/main amd64 libiterator-perl all 0.03+ds1-2 [18.8 kB]
Get:41 http://localhost:3142/debian sid/main amd64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB]
Get:42 http://localhost:3142/debian sid/main amd64 libdata-dpath-perl all 0.59-1 [43.6 kB]
Get:43 http://localhost:3142/debian sid/main amd64 libdata-messagepack-perl amd64 1.02-1+b3 [32.5 kB]
Get:44 http://localhost:3142/debian sid/main amd64 libnet-domain-tld-perl all 1.75-3 [31.9 kB]
Get:45 http://localhost:3142/debian sid/main amd64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB]
Get:46 http://localhost:3142/debian sid/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB]
Get:47 http://localhost:3142/debian sid/main amd64 libnet-netmask-perl all 2.0002-2 [28.6 kB]
Get:48 http://localhost:3142/debian sid/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-2+b3 [98.1 kB]
Get:49 http://localhost:3142/debian sid/main amd64 libdata-validate-ip-perl all 0.31-1 [20.6 kB]
Get:50 http://localhost:3142/debian sid/main amd64 libdata-validate-uri-perl all 0.07-3 [11.0 kB]
Get:51 http://localhost:3142/debian sid/main amd64 libdevel-size-perl amd64 0.83-2+b3 [24.3 kB]
Get:52 http://localhost:3142/debian sid/main amd64 libemail-address-xs-perl amd64 1.05-1+b3 [29.3 kB]
Get:53 http://localhost:3142/debian sid/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB]
Get:54 http://localhost:3142/debian sid/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB]
Get:55 http://localhost:3142/debian sid/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB]
Get:56 http://localhost:3142/debian sid/main amd64 libnumber-compare-perl all 0.03-3 [6332 B]
Get:57 http://localhost:3142/debian sid/main amd64 libtext-glob-perl all 0.11-3 [7676 B]
Get:58 http://localhost:3142/debian sid/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB]
Get:59 http://localhost:3142/debian sid/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB]
Get:60 http://localhost:3142/debian sid/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB]
Get:61 http://localhost:3142/debian sid/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB]
Get:62 http://localhost:3142/debian sid/main amd64 libfont-ttf-perl all 1.06-2 [318 kB]
Get:63 http://localhost:3142/debian sid/main amd64 libio-html-perl all 1.004-3 [16.2 kB]
Get:64 http://localhost:3142/debian sid/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB]
Get:65 http://localhost:3142/debian sid/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB]
Get:66 http://localhost:3142/debian sid/main amd64 libhtml-form-perl all 6.11-1 [33.1 kB]
Get:67 http://localhost:3142/debian sid/main amd64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB]
Get:68 http://localhost:3142/debian sid/main amd64 libhtml-tree-perl all 5.07-3 [211 kB]
Get:69 http://localhost:3142/debian sid/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB]
Get:70 http://localhost:3142/debian sid/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB]
Get:71 http://localhost:3142/debian sid/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B]
Get:72 http://localhost:3142/debian sid/main amd64 libnet-ssleay-perl amd64 1.94-1+b1 [339 kB]
Get:73 http://localhost:3142/debian sid/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB]
Get:74 http://localhost:3142/debian sid/main amd64 libnet-http-perl all 6.23-1 [23.9 kB]
Get:75 http://localhost:3142/debian sid/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB]
Get:76 http://localhost:3142/debian sid/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB]
Get:77 http://localhost:3142/debian sid/main amd64 libwww-perl all 6.77-1 [183 kB]
Get:78 http://localhost:3142/debian sid/main amd64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB]
Get:79 http://localhost:3142/debian sid/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB]
Get:80 http://localhost:3142/debian sid/main amd64 libio-interactive-perl all 1.025-1 [11.4 kB]
Get:81 http://localhost:3142/debian sid/main amd64 libipc-run3-perl all 0.049-1 [31.5 kB]
Get:82 http://localhost:3142/debian sid/main amd64 libjson-maybexs-perl all 1.004005-1 [12.9 kB]
Get:83 http://localhost:3142/debian sid/main amd64 liblist-compare-perl all 0.55-2 [65.7 kB]
Get:84 http://localhost:3142/debian sid/main amd64 liblist-someutils-perl all 0.59-1 [37.1 kB]
Get:85 http://localhost:3142/debian sid/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB]
Get:86 http://localhost:3142/debian sid/main amd64 liblz1 amd64 1.14-1 [38.5 kB]
Get:87 http://localhost:3142/debian sid/main amd64 liblzo2-2 amd64 2.10-2+b1 [54.8 kB]
Get:88 http://localhost:3142/debian sid/main amd64 libmarkdown2 amd64 2.2.7-2+b1 [35.6 kB]
Get:89 http://localhost:3142/debian sid/main amd64 libmldbm-perl all 2.05-4 [16.8 kB]
Get:90 http://localhost:3142/debian sid/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB]
Get:91 http://localhost:3142/debian sid/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB]
Get:92 http://localhost:3142/debian sid/main amd64 libmoo-perl all 2.005005-1 [58.0 kB]
Get:93 http://localhost:3142/debian sid/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB]
Get:94 http://localhost:3142/debian sid/main amd64 libmoox-aliases-perl all 0.001006-2 [7156 B]
Get:95 http://localhost:3142/debian sid/main amd64 libmouse-perl amd64 2.5.10-1+b5 [143 kB]
Get:96 http://localhost:3142/debian sid/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB]
Get:97 http://localhost:3142/debian sid/main amd64 libsub-identify-perl amd64 0.14-3+b2 [11.2 kB]
Get:98 http://localhost:3142/debian sid/main amd64 libsub-name-perl amd64 0.27-1+b2 [12.5 kB]
Get:99 http://localhost:3142/debian sid/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB]
Get:100 http://localhost:3142/debian sid/main amd64 libpath-tiny-perl all 0.144-1 [56.4 kB]
Get:101 http://localhost:3142/debian sid/main amd64 libperlio-gzip-perl amd64 0.20-1+b3 [17.5 kB]
Get:102 http://localhost:3142/debian sid/main amd64 libperlio-utf8-strict-perl amd64 0.010-1+b2 [11.4 kB]
Get:103 http://localhost:3142/debian sid/main amd64 libproc-processtable-perl amd64 0.636-1+b2 [42.2 kB]
Get:104 http://localhost:3142/debian sid/main amd64 libregexp-wildcards-perl all 1.05-3 [14.1 kB]
Get:105 http://localhost:3142/debian sid/main amd64 libsereal-decoder-perl amd64 5.004+ds-1+b2 [99.3 kB]
Get:106 http://localhost:3142/debian sid/main amd64 libsereal-encoder-perl amd64 5.004+ds-1+b2 [102 kB]
Get:107 http://localhost:3142/debian sid/main amd64 libsort-versions-perl all 1.62-3 [8928 B]
Get:108 http://localhost:3142/debian sid/main amd64 libxs-parse-keyword-perl amd64 0.39-1+b2 [57.6 kB]
Get:109 http://localhost:3142/debian sid/main amd64 libsyntax-keyword-try-perl amd64 0.29-2 [26.9 kB]
Get:110 http://localhost:3142/debian sid/main amd64 libterm-readkey-perl amd64 2.38-2+b3 [24.7 kB]
Get:111 http://localhost:3142/debian sid/main amd64 libtext-levenshteinxs-perl amd64 0.03-5+b3 [8700 B]
Get:112 http://localhost:3142/debian sid/main amd64 libtext-markdown-discount-perl amd64 0.16-1+b2 [13.0 kB]
Get:113 http://localhost:3142/debian sid/main amd64 libtext-xslate-perl amd64 3.5.9-2 [173 kB]
Get:114 http://localhost:3142/debian sid/main amd64 libtime-duration-perl all 1.21-2 [13.1 kB]
Get:115 http://localhost:3142/debian sid/main amd64 libtime-moment-perl amd64 0.44-2+b3 [72.8 kB]
Get:116 http://localhost:3142/debian sid/main amd64 libunicode-utf8-perl amd64 0.62-2+b2 [20.2 kB]
Get:117 http://localhost:3142/debian sid/main amd64 libwww-mechanize-perl all 2.18-1 [114 kB]
Get:118 http://localhost:3142/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB]
Get:119 http://localhost:3142/debian sid/main amd64 libyaml-libyaml-perl amd64 0.89+ds-1+b1 [35.0 kB]
Get:120 http://localhost:3142/debian sid/main amd64 plzip amd64 1.11-1 [63.9 kB]
Get:121 http://localhost:3142/debian sid/main amd64 lzop amd64 1.04-2 [84.2 kB]
Get:122 http://localhost:3142/debian sid/main amd64 patchutils amd64 0.4.2-1 [77.5 kB]
Get:123 http://localhost:3142/debian sid/main amd64 t1utils amd64 1.41-4 [62.1 kB]
Get:124 http://localhost:3142/debian sid/main amd64 unzip amd64 6.0-28 [166 kB]
Get:125 http://localhost:3142/debian sid/main amd64 lintian all 2.117.0 [1052 kB]
debconf: delaying package configuration, since apt-utils is not installed
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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) ...
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Setting up libdevel-size-perl (0.83-2+b3) ...
Setting up unzip (6.0-28) ...
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Setting up libmarkdown2:amd64 (2.2.7-2+b1) ...
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Processing triggers for libc-bin (2.37-15.1) ...
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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: amd64
Build Profiles: cross nocheck
Build Type: any
Build-Space: 564892
Build-Time: 520
Distribution: unstable
Foreign Architectures: armhf
Host Architecture: armhf
Install-Time: 25
Job: macromoleculebuilder_4.0.0+dfsg-3.1
Lintian: pass
Machine Architecture: amd64
Package: macromoleculebuilder
Package-Time: 556
Source-Version: 4.0.0+dfsg-3.1
Space: 564892
Status: successful
Version: 4.0.0+dfsg-3.1
--------------------------------------------------------------------------------
Finished at 2024-04-04T11:42:10Z
Build needed 00:09:16, 564892k disk space