Mon Dec  2 06:09:53 UTC 2024  I: starting to build macromoleculebuilder/trixie/amd64 on jenkins on '2024-12-02 06:09'
Mon Dec  2 06:09:53 UTC 2024  I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_13/25887/console.log
Mon Dec  2 06:09:53 UTC 2024  I: Downloading source for trixie/macromoleculebuilder=4.0.0+dfsg-5
--2024-12-02 06:09:53--  http://deb.debian.org/debian/pool/main/m/macromoleculebuilder/macromoleculebuilder_4.0.0%2bdfsg-5.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2491 (2.4K) [text/prs.lines.tag]
Saving to: ‘macromoleculebuilder_4.0.0+dfsg-5.dsc’

     0K ..                                                    100%  308M=0s

2024-12-02 06:09:53 (308 MB/s) - ‘macromoleculebuilder_4.0.0+dfsg-5.dsc’ saved [2491/2491]

Mon Dec  2 06:09:53 UTC 2024  I: macromoleculebuilder_4.0.0+dfsg-5.dsc
-----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-5
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: architecture-is-64-bit, asciidoc-base, cmake, debhelper-compat (= 13), docbook-xml, dpkg-dev (>= 1.22.5), 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
 92ca5482b680f90676592a9fd69ec77274b4269d 5964 macromoleculebuilder_4.0.0+dfsg-5.debian.tar.xz
Checksums-Sha256:
 2f50d11c886c36fd18476f942d7521536ded599584e0d83462a63ba5f9ccc449 2567256 macromoleculebuilder_4.0.0+dfsg.orig.tar.xz
 139eb1301e44a6b967bb990e97300618befc1784e04c2b62bf399c8b835f4afd 5964 macromoleculebuilder_4.0.0+dfsg-5.debian.tar.xz
Files:
 951370d06adf03fb858edccdee43c075 2567256 macromoleculebuilder_4.0.0+dfsg.orig.tar.xz
 69bbd609e8a36fbef46bcfbf9328d2c5 5964 macromoleculebuilder_4.0.0+dfsg-5.debian.tar.xz

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Mon Dec  2 06:09:53 UTC 2024  I: Checking whether the package is not for us
Mon Dec  2 06:09:53 UTC 2024  I: Starting 1st build on remote node ionos11-amd64.debian.net.
Mon Dec  2 06:09:53 UTC 2024  I: Preparing to do remote build '1' on ionos11-amd64.debian.net.
Mon Dec  2 06:42:19 UTC 2024  I: Deleting $TMPDIR on ionos11-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sun Dec  1 18:09:56 -12 2024
I: pbuilder-time-stamp: 1733119796
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [macromoleculebuilder_4.0.0+dfsg-5.dsc]
I: copying [./macromoleculebuilder_4.0.0+dfsg.orig.tar.xz]
I: copying [./macromoleculebuilder_4.0.0+dfsg-5.debian.tar.xz]
I: Extracting source
gpgv: Signature made Wed Nov 27 07:10:58 2024 
gpgv:                using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287
gpgv:                issuer "merkys@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./macromoleculebuilder_4.0.0+dfsg-5.dsc: no acceptable signature found
dpkg-source: info: extracting macromoleculebuilder in macromoleculebuilder-4.0.0+dfsg
dpkg-source: info: unpacking macromoleculebuilder_4.0.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking macromoleculebuilder_4.0.0+dfsg-5.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
dpkg-source: info: applying 27.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/2405886/tmp/hooks/D02_print_environment starting
I: set
  BUILDDIR='/build/reproducible-path'
  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
  BUILDUSERNAME='pbuilder1'
  BUILD_ARCH='amd64'
  DEBIAN_FRONTEND='noninteractive'
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
  DISTRIBUTION='trixie'
  HOME='/root'
  HOST_ARCH='amd64'
  IFS=' 	
  '
  INVOCATION_ID='79db9fd38936424aba93b7d67b02a88a'
  LANG='C'
  LANGUAGE='en_US:en'
  LC_ALL='C'
  MAIL='/var/mail/root'
  OPTIND='1'
  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
  PBCURRENTCOMMANDLINEOPERATION='build'
  PBUILDER_OPERATION='build'
  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
  PBUILDER_SYSCONFDIR='/etc'
  PPID='2405886'
  PS1='# '
  PS2='> '
  PS4='+ '
  PWD='/'
  SHELL='/bin/bash'
  SHLVL='2'
  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.6CmBvtqs/pbuilderrc_qAm1 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6CmBvtqs/b1 --logfile b1/build.log macromoleculebuilder_4.0.0+dfsg-5.dsc'
  SUDO_GID='111'
  SUDO_UID='106'
  SUDO_USER='jenkins'
  TERM='unknown'
  TZ='/usr/share/zoneinfo/Etc/GMT+12'
  USER='root'
  _='/usr/bin/systemd-run'
  http_proxy='http://46.16.76.132:3128'
I: uname -a
  Linux ionos11-amd64 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/2405886/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: architecture-is-64-bit, asciidoc-base, cmake, debhelper-compat (= 13), docbook-xml, dpkg-dev (>= 1.22.5), 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
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19962 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on architecture-is-64-bit; however:
  Package architecture-is-64-bit is not installed.
 pbuilder-satisfydepends-dummy depends on asciidoc-base; however:
  Package asciidoc-base is not installed.
 pbuilder-satisfydepends-dummy depends on cmake; however:
  Package cmake is not installed.
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on docbook-xml; however:
  Package docbook-xml is not installed.
 pbuilder-satisfydepends-dummy depends on gemmi-dev (>= 0.6.2+ds-2); however:
  Package gemmi-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libopenmm-dev; however:
  Package libopenmm-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libseqan2-dev; however:
  Package libseqan2-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libsimbody-dev; however:
  Package libsimbody-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libsimtkmolmodel-dev (>= 3.1.0); however:
  Package libsimtkmolmodel-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libsimtkmolmodel-plugins; however:
  Package libsimtkmolmodel-plugins is not installed.
 pbuilder-satisfydepends-dummy depends on libstb-dev; however:
  Package libstb-dev is not installed.
 pbuilder-satisfydepends-dummy depends on tao-pegtl-dev; however:
  Package tao-pegtl-dev is not installed.
 pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
  Package zlib1g-dev is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  architecture-properties{a} asciidoc-base{a} asciidoc-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docbook-xml{a} docbook-xsl{a} dwz{a} file{a} freeglut3-dev{a} gemmi-dev{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libblas-dev{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libegl-dev{a} libegl-mesa0{a} libegl1{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgbm1{a} libgfortran5{a} libgl-dev{a} libgl1{a} libgl1-mesa-dev{a} libgl1-mesa-dri{a} libglapi-mesa{a} libgles-dev{a} libgles1{a} libgles2{a} libglu1-mesa{a} libglu1-mesa-dev{a} libglut-dev{a} libglut3.12{a} libglvnd-core-dev{a} libglvnd-dev{a} libglvnd0{a} libglx-dev{a} libglx-mesa0{a} libglx0{a} libgssapi-krb5-2{a} libice-dev{a} libice6{a} libicu72{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libllvm19{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnsl2{a} libopengl-dev{a} libopengl0{a} libopenmm-dev{a} libopenmm8.1{a} libpciaccess0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libseqan2-dev{a} libsimbody-dev{a} libsimbody3.7{a} libsimtkmolmodel-dev{a} libsimtkmolmodel-plugins{a} libsimtkmolmodel3.1t64{a} libsm-dev{a} libsm6{a} libssh2-1t64{a} libstb-dev{a} libstb0t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libvulkan1{a} libwayland-client0{a} libwayland-server0{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx11-xcb1{a} libxau-dev{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxfixes-dev{a} libxfixes3{a} libxi-dev{a} libxi6{a} libxml2{a} libxml2-utils{a} libxmu-dev{a} libxmu-headers{a} libxmu6{a} libxshmfence1{a} libxslt1.1{a} libxt-dev{a} libxt6t64{a} libxxf86vm1{a} libz3-4{a} m4{a} man-db{a} media-types{a} mesa-libgallium{a} netbase{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sgml-data{a} tao-pegtl-dev{a} tzdata{a} uuid-dev{a} x11-common{a} x11proto-dev{a} xml-core{a} xorg-sgml-doctools{a} xsltproc{a} xtrans-dev{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx mesa-vulkan-drivers psmisc publicsuffix wget xmlto 
0 packages upgraded, 177 newly installed, 0 to remove and 0 not upgraded.
Need to get 121 MB of archives. After unpacking 511 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB]
Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB]
Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB]
Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB]
Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-3 [255 kB]
Get: 8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB]
Get: 9 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB]
Get: 10 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB]
Get: 11 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 12 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB]
Get: 13 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB]
Get: 14 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB]
Get: 16 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB]
Get: 17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB]
Get: 18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB]
Get: 19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB]
Get: 20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.7-3 [671 kB]
Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B]
Get: 22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB]
Get: 23 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB]
Get: 24 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB]
Get: 25 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-6 [879 kB]
Get: 26 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 27 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 28 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 29 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 30 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB]
Get: 31 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 32 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB]
Get: 33 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB]
Get: 34 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 35 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 36 http://deb.debian.org/debian trixie/main amd64 architecture-properties amd64 0.2.3 [2184 B]
Get: 37 http://deb.debian.org/debian trixie/main amd64 asciidoc-common all 10.2.1-1 [104 kB]
Get: 38 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB]
Get: 39 http://deb.debian.org/debian trixie/main amd64 docbook-xsl all 1.79.2+dfsg-7 [1221 kB]
Get: 40 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB]
Get: 41 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
Get: 42 http://deb.debian.org/debian trixie/main amd64 libxml2-utils amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [99.4 kB]
Get: 43 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB]
Get: 44 http://deb.debian.org/debian trixie/main amd64 xsltproc amd64 1.1.35-1.1+b1 [115 kB]
Get: 45 http://deb.debian.org/debian trixie/main amd64 asciidoc-base all 10.2.1-1 [84.9 kB]
Get: 46 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB]
Get: 47 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB]
Get: 48 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 49 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 50 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB]
Get: 51 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.30.5-1 [2223 kB]
Get: 52 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB]
Get: 53 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB]
Get: 54 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB]
Get: 55 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB]
Get: 56 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB]
Get: 57 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get: 58 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get: 59 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get: 60 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get: 61 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB]
Get: 62 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB]
Get: 63 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB]
Get: 64 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB]
Get: 65 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.30.5-1 [11.4 MB]
Get: 66 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB]
Get: 67 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB]
Get: 68 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 69 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 70 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 71 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 72 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 73 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 74 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB]
Get: 75 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 76 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 77 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB]
Get: 78 http://deb.debian.org/debian trixie/main amd64 sgml-data all 2.0.11+nmu1 [179 kB]
Get: 79 http://deb.debian.org/debian trixie/main amd64 docbook-xml all 4.5-13 [77.4 kB]
Get: 80 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB]
Get: 81 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get: 82 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get: 83 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get: 84 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB]
Get: 85 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB]
Get: 86 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B]
Get: 87 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB]
Get: 88 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 24.2.7-1 [37.9 kB]
Get: 89 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB]
Get: 90 http://deb.debian.org/debian trixie/main amd64 libxcb-dri2-0 amd64 1.17.0-2+b1 [107 kB]
Get: 91 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB]
Get: 92 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB]
Get: 93 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB]
Get: 94 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB]
Get: 95 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB]
Get: 96 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB]
Get: 97 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB]
Get: 98 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB]
Get: 99 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b2 [20.3 kB]
Get: 100 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b2 [8848 B]
Get: 101 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b3 [19.3 kB]
Get: 102 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB]
Get: 103 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b2 [51.9 kB]
Get: 104 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB]
Get: 105 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB]
Get: 106 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB]
Get: 107 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB]
Get: 108 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.4-1 [26.0 MB]
Get: 109 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB]
Get: 110 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB]
Get: 111 http://deb.debian.org/debian trixie/main amd64 mesa-libgallium amd64 24.2.7-1 [9186 kB]
Get: 112 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.3.296.0-1 [126 kB]
Get: 113 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.23.0-1+b1 [34.2 kB]
Get: 114 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 24.2.7-1 [42.8 kB]
Get: 115 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 24.2.7-1 [43.9 kB]
Get: 116 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 24.2.7-1 [154 kB]
Get: 117 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB]
Get: 118 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB]
Get: 119 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB]
Get: 120 http://deb.debian.org/debian trixie/main amd64 libglut3.12 amd64 3.4.0-1+b2 [139 kB]
Get: 121 http://deb.debian.org/debian trixie/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get: 122 http://deb.debian.org/debian trixie/main amd64 x11proto-dev all 2024.1-1 [603 kB]
Get: 123 http://deb.debian.org/debian trixie/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB]
Get: 124 http://deb.debian.org/debian trixie/main amd64 libxdmcp-dev amd64 1:1.1.5-1 [44.3 kB]
Get: 125 http://deb.debian.org/debian trixie/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB]
Get: 126 http://deb.debian.org/debian trixie/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB]
Get: 127 http://deb.debian.org/debian trixie/main amd64 libx11-dev amd64 2:1.8.10-2 [891 kB]
Get: 128 http://deb.debian.org/debian trixie/main amd64 libglx-dev amd64 1.7.0-1+b2 [15.8 kB]
Get: 129 http://deb.debian.org/debian trixie/main amd64 libgl-dev amd64 1.7.0-1+b2 [101 kB]
Get: 130 http://deb.debian.org/debian trixie/main amd64 libglvnd-core-dev amd64 1.7.0-1+b2 [13.4 kB]
Get: 131 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.23.0-1+b1 [26.6 kB]
Get: 132 http://deb.debian.org/debian trixie/main amd64 libegl-mesa0 amd64 24.2.7-1 [133 kB]
Get: 133 http://deb.debian.org/debian trixie/main amd64 libegl1 amd64 1.7.0-1+b2 [34.6 kB]
Get: 134 http://deb.debian.org/debian trixie/main amd64 libegl-dev amd64 1.7.0-1+b2 [19.5 kB]
Get: 135 http://deb.debian.org/debian trixie/main amd64 libgles1 amd64 1.7.0-1+b2 [12.1 kB]
Get: 136 http://deb.debian.org/debian trixie/main amd64 libgles2 amd64 1.7.0-1+b2 [17.3 kB]
Get: 137 http://deb.debian.org/debian trixie/main amd64 libgles-dev amd64 1.7.0-1+b2 [50.8 kB]
Get: 138 http://deb.debian.org/debian trixie/main amd64 libopengl0 amd64 1.7.0-1+b2 [30.9 kB]
Get: 139 http://deb.debian.org/debian trixie/main amd64 libopengl-dev amd64 1.7.0-1+b2 [5388 B]
Get: 140 http://deb.debian.org/debian trixie/main amd64 libglvnd-dev amd64 1.7.0-1+b2 [5148 B]
Get: 141 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dev amd64 24.2.7-1 [18.5 kB]
Get: 142 http://deb.debian.org/debian trixie/main amd64 libglu1-mesa amd64 9.0.2-1.1+b2 [185 kB]
Get: 143 http://deb.debian.org/debian trixie/main amd64 libglu1-mesa-dev amd64 9.0.2-1.1+b2 [223 kB]
Get: 144 http://deb.debian.org/debian trixie/main amd64 libxext-dev amd64 2:1.3.4-1+b2 [104 kB]
Get: 145 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB]
Get: 146 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB]
Get: 147 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB]
Get: 148 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB]
Get: 149 http://deb.debian.org/debian trixie/main amd64 libice-dev amd64 2:1.1.1-1 [73.8 kB]
Get: 150 http://deb.debian.org/debian trixie/main amd64 uuid-dev amd64 2.40.2-11 [47.2 kB]
Get: 151 http://deb.debian.org/debian trixie/main amd64 libsm-dev amd64 2:1.2.4-1 [37.7 kB]
Get: 152 http://deb.debian.org/debian trixie/main amd64 libxt-dev amd64 1:1.2.1-1.2+b1 [407 kB]
Get: 153 http://deb.debian.org/debian trixie/main amd64 libglut-dev amd64 3.4.0-1+b2 [163 kB]
Get: 154 http://deb.debian.org/debian trixie/main amd64 freeglut3-dev amd64 3.4.0-1+b2 [53.4 kB]
Get: 155 http://deb.debian.org/debian trixie/main amd64 tao-pegtl-dev all 3.2.7-1 [69.4 kB]
Get: 156 http://deb.debian.org/debian trixie/main amd64 gemmi-dev amd64 0.6.5+ds-2 [1139 kB]
Get: 157 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-4 [152 kB]
Get: 158 http://deb.debian.org/debian trixie/main amd64 libblas-dev amd64 3.12.0-4 [161 kB]
Get: 159 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB]
Get: 160 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB]
Get: 161 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.0-4 [4991 kB]
Get: 162 http://deb.debian.org/debian trixie/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-1+b1 [1058 kB]
Get: 163 http://deb.debian.org/debian trixie/main amd64 libopenmm-dev amd64 8.1.2+dfsg-1+b1 [346 kB]
Get: 164 http://deb.debian.org/debian trixie/main amd64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB]
Get: 165 http://deb.debian.org/debian trixie/main amd64 libxfixes-dev amd64 1:6.0.0-2+b2 [22.3 kB]
Get: 166 http://deb.debian.org/debian trixie/main amd64 libxi-dev amd64 2:1.8.2-1 [241 kB]
Get: 167 http://deb.debian.org/debian trixie/main amd64 libxmu6 amd64 2:1.1.3-3+b3 [58.8 kB]
Get: 168 http://deb.debian.org/debian trixie/main amd64 libxmu-headers all 2:1.1.3-3 [68.5 kB]
Get: 169 http://deb.debian.org/debian trixie/main amd64 libxmu-dev amd64 2:1.1.3-3+b3 [65.2 kB]
Get: 170 http://deb.debian.org/debian trixie/main amd64 libsimbody3.7 amd64 3.7+dfsg-3+b1 [3363 kB]
Get: 171 http://deb.debian.org/debian trixie/main amd64 libsimbody-dev amd64 3.7+dfsg-3+b1 [2728 kB]
Get: 172 http://deb.debian.org/debian trixie/main amd64 libsimtkmolmodel3.1t64 amd64 3.1.0-4.1+b3 [667 kB]
Get: 173 http://deb.debian.org/debian trixie/main amd64 libsimtkmolmodel-dev amd64 3.1.0-4.1+b3 [1864 kB]
Get: 174 http://deb.debian.org/debian trixie/main amd64 libsimtkmolmodel-plugins amd64 3.1.0-4.1+b3 [19.6 kB]
Get: 175 http://deb.debian.org/debian trixie/main amd64 libstb0t64 amd64 0.0~git20240715.f7f20f39fe4f+ds-1 [220 kB]
Get: 176 http://deb.debian.org/debian trixie/main amd64 libstb-dev amd64 0.0~git20240715.f7f20f39fe4f+ds-1 [654 kB]
Get: 177 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Fetched 121 MB in 11s (11.3 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libpython3.12-minimal:amd64.
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Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ...
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Unpacking python3.12-minimal (3.12.7-3) ...
Setting up libpython3.12-minimal:amd64 (3.12.7-3) ...
Setting up libexpat1:amd64 (2.6.4-1) ...
Setting up python3.12-minimal (3.12.7-3) ...
Selecting previously unselected package python3-minimal.
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Unpacking python3-minimal (3.12.6-1) ...
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Unpacking media-types (10.1.0) ...
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Unpacking netbase (6.4) ...
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Unpacking tzdata (2024b-3) ...
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Unpacking libkrb5support0:amd64 (1.21.3-3) ...
Selecting previously unselected package libcom-err2:amd64.
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Unpacking libcom-err2:amd64 (1.47.1-1+b1) ...
Selecting previously unselected package libk5crypto3:amd64.
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Unpacking libk5crypto3:amd64 (1.21.3-3) ...
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Unpacking libkeyutils1:amd64 (1.6.3-4) ...
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Unpacking libkrb5-3:amd64 (1.21.3-3) ...
Selecting previously unselected package libgssapi-krb5-2:amd64.
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Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ...
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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ...
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Unpacking libnsl2:amd64 (1.3.0-3+b3) ...
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Unpacking readline-common (8.2-5) ...
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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
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Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ...
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Setting up python3-minimal (3.12.6-1) ...
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Setting up media-types (10.1.0) ...
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Setting up libkeyutils1:amd64 (1.6.3-4) ...
Setting up libxcb1:amd64 (1.17.0-2+b1) ...
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Setting up libxcb-glx0:amd64 (1.17.0-2+b1) ...
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Setting up libmagic1t64:amd64 (1:5.45-3+b1) ...
Setting up x11-common (1:7.7+23.1) ...
invoke-rc.d: could not determine current runlevel
Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix.
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Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ...
Setting up libnghttp2-14:amd64 (1.64.0-1) ...
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Setting up m4 (1.4.19-4) ...
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Setting up libkrb5support0:amd64 (1.21.3-3) ...
Setting up libseqan2-dev (2.4.0+dfsg-16) ...
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Current default time zone: 'Etc/UTC'
Local time is now:      Mon Dec  2 06:14:06 UTC 2024.
Universal Time is now:  Mon Dec  2 06:14:06 UTC 2024.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

Setting up libxcb-present0:amd64 (1.17.0-2+b1) ...
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update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
Setting up libgles2:amd64 (1.7.0-1+b2) ...
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Setting up libglu1-mesa:amd64 (9.0.2-1.1+b2) ...
Setting up libssh2-1t64:amd64 (1.11.1-1) ...
Setting up libopengl-dev:amd64 (1.7.0-1+b2) ...
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Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up libblas-dev:amd64 (3.12.0-4) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode
Setting up tao-pegtl-dev (3.2.7-1) ...
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Setting up liblapack3:amd64 (3.12.0-4) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
Setting up gettext (0.22.5-2) ...
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Setting up libice-dev:amd64 (2:1.1.1-1) ...
Setting up libtool (2.4.7-8) ...
Setting up gemmi-dev (0.6.5+ds-2) ...
Setting up libxext6:amd64 (2:1.3.4-1+b2) ...
Setting up libopenmm-dev (8.1.2+dfsg-1+b1) ...
Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ...
Setting up libxxf86vm1:amd64 (1:1.1.4-1+b3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
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Setting up libxfixes3:amd64 (1:6.0.0-2+b2) ...
Setting up liblapack-dev:amd64 (3.12.0-4) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode
Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ...
Setting up libreadline8t64:amd64 (8.2-5) ...
Setting up dh-strip-nondeterminism (1.14.0-1) ...
Setting up libdrm2:amd64 (2.4.123-1) ...
Setting up libstb-dev:amd64 (0.0~git20240715.f7f20f39fe4f+ds-1) ...
Setting up groff-base (1.23.0-5) ...
Setting up xml-core (0.19) ...
Setting up libxslt1.1:amd64 (1.1.35-1.1+b1) ...
Setting up libxml2-utils (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up libsm6:amd64 (2:1.2.4-1) ...
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Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ...
Setting up libxcb1-dev:amd64 (1.17.0-2+b1) ...
Setting up libxi6:amd64 (2:1.8.2-1) ...
Setting up libcurl4t64:amd64 (8.11.0-1) ...
Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ...
Setting up libsm-dev:amd64 (2:1.2.4-1) ...
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Setting up po-debconf (1.0.21+nmu1) ...
Setting up libdrm-intel1:amd64 (2.4.123-1) ...
Setting up xsltproc (1.1.35-1.1+b1) ...
Setting up libx11-dev:amd64 (2:1.8.10-2) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up libxext-dev:amd64 (2:1.3.4-1+b2) ...
Setting up libnsl2:amd64 (1.3.0-3+b3) ...
Setting up cmake (3.30.5-1) ...
Setting up libxi-dev:amd64 (2:1.8.2-1) ...
Setting up mesa-libgallium:amd64 (24.2.7-1) ...
Setting up libxmu-headers (2:1.1.3-3) ...
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Setting up libpython3.12-stdlib:amd64 (3.12.7-3) ...
Setting up libgbm1:amd64 (24.2.7-1) ...
Setting up python3.12 (3.12.7-3) ...
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Setting up debhelper (13.20) ...
Setting up libegl-mesa0:amd64 (24.2.7-1) ...
Setting up libxt-dev:amd64 (1:1.2.1-1.2+b1) ...
Setting up libegl1:amd64 (1.7.0-1+b2) ...
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Setting up python3 (3.12.6-1) ...
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Setting up libgl1:amd64 (1.7.0-1+b2) ...
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Setting up libsimbody3.7:amd64 (3.7+dfsg-3+b1) ...
Setting up libglx-dev:amd64 (1.7.0-1+b2) ...
Setting up libgl-dev:amd64 (1.7.0-1+b2) ...
Setting up libegl-dev:amd64 (1.7.0-1+b2) ...
Setting up libsimtkmolmodel3.1t64:amd64 (3.1.0-4.1+b3) ...
Setting up libglu1-mesa-dev:amd64 (9.0.2-1.1+b2) ...
Setting up libgles-dev:amd64 (1.7.0-1+b2) ...
Setting up libsimtkmolmodel-plugins (3.1.0-4.1+b3) ...
Setting up libsimtkmolmodel-dev:amd64 (3.1.0-4.1+b3) ...
Setting up libglvnd-dev:amd64 (1.7.0-1+b2) ...
Setting up libgl1-mesa-dev:amd64 (24.2.7-1) ...
Setting up libglut-dev:amd64 (3.4.0-1+b2) ...
Setting up freeglut3-dev:amd64 (3.4.0-1+b2) ...
Setting up libsimbody-dev:amd64 (3.7+dfsg-3+b1) ...
Processing triggers for libc-bin (2.40-3) ...
Processing triggers for sgml-base (1.31) ...
Setting up docbook-xsl (1.79.2+dfsg-7) ...
Setting up sgml-data (2.0.11+nmu1) ...
Setting up asciidoc-base (10.2.1-1) ...
Processing triggers for sgml-base (1.31) ...
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Reading package lists...
Building dependency tree...
Reading state information...
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Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../macromoleculebuilder_4.0.0+dfsg-5_source.changes
dpkg-buildpackage: info: source package macromoleculebuilder
dpkg-buildpackage: info: source version 4.0.0+dfsg-5
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andrius Merkys <merkys@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean
   dh_clean
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg'
dh_auto_configure -- \
	-DCMAKE_BUILD_TYPE=Release \
	-DENABLE_LEPTON=OFF \
	-DGEMMI_DIR=/usr \
	-DOpenMM_INCLUDE_DIR=/usr/include \
	-DSimTKmolmodel=/usr \
	-DCMAKE_CXX_FLAGS="-D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0"
	cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCMAKE_BUILD_TYPE=Release -DENABLE_LEPTON=OFF -DGEMMI_DIR=/usr -DOpenMM_INCLUDE_DIR=/usr/include -DSimTKmolmodel=/usr "-DCMAKE_CXX_FLAGS=-D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0" ..
-- The CXX compiler identification is GNU 14.2.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMM: /usr/include
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1")
-- Found gemmi version 0.6.5
-- Looking for copy_file_range
-- Looking for copy_file_range - found
-- Looking for sendfile
-- Looking for sendfile - found
-- Configuring done (7.6s)
-- Generating done (0.1s)
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_EXPORT_NO_PACKAGE_REGISTRY
    CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
    FETCHCONTENT_FULLY_DISCONNECTED
    SimTKmolmodel


-- Build files have been written to: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu
make[1]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg'
   dh_auto_build
	cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1
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/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ParameterReader.cpp.o -MF CMakeFiles/MMB.dir/src/ParameterReader.cpp.o.d -o CMakeFiles/MMB.dir/src/ParameterReader.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp
[ 59%] Building CXX object CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/TetherForce.cpp.o -MF CMakeFiles/MMB.dir/src/TetherForce.cpp.o.d -o CMakeFiles/MMB.dir/src/TetherForce.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/TetherForce.cpp
[ 56%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o -MF CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o.d -o CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp
[ 62%] Building CXX object CMakeFiles/MMB.dir/src/DensityMap.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o -MF CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o.d -o CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/WaterDroplet.cpp
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DensityMap.cpp.o -MF CMakeFiles/MMB.dir/src/DensityMap.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityMap.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:12:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Utils.cpp:12:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ThreadingStruct>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'double AtomSpringContainer::calcRmsd(SimTK::State&, BiopolymerClassContainer&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:65:12: warning: unused variable 'myExtension' [-Wunused-variable]
   65 |     double myExtension = 0.0;
      |            ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::deleteAtomSpring(int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:194:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<AtomSpring>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  194 |     if(id < 0 || id >= atomSpringVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateAtomSpring(int, const AtomSpring&, BiopolymerClassContainer&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:201:21: warning: comparison of integer expressions of different signedness: 'const int' and 'std::vector<AtomSpring>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  201 |     if(id < 0 || id >= atomSpringVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::deleteThreading(int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:260:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ThreadingStruct>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  260 |     if(id < 0 || id >= threadingStructVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateThreading(int, const ThreadingStruct&, BiopolymerClassContainer&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:268:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ThreadingStruct>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  268 |     if(id < 0 || id >= threadingStructVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateThreading(int, SimTK::String, ResidueID, ResidueID, SimTK::String, ResidueID, ResidueID, double, bool, BiopolymerClassContainer&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:279:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ThreadingStruct>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  279 |     if(id < 0 || id >= threadingStructVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::deleteGappedThreading(int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:441:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ThreadingStruct>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  441 |     if(id < 0 || id >= gappedThreadingStructVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateGappedThreading(int, const ThreadingStruct&, BiopolymerClassContainer&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:449:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ThreadingStruct>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  449 |     if(id < 0 || id >= gappedThreadingStructVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateGappedThreading(int, SimTK::String, SimTK::String, double, bool, BiopolymerClassContainer&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:458:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ThreadingStruct>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  458 |     if(id < 0 || id >= gappedThreadingStructVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::createSpringsFromGappedThreading(BiopolymerClassContainer&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:488:24: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size<seqan::String<char, seqan::Alloc<> > >::Type' {aka 'long unsigned int'} [-Wsign-compare]
  488 |         while ((aIndex < length(thread.updThreadingPartner(0).sequence)) &&
      |                 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:489:24: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size<seqan::String<char, seqan::Alloc<> > >::Type' {aka 'long unsigned int'} [-Wsign-compare]
  489 |                (bIndex < length(thread.updThreadingPartner(1).sequence)))
      |                 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ConstraintContainer.h:14,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/MoleculeContainer.h:8,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MoleculeContainer.cpp:3:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClassTwoTransformForces.h:17,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:10:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Spiral.h:16,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp:11:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MoleculeContainer.cpp: In constructor 'CustomMolecule::CustomMolecule(std::vector<std::vector<SimTK::String> >, SimTK::DuMMForceFieldSubsystem&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MoleculeContainer.cpp:324:15: warning: unused variable 'myAngle1' [-Wunused-variable]
  324 |         Angle myAngle1 = 180*Deg2Rad; // this is a bond angle
      |               ^~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DisplacementContainer.h:14,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DisplacementContainer.cpp:12:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/PeriodicScrubber.h:16,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:24,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:12:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BasePairContainer.h:17,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BasePairContainer.cpp:11:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp: In member function 'void Spiral::clear()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp:92:12: warning: unused variable 'helixAdvancePerBasePair' [-Wunused-variable]
   92 |     double helixAdvancePerBasePair = -11111. ;  // in nm // should be user specified.
      |            ^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp: In member function 'double Spiral::harmonicThetaAdjustment(double)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp:124:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<frequencyPhaseAmplitude>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  124 |     for (int i =0; i < frequencyPhaseAmplitudeVector.size(); i++){
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp:11:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ThreadingStruct>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp: In member function 'void Spiral::writeCylindricalSpiralCommandFile(MonoAtomsContainer&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp:140:10: warning: variable 'deltaZ' set but not used [-Wunused-but-set-variable]
  140 |     Vec3 deltaZ = Vec3(0,0,1) * sin(cylindricalSpiralSlopeAngle(pitch,radius))*helixAdvancePerBasePair ;
      |          ^~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ConstraintContainer.h:14,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp:10:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp: In member function 'void Spiral::writeSphericalSpiralCommandFile(MonoAtomsContainer&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp:238:16: warning: unused variable 'currentPhi' [-Wunused-variable]
  238 |         double currentPhi = priorPhi + deltaPhi ; // phiFromTheta(currentTheta, pitch, radius, phiOffset);
      |                ^~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp:221:12: warning: unused variable 'phiOffsetFromStartingTheta' [-Wunused-variable]
  221 |     double phiOffsetFromStartingTheta = phiFromTheta(startTheta, pitch, radius, 0.0, spiralIsRightHanded); // use offset = 0 to retreive the original, non-offset phi
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ThreadingStruct>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:17:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:11:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp:12:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:4,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:14,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityContainer.cpp:11:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BasePairContainer.cpp: In member function 'void BasePairContainer::updateBasePair(int, SimTK::String, int, SimTK::String, SimTK::String, int, SimTK::String, SimTK::String, BiopolymerClassContainer&, const LeontisWesthofClass&, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BasePairContainer.cpp:44:28: warning: ignoring return value of 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::at(size_type) [with _Tp = BaseInteraction; _Alloc = std::allocator<BaseInteraction>; reference = BaseInteraction&; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result]
   44 |         myBasePairVector.at(index);
      |         ~~~~~~~~~~~~~~~~~~~^~~~~~~
In file included from /usr/include/c++/14/vector:66,
                 from /usr/include/simbody/SimTKcommon/internal/Array.h:39,
                 from /usr/include/simbody/SimTKcommon/basics.h:53,
                 from /usr/include/simbody/SimTKcommon.h:32,
                 from /usr/include/simbody/Simbody.h:38,
                 from /usr/include/molmodel/SimTKmolmodel.h:47,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BasePairContainer.h:16:
/usr/include/c++/14/bits/stl_vector.h:1180:7: note: declared here
 1180 |       at(size_type __n)
      |       ^~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:11:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  292 |              return 0;
      |              ^~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp:11:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:14:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp: In member function 'void MobilizerContainer::addMobilizerDomainsInterfacesToVector(const std::vector<MobilizerDomainsInterface>&, BiopolymerClassContainer&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp:190:37: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
  190 |             if( (dist <= it->range) &&
      |                 ~~~~~~~~~~~~~~~~~~~~^~
  191 |                 (it->domain1.contains(chain1, res1) && it->domain2.contains(chain2, res2)) ||
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/WaterDroplet.h:16,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/WaterDroplet.cpp:11:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MonoAtoms.cpp:11:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::resizeVectorOfAmplitudeAndRandomPhases()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:177:62: warning: comparison of integer expressions of different signedness: 'std::vector<std::vector<std::vector<AmplitudeFrequencyAndRandomPhases> > >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  177 |         if (vectorOfAmplitudeFrequencyAndRandomPhases.size() != (unitCellParameters.calcMaxFrequencyDoublingsZ()+1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:181:78: warning: comparison of integer expressions of different signedness: 'std::vector<std::vector<AmplitudeFrequencyAndRandomPhases> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  181 |                 if (vectorOfAmplitudeFrequencyAndRandomPhases[zIndex].size() != (unitCellParameters.calcMaxFrequencyDoublingsY()+1) ) {
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:185:90: warning: comparison of integer expressions of different signedness: 'std::vector<AmplitudeFrequencyAndRandomPhases>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  185 |                     if (vectorOfAmplitudeFrequencyAndRandomPhases[zIndex][yIndex].size() != (unitCellParameters.calcMaxFrequencyDoublingsX()+1 )) {
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ThreadingStruct>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp: In member function 'void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp:129:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ConstraintClass>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  129 |     if(index < 0 || index >= constraintClassVector.size())
      |                     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:12:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp: In member function 'void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp:146:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ConstraintClass>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  146 |     if(index < 0 || index >= constraintClassVector.size())
      |                     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::densityAutocorrelation(bool, bool) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:209:12: warning: unused variable 'ySquared' [-Wunused-variable]
  209 |     double ySquared = 0.;
      |            ^~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:210:12: warning: unused variable 'zSquared' [-Wunused-variable]
  210 |     double zSquared = 0.;
      |            ^~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:279:16: warning: variable 'dutyCycle' set but not used [-Wunused-but-set-variable]
  279 |         double dutyCycle; //must be between 0 and 1.  at 1, force is applied all the time.  at 0, basically never applied.
      |                ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:280:16: warning: variable 'scrubberPeriod' set but not used [-Wunused-but-set-variable]
  280 |         double scrubberPeriod;
      |                ^~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::populateNoiseMap()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:307:12: warning: unused variable 'groundFrequencyX' [-Wunused-variable]
  307 |     double groundFrequencyX = 1/unitCellParameters.getNa()/unitCellParameters.geta()/2;
      |            ^~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:308:12: warning: unused variable 'groundFrequencyY' [-Wunused-variable]
  308 |     double groundFrequencyY = 1/unitCellParameters.getNb()/unitCellParameters.getb()/2;
      |            ^~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:309:12: warning: unused variable 'groundFrequencyZ' [-Wunused-variable]
  309 |     double groundFrequencyZ = 1/unitCellParameters.getNc()/unitCellParameters.getc()/2;
      |            ^~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:311:12: warning: unused variable 'maxFrequencyX' [-Wunused-variable]
  311 |     double maxFrequencyX = 1/unitCellParameters.geta()/2;
      |            ^~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:312:12: warning: unused variable 'maxFrequencyY' [-Wunused-variable]
  312 |     double maxFrequencyY = 1/unitCellParameters.getb()/2;
      |            ^~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:313:12: warning: unused variable 'maxFrequencyZ' [-Wunused-variable]
  313 |     double maxFrequencyZ = 1/unitCellParameters.getc()/2;
      |            ^~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:318:12: warning: variable 'signalToNoiseRatio' set but not used [-Wunused-but-set-variable]
  318 |     double signalToNoiseRatio = 0.;
      |            ^~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:319:12: warning: unused variable 'inverseNoiseTemperatureToPower4' [-Wunused-variable]
  319 |     double inverseNoiseTemperatureToPower4 = 1/pow(noiseTemperature,4); //Stefan–Boltzmann law says total radiance goes like T^4. So we normalize by this number to keep noise sort of constant with temperatuere. Of course our oven has a maximum wavenumber, so this won't be perfect.
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/WaterDroplet.h:17:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BaseInteractionParameterReader.h:22,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BaseInteractionParameterReader.cpp:18:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::validateContact(ContactStretch, BiopolymerClassContainer&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:26:10: warning: variable 'myEndCapsOn' set but not used [-Wunused-but-set-variable]
   26 |     bool myEndCapsOn;
      |          ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::deleteContactWithin(int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:70:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ContactWithin>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   70 |     if(id < 0 || id >= contactWithinVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::updateContactWithin(int, SimTK::String, int, double, SimTK::String, BiopolymerClassContainer&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:77:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ContactWithin>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   77 |     if(id < 0 || id >= contactWithinVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::loadParametersAndDensity_CCP4MAP()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:543:13: warning: unused variable 'newU' [-Wunused-variable]
  543 |         int newU, newV, newW;
      |             ^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:543:19: warning: unused variable 'newV' [-Wunused-variable]
  543 |         int newU, newV, newW;
      |                   ^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:543:25: warning: unused variable 'newW' [-Wunused-variable]
  543 |         int newU, newV, newW;
      |                         ^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:507:9: warning: unused variable 'xGridInds' [-Wunused-variable]
  507 |     int xGridInds                                     = xDimInds;
      |         ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:508:9: warning: unused variable 'yGridInds' [-Wunused-variable]
  508 |     int yGridInds                                     = yDimInds;
      |         ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:509:9: warning: unused variable 'zGridInds' [-Wunused-variable]
  509 |     int zGridInds                                     = zDimInds;
      |         ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityContainer.cpp: In member function 'void DensityContainer::updateDensityStretch(int, const DensityStretch&, BiopolymerClassContainer&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityContainer.cpp:18:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   18 |     if(id < 0 || id >= residueStretchVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::writeDensityMapXplor(SimTK::String, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:689:13: warning: unused variable 'densitiesPerLine' [-Wunused-variable]
  689 |         int densitiesPerLine = 6;
      |             ^~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsPurine(char)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:51:14: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
   51 |     return c == 'A' | c == 'G';
      |            ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsRNA(char)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:57:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
   57 |         c == 'A' |
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:59:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
   59 |         c == 'G' |
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:60:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
   60 |         c == 'U'
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsDNA(char)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:67:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
   67 |         c == 'A' |
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:69:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
   69 |         c == 'G' |
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:70:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
   70 |         c == 'T'
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsProtein(char)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:77:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
   77 |         c == 'C' |
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:79:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
   79 |         c == 'H' |
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:80:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
   80 |         c == 'I'
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:86:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
   86 |         c == 'M' |
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:88:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
   88 |         c == 'V' |
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:89:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
   89 |         c == 'A'
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:95:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
   95 |         c == 'G' |
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:97:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
   97 |         c == 'P' |
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:98:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
   98 |         c == 'T'
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:104:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  104 |         c == 'R' |
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:106:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  106 |         c == 'Y' |
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:107:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  107 |         c == 'W'
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:113:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  113 |         c == 'D' |
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:115:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  115 |         c == 'E' |
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:116:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  116 |         c == 'Q' |
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:117:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  117 |         c == 'K'
      |         ~~^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ThreadingStruct>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::modifyResidue(BiopolymerModification, SimTK::Compound, SimTK::DuMMForceFieldSubsystem&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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)));
      |                                         ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:135:29: warning: unused variable 'myOrdinality' [-Wunused-variable]
  135 |         Ordinality::Residue myOrdinality(SimTK::Ordinality::Any);
      |                             ^~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:147:32: warning: unused variable 'myBondMobility' [-Wunused-variable]
  147 |         BondMobility::Mobility myBondMobility = stringToBondMobility("Rigid");
      |                                ^~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::constraintsAndRestraints(ParameterReader&, BiopolymerClassContainer&, SimTK::GeneralForceSubsystem&, SimTK::SimbodyMatterSubsystem&, SimTK::State&, SimTK::CompoundSystem&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:172:31: warning: variable 'myResidueID' set but not used [-Wunused-but-set-variable]
  172 |                     ResidueID myResidueID = myConstraintClass.getResidueID1();
      |                               ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'int BiopolymerClass::checkResidueNumbersAndInsertionCodes()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:244:15: warning: variable 'myResidueID' set but not used [-Wunused-but-set-variable]
  244 |     ResidueID myResidueID = getFirstResidueID();
      |               ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::deleteContact(int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:275:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ContactStretch, std::allocator<ContactStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  275 |     if(id < 0 || id >= residueStretchVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::updateContact(int, std::string, int, int, std::string, BiopolymerClassContainer&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:283:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ContactStretch, std::allocator<ContactStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  283 |     if(id < 0 || id >= residueStretchVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'bool ContactContainer::hasSharedContact(SimTK::String, ResidueID, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:313:71: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
  313 |             ((tempContactStretch.getStartResidue() <= endResidueID)   && (tempContactStretch.getEndResidue() >= endResidueID) ||   // the supplied end residue is in the range of this ContactStretch (with index $i).
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/TetherForce.h:19,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/TetherForce.cpp:11:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Repel.h: In constructor 'ConstrainedDynamics::ConstrainedDynamics(ParameterReader*)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:269:29: warning: 'ConstrainedDynamics::_parameterReader' will be initialized after [-Wreorder]
  269 |     ParameterReader *       _parameterReader;
      |                             ^~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:259:29: warning:   'SimTK::SimbodyMatterSubsystem ConstrainedDynamics::_matter' [-Wreorder]
  259 |     SimbodyMatterSubsystem  _matter;
      |                             ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:342:1: warning:   when initialized here [-Wreorder]
  342 | ConstrainedDynamics::ConstrainedDynamics(ParameterReader * myParameterReader) : _parameterReader(myParameterReader),
      | ^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::initializeBiopolymer(SimTK::String, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:405:10: warning: variable 'readFromFile' set but not used [-Wunused-but-set-variable]
  405 |     bool readFromFile = false;
      |          ^~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::setPdbResidueNumbersFromResidueIDVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:518:15: warning: variable 'myFirstResidueID' set but not used [-Wunused-but-set-variable]
  518 |     ResidueID myFirstResidueID = getFirstResidueID() ;
      |               ^~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:520:9: warning: unused variable 'numResidues' [-Wunused-variable]
  520 |     int numResidues = -1;
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::renumberPdbResidues(ResidueID)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:551:9: warning: unused variable 'myNewResidueNumberWithoutInsertionCode' [-Wunused-variable]
  551 |     int myNewResidueNumberWithoutInsertionCode = firstResidueID.getResidueNumber() ;
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::removeNonPriorityBasePairs(int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:727:9: warning: unused variable 'oldDutyCyclePriority' [-Wunused-variable]
  727 |     int oldDutyCyclePriority=0;
      |         ^~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::updateAllResiduesWithin(int, SimTK::String, int, double)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:776:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<AllResiduesWithin>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  776 |     if(index < 0 || index >= includeAllResiduesWithinVector.size()){
      |                     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::deleteAllResiduesWithin(int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:785:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<AllResiduesWithin>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  785 |     if(index < 0 || index >= includeAllResiduesWithinVector.size()){
      |                     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ThreadingStruct>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'int BiopolymerClass::matchCoordinates(const SimTK::PdbStructure&, bool, bool, bool, bool, bool, bool, double, double)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:669:45: warning: variable 'biopolymerAtomTargetsIterator' set but not used [-Wunused-but-set-variable]
  669 |     Compound::AtomTargetLocations::iterator biopolymerAtomTargetsIterator = biopolymerAtomTargets.begin();
      |                                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'bool BiopolymerClass::hasAtom(ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1053:9: warning: unused variable 'myResidueIndex' [-Wunused-variable]
 1053 |     int myResidueIndex = getResidueIndex(myResidueID);
      |         ^~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::runAllSteps()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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++){
      |           ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'SimTK::Vec3 BiopolymerClass::calcDefaultAtomLocationInGroundFrame(const ResidueID&, const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1316:25: warning: variable 'myAtomIndex' set but not used [-Wunused-but-set-variable]
 1316 |     Compound::AtomIndex myAtomIndex = atomIndex(myResidueID,atomName);
      |                         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::addGeneralSterics(SimTK::GeneralContactSubsystem&, SimTK::ContactSetIndex, SimTK::HuntCrossleyForce&, SimTK::SimbodyMatterSubsystem&, double, double, ResidueID, ResidueID, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1437:12: warning: unused variable 'huntCrossleyDissipation' [-Wunused-variable]
 1437 |     double huntCrossleyDissipation  =.0;
      |            ^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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.
      |                 ^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'ResidueID BiopolymerClass::sum(ResidueID, int) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:2172:55: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 2172 |         if ((newResidueIndex < 0) || (newResidueIndex >= residueIDVector.size())) {
      |                                       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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))
      |                ^
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClassContainer::waterDropletAboutResidues(std::vector<WaterDropletAboutResidueStruct>, WaterDropletContainer&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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
      |                       ^~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClassContainer::substituteResidue(SimTK::String, ResidueID, SimTK::String, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4130:15: warning: variable 'myFirstResidueNumber' set but not used [-Wunused-but-set-variable]
 4130 |     ResidueID myFirstResidueNumber = myOldBiopolymerClass.getFirstResidueID();
      |               ^~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2658:27: warning: variable 'residueID1' set but not used [-Wunused-but-set-variable]
 2658 |                 ResidueID residueID1 = ResidueID(-11111,'X');
      |                           ^~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2659:27: warning: variable 'residueID2' set but not used [-Wunused-but-set-variable]
 2659 |                 ResidueID residueID2 = ResidueID(-11111,'X');
      |                           ^~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2735:16: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
 2735 |             if ((parameterStringClass.getString(0).compare("constraint") == 0) || (parameterStringClass.getString(0).compare("restraint") == 0))
      |                ^
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClassContainer::substituteResidue(Mutation, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4519:15: warning: variable 'myFirstResidueNumber' set but not used [-Wunused-but-set-variable]
 4519 |     ResidueID myFirstResidueNumber = myOldBiopolymerClass.getFirstResidueID();
      |               ^~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::addAllMutualChainResidues(double, std::vector<SimTK::String>, std::vector<SimTK::String>, BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:210:4:   required from 'void ResidueStretchContainer<ResidueStretchType>::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]'
  210 |                         addAllMutualChainResidues(tempInterface.Depth, tempInterface.Chains, tempInterface.PartnerChains, myBiopolymerClassContainer);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:470:84:   required from here
  470 |     _parameterReader->mobilizerContainer.addStretchesToVectorFromInterfaceContainer(_parameterReader->myBiopolymerClassContainer);
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:232:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  232 |             for (int i = 0; i < concatenatedAtomInfoVector.size() ; i++) {
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:244:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<unsigned int, unsigned int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  244 |             for ( int j = 0 ; j < neighborList.size(); j++) {
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::addAllMutualChainResidues(double, std::vector<SimTK::String>, std::vector<SimTK::String>, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:210:4:   required from 'void ResidueStretchContainer<ResidueStretchType>::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]'
  210 |                         addAllMutualChainResidues(tempInterface.Depth, tempInterface.Chains, tempInterface.PartnerChains, myBiopolymerClassContainer);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:573:84:   required from here
  573 |     _parameterReader->  physicsContainer.addStretchesToVectorFromInterfaceContainer(_parameterReader->myBiopolymerClassContainer);
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:232:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  232 |             for (int i = 0; i < concatenatedAtomInfoVector.size() ; i++) {
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:244:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<unsigned int, unsigned int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  244 |             for ( int j = 0 ; j < neighborList.size(); j++) {
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
[ 65%] Building CXX object CMakeFiles/MMB.dir/src/DensityForce.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DensityForce.cpp.o -MF CMakeFiles/MMB.dir/src/DensityForce.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityForce.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityForce.cpp
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:16:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4682:61:   required from here
 4682 |     myResidueStretchContainer.addIntraChainInterfaceResidues( radius, chain, *this );
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:283:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  283 |             for (int i = 0; i < chainAtomInfoVector.size() ; i++) {
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:300:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<unsigned int, unsigned int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  300 |             for ( int j = 0 ; j < neighborList.size(); j++) {
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'bool ResidueStretchContainer<ResidueStretchType>::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = MobilizerStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:264:27:   required from 'void ResidueStretchContainer<ResidueStretchType>::addAllMutualChainResidues(double, std::vector<SimTK::String>, std::vector<SimTK::String>, BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]'
  264 |                     if (!(vectorHasResidueStretch(myResidueStretch1))) {addStretch(myResidueStretch1);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:210:4:   required from 'void ResidueStretchContainer<ResidueStretchType>::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]'
  210 |                         addAllMutualChainResidues(tempInterface.Depth, tempInterface.Chains, tempInterface.PartnerChains, myBiopolymerClassContainer);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:470:84:   required from here
  470 |     _parameterReader->mobilizerContainer.addStretchesToVectorFromInterfaceContainer(_parameterReader->myBiopolymerClassContainer);
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:104:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MobilizerStretch>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  104 |                 for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'bool ResidueStretchContainer<ResidueStretchType>::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:264:27:   required from 'void ResidueStretchContainer<ResidueStretchType>::addAllMutualChainResidues(double, std::vector<SimTK::String>, std::vector<SimTK::String>, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]'
  264 |                     if (!(vectorHasResidueStretch(myResidueStretch1))) {addStretch(myResidueStretch1);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:210:4:   required from 'void ResidueStretchContainer<ResidueStretchType>::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]'
  210 |                         addAllMutualChainResidues(tempInterface.Depth, tempInterface.Chains, tempInterface.PartnerChains, myBiopolymerClassContainer);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:573:84:   required from here
  573 |     _parameterReader->  physicsContainer.addStretchesToVectorFromInterfaceContainer(_parameterReader->myBiopolymerClassContainer);
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:104:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SingleResidue>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  104 |                 for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = SingleResidue]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:814:42:   required from here
  814 |     physicsContainer.deleteResidueStretch(index);
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SingleResidue>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o -MF CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o.d -o CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ElectrostaticPotentialGridForce.cpp
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = MobilizerStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:2584:54:   required from 'void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch&, ResidueStretchContainer<ResidueStretchType>&) [with ResidueStretchType = MobilizerStretch]'
 2584 |     residueStretchContainer.printResidueStretchVector();
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:2588:181:   required from here
 2588 | template void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch &residueStretch, ResidueStretchContainer<MobilizerStretch> &residueStretchContainer);
      |                                                                                                                                                                                     ^
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MobilizerStretch>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'bool ResidueStretchContainer<ResidueStretchType>::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:320:27:   required from 'void ResidueStretchContainer<ResidueStretchType>::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]'
  320 |                     if (!(vectorHasResidueStretch(myResidueStretch1))) {addResidueStretchToVector(myResidueStretch1);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4682:61:   required from here
 4682 |     myResidueStretchContainer.addIntraChainInterfaceResidues( radius, chain, *this );
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:104:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SingleResidue>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  104 |                 for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4827:54:   required from 'void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer&, ResidueStretchContainer<ResidueStretchType>&) [with ResidueStretchType = DensityStretch]'
 4827 |     residueStretchContainer.printResidueStretchVector();
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4830:213:   required from here
 4830 | template void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer &mobilizerContainer, ResidueStretchContainer<DensityStretch> &residueStretchContainer);
      |                                                                                                                                                                                                                     ^
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93,
                 from /usr/include/simbody/SimTKcommon/Simmatrix.h:37,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22:
In member function 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]',
    inlined from 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Mat<3, 3> [1]' [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
In file included from /usr/include/molmodel/molmodel/internal/Compound.h:41,
                 from /usr/include/molmodel/SimTKmolmodel.h:53,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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:201:33:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<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:201:33:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<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:201:33:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<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();
      |                                 ^
[ 71%] Building CXX object CMakeFiles/MMB.dir/src/MMBLogger.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/MMBLogger.cpp.o -MF CMakeFiles/MMB.dir/src/MMBLogger.cpp.o.d -o CMakeFiles/MMB.dir/src/MMBLogger.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/MMBLogger.cpp
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93,
                 from /usr/include/simbody/SimTKcommon/Simmatrix.h:37,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/Simbody.h:38,
                 from /usr/include/molmodel/SimTKmolmodel.h:47,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClassTwoTransformForces.h:16:
In member function 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]',
    inlined from 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from 'SimTK::Rotation_<P>::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from 'virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:117:50:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:117:50:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:117:50:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72
  116 |             Rotation rotation2;
      |                      ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 ) {
      |                 ^~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 75%] Building CXX object CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -MF CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o.d -o CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:254:29: warning: 'myFrcScalar' may be used uninitialized [-Wmaybe-uninitialized]
  254 |                 myFrcScalar *= myParameterReader.twoTransformForceMultiplier;
      |                 ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:167:20: note: 'myFrcScalar' was declared here
  167 |             double myFrcScalar;
      |                    ^~~~~~~~~~~
[ 78%] Building CXX object CMakeFiles/MMB.dir/src/CifOutput.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/CifOutput.cpp.o -MF CMakeFiles/MMB.dir/src/CifOutput.cpp.o.d -o CMakeFiles/MMB.dir/src/CifOutput.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/CifOutput.cpp
[ 81%] Building CXX object CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o -MF CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o.d -o CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ProgressWriter.cpp
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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:319:22:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:319:22:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:319:22:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:320:50:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:320:50:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:320:50:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object 'rotation2' of size 72
  319 |             Rotation rotation2;
      |                      ^~~~~~~~~
[ 84%] Building CXX object CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o -MF CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o.d -o CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/NTC_PARAMETER_READER.cpp
[ 87%] Building CXX object CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o -MF CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/NtCClassContainer.cpp
[ 90%] Building CXX object CMakeFiles/MMB.dir/src/NtCForces.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NtCForces.cpp.o -MF CMakeFiles/MMB.dir/src/NtCForces.cpp.o.d -o CMakeFiles/MMB.dir/src/NtCForces.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/NtCForces.cpp
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityForce.h:20,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/DensityForce.cpp:11:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ThreadingStruct>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ElectrostaticPotentialGridForce.h:19,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ElectrostaticPotentialGridForce.cpp:11:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ThreadingStruct>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/PeriodicPdbAndEnergyWriter.h:13,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:18:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ThreadingStruct>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/CifOutput.h:5,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/CifOutput.cpp:1:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp: In member function 'virtual void SimTK::PeriodicPdbAndEnergyWriter::handleEvent(SimTK::State&, SimTK::Real, bool&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:201:30: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  201 |         if(myEnergies.size() > myParameterReader.convergenceTimeout) {
      |            ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:202:20: warning: unused variable 'lastEnergy' [-Wunused-variable]
  202 |             double lastEnergy = myEnergies.back();
      |                    ^~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:49:9: warning: unused variable 'compoundNumber' [-Wunused-variable]
   49 |     int compoundNumber                                = 1;
      |         ^~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:50:9: warning: unused variable 'requiredPrecision' [-Wunused-variable]
   50 |     int requiredPrecision                             = 12;
      |         ^~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/PeriodicPdbAndEnergyWriter.h:13,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/CifOutput.h:12:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ThreadingStruct>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/NtC_Class_Container.h:14,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/NTC_PARAMETER_READER.cpp:16:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/NTC_FORCE_CLASS.h:4,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/NTC_PARAMETER_READER.cpp:17:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/NtCForces.h:13,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/NtCForces.cpp:11:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/NtCClassContainer.cpp:13:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ThreadingStruct>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93,
                 from /usr/include/simbody/SimTKcommon/Simmatrix.h:37,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /usr/include/molmodel/molmodel/internal/Compound.h:36,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:16:
In member function 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]',
    inlined from 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from 'SimTK::Rotation_<P>::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from 'int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:875:14:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:875:14:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:875:14:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:876:44:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:876:44:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:876:44:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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&)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:875:14: note: object 'myRotation' of size 72
  875 |     Rotation myRotation;
      |              ^~~~~~~~~~
In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93,
                 from /usr/include/simbody/SimTKcommon/Simmatrix.h:37,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22:
In member function 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]',
    inlined from 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from 'SimTK::Rotation_<P>::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from 'Displacement::Displacement()' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:544:8,
    inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2223:19:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'Displacement [1]' [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2223:26: note: at offset 56 into object 'myDisplacement' of size 128
 2223 |             Displacement myDisplacement;
      |                          ^~~~~~~~~~~~~~
In member function 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]',
    inlined from 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from 'SimTK::Rotation_<P>::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from 'Displacement::Displacement()' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:544:8,
    inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2223:19:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'Displacement [1]' [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2223:26: note: at offset 56 into object 'myDisplacement' of size 128
 2223 |             Displacement myDisplacement;
      |                          ^~~~~~~~~~~~~~
In member function 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]',
    inlined from 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from 'SimTK::Rotation_<P>::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from 'Displacement::Displacement()' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:544:8,
    inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2223:19:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'Displacement [1]' [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2223:26: note: at offset 56 into object 'myDisplacement' of size 128
 2223 |             Displacement myDisplacement;
      |                          ^~~~~~~~~~~~~~
In member function 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]',
    inlined from 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from 'SimTK::Rotation_<P>::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2224:22: note: object 'myRotation' of size 72
 2224 |             Rotation myRotation;
      |                      ^~~~~~~~~~
In member function 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]',
    inlined from 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from 'SimTK::Rotation_<P>::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from 'Displacement::Displacement()' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:544:8,
    inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2207:30:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'Displacement [1]' [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2207:30: note: at offset 56 into object 'myDisplacement' of size 128
 2207 |                 Displacement myDisplacement;
      |                              ^~~~~~~~~~~~~~
In member function 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]',
    inlined from 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from 'SimTK::Rotation_<P>::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from 'Displacement::Displacement()' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:544:8,
    inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2207:30:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'Displacement [1]' [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2207:30: note: at offset 56 into object 'myDisplacement' of size 128
 2207 |                 Displacement myDisplacement;
      |                              ^~~~~~~~~~~~~~
In member function 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]',
    inlined from 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from 'SimTK::Rotation_<P>::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from 'Displacement::Displacement()' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:544:8,
    inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2207:30:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'Displacement [1]' [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2207:30: note: at offset 56 into object 'myDisplacement' of size 128
 2207 |                 Displacement myDisplacement;
      |                              ^~~~~~~~~~~~~~
In member function 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]',
    inlined from 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from 'SimTK::Rotation_<P>::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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 /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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; }
      |                              ~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2209:26: note: object 'myRotation' of size 72
 2209 |                 Rotation myRotation;
      |                          ^~~~~~~~~~
[ 93%] Linking CXX shared library libMMB.so
/usr/bin/cmake -E cmake_link_script CMakeFiles/MMB.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -Wl,-z,relro -shared -Wl,-soname,libMMB.so.4.0 -o libMMB.so.4.0 CMakeFiles/MMB.dir/src/Utils.cpp.o CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o CMakeFiles/MMB.dir/src/DensityContainer.cpp.o CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o CMakeFiles/MMB.dir/src/ContactContainer.cpp.o CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o CMakeFiles/MMB.dir/src/Repel.cpp.o CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o CMakeFiles/MMB.dir/src/Spiral.cpp.o CMakeFiles/MMB.dir/src/ParameterReader.cpp.o CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o CMakeFiles/MMB.dir/src/TetherForce.cpp.o CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o CMakeFiles/MMB.dir/src/DensityMap.cpp.o CMakeFiles/MMB.dir/src/DensityForce.cpp.o CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o CMakeFiles/MMB.dir/src/MMBLogger.cpp.o CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o CMakeFiles/MMB.dir/src/CifOutput.cpp.o CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o CMakeFiles/MMB.dir/src/NtCForces.cpp.o   -L/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/SYSTEM  -Wl,-rpath,/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/SYSTEM: /usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 /usr/lib/x86_64-linux-gnu/libOpenMM.so /usr/lib/x86_64-linux-gnu/libz.so -lgemmi_cpp /usr/lib/x86_64-linux-gnu/libSimTKsimbody.so.3.7 /usr/lib/x86_64-linux-gnu/libSimTKmath.so.3.7 /usr/lib/x86_64-linux-gnu/libSimTKcommon.so.3.7 /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lpthread -lrt -ldl -lm
/usr/bin/cmake -E cmake_symlink_library libMMB.so.4.0 libMMB.so.4.0 libMMB.so
make[3]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu'
[ 93%] Built target MMB
make  -f CMakeFiles/MMB_EXEC.dir/build.make CMakeFiles/MMB_EXEC.dir/depend
make[3]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu'
cd /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu/CMakeFiles/MMB_EXEC.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu'
make  -f CMakeFiles/MMB_EXEC.dir/build.make CMakeFiles/MMB_EXEC.dir/build
make[3]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu'
[ 96%] Building CXX object CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DUSE_MMB_CONSTEXPR -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -I/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -MD -MT CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o -MF CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o.d -o CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o -c /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/RNABuilder.cpp
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/src/RNABuilder.cpp:22:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/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;
      |              ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:321:14: warning: unused variable 'endChar' [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning:   'ResidueID MMBAtomInfo::residueID' [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<SimTK::String>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<MMBAtomInfo>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ResidueID>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ThreadingStruct>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
                 from /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[100%] Linking CXX executable MMB
/usr/bin/cmake -E cmake_link_script CMakeFiles/MMB_EXEC.dir/link.txt --verbose=1
/usr/bin/c++ -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -Wl,-z,relro CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o -o MMB   -L/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/SYSTEM  -Wl,-rpath,/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/SYSTEM:/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu: libMMB.so.4.0 /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libSimTKmolmodel.so.3.1 /usr/lib/x86_64-linux-gnu/libSimTKsimbody.so.3.7 /usr/lib/x86_64-linux-gnu/libSimTKmath.so.3.7 /usr/lib/x86_64-linux-gnu/libSimTKcommon.so.3.7 /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/liblapack.so -lpthread -lrt -ldl -lm
make[3]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu'
[100%] Built target MMB_EXEC
make[2]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu'
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0
make[1]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu'
   dh_auto_test
   create-stamp debian/debhelper-build-stamp
   dh_prep
   dh_auto_install
	cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/macromoleculebuilder-4.0.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg -B/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
make  -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/AddBackboneOxygenForces.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/AddNASTForces.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/AtomSpringContainer.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/BaseInteractionParameterReader.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/BasePairContainer.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/BiopolymerClass.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/BiopolymerClassTwoTransformForces.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/CalcTransformCorrection.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/CenterOfMass.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/CifOutput.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Constexpr.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/ConstraintContainer.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/ContactContainer.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/DensityContainer.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/DensityForce.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/DensityMap.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/DisplacementContainer.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/ElectrostaticPotentialGridForce.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/ExportMacros.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/ExtraMath.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/GeometricCenter.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/HarmonicVelocityRescalingThermostat.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Impossible.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/KBBackboneTorsionForce.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Lepton.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/LigandDroplet.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Ligands.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Ligands.sam.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/MMBLogger.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/MobilizerContainer.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/MoleculeContainer.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/MonoAtoms.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Mutation.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/NTC_FORCE_CLASS.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/NTC_PARAMETER_READER.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/NtCBackboneTorsionForce.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/NtCForces.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/NtCInteractionParameterReader.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/NtC_Class_Container.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/ParameterReader.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/ParameterReader_wrapper.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/PeriodicParameterReaderUpdater.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/PeriodicPdbAndCOMWriter.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/PeriodicPdbAndEnergySingleFrameWriter.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/PeriodicPdbAndEnergyWriter.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/PeriodicPdbSingleFrameWriter.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/PeriodicScrubber.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/ProgressWriter.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/RandomizeRNACoordinates.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Repel.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/ResidueStretchContainer.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/RigidifyFormedHelices.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/SetChiMobility.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/SetSingleBondMobility.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Spiral.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/StackingForceSubsystem.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Sterics.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/TetherForce.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Threading.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/UnitCellParameters.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Utils.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/WadleyKeatingDuartePyleTorsionForce.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Water.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/WaterDroplet.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/superimposer.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/MMB_config.h
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libMMB.so.4.0
-- Set non-toolchain portion of runtime path of "/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libMMB.so.4.0" to ""
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libMMB.so
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/share/MMB/parameters.csv
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/bin/MMB
-- Set non-toolchain portion of runtime path of "/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/bin/MMB" to ""
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/mmb/MmbConfigVersion.cmake
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/mmb/MmbTargets.cmake
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/mmb/MmbTargets-release.cmake
-- Installing: /build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/mmb.pc
make[1]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg/obj-x86_64-linux-gnu'
   dh_install
   dh_installdocs
   dh_installchangelogs
   debian/rules override_dh_installman
make[1]: Entering directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg'
a2x -d manpage -f manpage -D debian/tmp debian/MMB.1.asciidoc
dh_installman
make[1]: Leaving directory '/build/reproducible-path/macromoleculebuilder-4.0.0+dfsg'
   dh_lintian
   dh_perl
   dh_link
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_dwz -a
   dh_strip -a
   dh_makeshlibs -a
   dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mmb/usr/bin/MMB was not linked against libz.so.1 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: symbol gzread used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzbuffer used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzeof used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzerror used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzgets used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzclose_r used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzgetc used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzungetc used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzopen used by debian/libmmb4.0t64/usr/lib/x86_64-linux-gnu/libMMB.so.4.0 found in none of the libraries
   dh_installdeb
   dh_gencontrol
   dh_md5sums
   dh_builddeb
dpkg-deb: building package 'libmmb-dev' in '../libmmb-dev_4.0.0+dfsg-5_amd64.deb'.
dpkg-deb: building package 'libmmb4.0t64' in '../libmmb4.0t64_4.0.0+dfsg-5_amd64.deb'.
dpkg-deb: building package 'mmb' in '../mmb_4.0.0+dfsg-5_amd64.deb'.
dpkg-deb: building package 'libmmb4.0t64-dbgsym' in '../libmmb4.0t64-dbgsym_4.0.0+dfsg-5_amd64.deb'.
dpkg-deb: building package 'mmb-common' in '../mmb-common_4.0.0+dfsg-5_all.deb'.
dpkg-deb: building package 'mmb-dbgsym' in '../mmb-dbgsym_4.0.0+dfsg-5_amd64.deb'.
 dpkg-genbuildinfo --build=binary -O../macromoleculebuilder_4.0.0+dfsg-5_amd64.buildinfo
 dpkg-genchanges --build=binary -O../macromoleculebuilder_4.0.0+dfsg-5_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env 
I: removing directory /srv/workspace/pbuilder/2405886 and its subdirectories
I: Current time: Sun Dec  1 18:42:18 -12 2024
I: pbuilder-time-stamp: 1733121738
Mon Dec  2 06:42:20 UTC 2024  I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net.
Mon Dec  2 06:42:20 UTC 2024  I: Preparing to do remote build '2' on ionos5-amd64.debian.net.
Mon Dec  2 06:52:43 UTC 2024  I: Deleting $TMPDIR on ionos5-amd64.debian.net.
Mon Dec  2 06:52:44 UTC 2024  I: macromoleculebuilder_4.0.0+dfsg-5_amd64.changes:
Format: 1.8
Date: Wed, 27 Nov 2024 02:07:37 -0500
Source: macromoleculebuilder
Binary: libmmb-dev libmmb4.0t64 libmmb4.0t64-dbgsym mmb mmb-common mmb-dbgsym
Architecture: amd64 all
Version: 4.0.0+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Changed-By: Andrius Merkys <merkys@debian.org>
Description:
 libmmb-dev - development files of MacroMoleculeBuilder
 libmmb4.0t64 - shared library of MacroMoleculeBuilder
 mmb        - model the structure and dynamics of macromolecules
 mmb-common - model the structure and dynamics of macromolecules (common files)
Closes: 1086362
Changes:
 macromoleculebuilder (4.0.0+dfsg-5) unstable; urgency=medium
 .
   * Link MMB_SHARED_TARGET with ZLIB_LIBRARIES via patch (Closes: #1086362)
Checksums-Sha1:
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Files:
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 e2c6071fa807cb1b2492940a7060bc51 25590636 debug optional libmmb4.0t64-dbgsym_4.0.0+dfsg-5_amd64.deb
 d2c571c15fc04b5ccb3b1b823ea54c21 1191904 libs optional libmmb4.0t64_4.0.0+dfsg-5_amd64.deb
 8874e060cd5c93b5da013597e5ac82e8 10940 science optional macromoleculebuilder_4.0.0+dfsg-5_amd64.buildinfo
 fec86aed585cadcbc24c20d65cd22806 339424 science optional mmb-common_4.0.0+dfsg-5_all.deb
 1bbabb838d3b0791ba2cc98605079650 1641624 debug optional mmb-dbgsym_4.0.0+dfsg-5_amd64.deb
 ab277d1a8603e3fd77bec0835e932c71 30344 science optional mmb_4.0.0+dfsg-5_amd64.deb
Mon Dec  2 06:52:45 UTC 2024  I: diffoscope 283 will be used to compare the two builds:
Running as unit: rb-diffoscope-amd64_13-25887.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.6CmBvtqs/macromoleculebuilder_4.0.0+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.6CmBvtqs/macromoleculebuilder_4.0.0+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.6CmBvtqs/macromoleculebuilder_4.0.0+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.6CmBvtqs/b1/macromoleculebuilder_4.0.0+dfsg-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.6CmBvtqs/b2/macromoleculebuilder_4.0.0+dfsg-5_amd64.changes

## command (total time: 0.000s)
       0.000s      1 call     cmp (internal)

## has_same_content_as (total time: 0.000s)
       0.000s      1 call     abc.DotChangesFile

## main (total time: 0.762s)
       0.762s      2 calls    outputs
       0.000s      1 call     cleanup

## recognizes (total time: 0.362s)
       0.362s     12 calls    diffoscope.comparators.binary.FilesystemFile

## specialize (total time: 0.000s)
       0.000s      1 call     specialize
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 1.111s
CPU time consumed: 1.110s
Mon Dec  2 06:52:47 UTC 2024  I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists.
Mon Dec  2 06:52:47 UTC 2024  I: macromoleculebuilder from trixie built successfully and reproducibly on amd64.
Mon Dec  2 06:52:48 UTC 2024  I: Submitting .buildinfo files to external archives:
Mon Dec  2 06:52:48 UTC 2024  I: Submitting 12K	b1/macromoleculebuilder_4.0.0+dfsg-5_amd64.buildinfo.asc
Mon Dec  2 06:52:49 UTC 2024  I: Submitting 12K	b2/macromoleculebuilder_4.0.0+dfsg-5_amd64.buildinfo.asc
Mon Dec  2 06:52:50 UTC 2024  I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Mon Dec  2 06:52:50 UTC 2024  I: Done submitting .buildinfo files.
Mon Dec  2 06:52:50 UTC 2024  I: Removing signed macromoleculebuilder_4.0.0+dfsg-5_amd64.buildinfo.asc files:
removed './b1/macromoleculebuilder_4.0.0+dfsg-5_amd64.buildinfo.asc'
removed './b2/macromoleculebuilder_4.0.0+dfsg-5_amd64.buildinfo.asc'