macromoleculebuilder →
4.0.0+dfsg-3 →
armhf → 2023-12-01 18:48:12
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| macromoleculebuilder 4.0.0+dfsg-3 (armhf) Fri, 01 Dec 2023 18:24:33 +0000 |
+==============================================================================+
Package: macromoleculebuilder
Version: 4.0.0+dfsg-3
Source Version: 4.0.0+dfsg-3
Distribution: trixie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/trixie-staging-armhf-sbuild-ddefe575-45ad-4034-9ce0-28cd56182269' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.3 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.0 MB]
Fetched 29.2 MB in 11s (2599 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'macromoleculebuilder' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/debichem-team/macromoleculebuilder.git
Please use:
git clone https://salsa.debian.org/debichem-team/macromoleculebuilder.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 2575 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main macromoleculebuilder 4.0.0+dfsg-3 (dsc) [2439 B]
Get:2 http://172.17.4.1/private trixie-staging/main macromoleculebuilder 4.0.0+dfsg-3 (tar) [2567 kB]
Get:3 http://172.17.4.1/private trixie-staging/main macromoleculebuilder 4.0.0+dfsg-3 (diff) [5516 B]
Fetched 2575 kB in 0s (6572 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-yAvsvy/macromoleculebuilder-4.0.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-yAvsvy' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-l0p8bh/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-l0p8bh/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-l0p8bh/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-l0p8bh/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-l0p8bh/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-l0p8bh/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-l0p8bh/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-l0p8bh/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2938 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase sensible-utils sgml-base util-linux-extra
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 40 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-l0p8bh/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (28.5 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12856 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: asciidoc-base, cmake, debhelper-compat (= 13), docbook-xml, gemmi-dev (>= 0.6.2+ds-2), libopenmm-dev, libseqan2-dev, libsimbody-dev, libsimtkmolmodel-dev (>= 3.1.0), libsimtkmolmodel-plugins, libstb-dev, tao-pegtl-dev, zlib1g-dev
Filtered Build-Depends: asciidoc-base, cmake, debhelper-compat (= 13), docbook-xml, gemmi-dev (>= 0.6.2+ds-2), libopenmm-dev, libseqan2-dev, libsimbody-dev, libsimtkmolmodel-dev (>= 3.1.0), libsimtkmolmodel-plugins, libstb-dev, tao-pegtl-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-macromoleculebuilder-dummy' in '/<<BUILDDIR>>/resolver-l0p8bh/apt_archive/sbuild-build-depends-macromoleculebuilder-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-macromoleculebuilder-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-l0p8bh/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-l0p8bh/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-l0p8bh/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-l0p8bh/apt_archive ./ Sources [610 B]
Get:5 copy:/<<BUILDDIR>>/resolver-l0p8bh/apt_archive ./ Packages [689 B]
Fetched 2632 B in 1s (4288 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install macromoleculebuilder build dependencies (apt-based resolver)
--------------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase util-linux-extra
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
asciidoc-base asciidoc-common autoconf automake autopoint autotools-dev
bsdextrautils bsdutils cmake cmake-data debhelper dh-autoreconf
dh-strip-nondeterminism docbook-xml docbook-xsl dwz file freeglut3-dev
gemmi-dev gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libarchive13 libblas-dev libblas3 libblkid1 libbrotli1
libbsd0 libcurl4 libdebhelper-perl libdrm-amdgpu1 libdrm-common
libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libegl-dev libegl-mesa0
libegl1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgbm1
libgfortran5 libgl-dev libgl1 libgl1-mesa-dev libgl1-mesa-dri libglapi-mesa
libgles-dev libgles1 libgles2 libglu1-mesa libglu1-mesa-dev libglut-dev
libglut3.12 libglvnd-core-dev libglvnd-dev libglvnd0 libglx-dev libglx-mesa0
libglx0 libice-dev libice6 libicu72 libjsoncpp25 liblapack-dev liblapack3
libllvm15 libmagic-mgc libmagic1 libmount1 libnghttp2-14 libopengl-dev
libopengl0 libopenmm-dev libopenmm8.0 libpipeline1 libproc2-0 libpsl5
libpthread-stubs0-dev libpython3-stdlib libpython3.11-minimal
libpython3.11-stdlib librhash0 librtmp1 libsensors-config libsensors5
libseqan2-dev libsimbody-dev libsimbody3.7 libsimtkmolmodel-dev
libsimtkmolmodel-plugins libsimtkmolmodel3.1 libsm-dev libsm6 libsmartcols1
libssh2-1 libstb-dev libstb0 libsub-override-perl libtool libuchardet0
libuuid1 libuv1 libwayland-client0 libwayland-server0 libx11-6 libx11-data
libx11-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri3-0
libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-shm0 libxcb-sync1
libxcb-xfixes0 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev
libxext6 libxfixes-dev libxfixes3 libxi-dev libxi6 libxml2 libxml2-utils
libxmu-dev libxmu-headers libxmu6 libxshmfence1 libxslt1.1 libxt-dev libxt6
libxxf86vm1 libz3-4 m4 man-db media-types mount po-debconf procps python3
python3-minimal python3.11 python3.11-minimal sgml-data tao-pegtl-dev
util-linux util-linux-extra x11-common x11proto-dev xml-core
xorg-sgml-doctools xsltproc xtrans-dev zlib1g-dev
Suggested packages:
asciidoc-doc docbook-utils source-highlight autoconf-archive gnu-standards
autoconf-doc cmake-doc cmake-format elpa-cmake-mode ninja-build dh-make
docbook docbook-dsssl docbook-defguide dbtoepub docbook-xsl-doc-html
| docbook-xsl-doc-pdf | docbook-xsl-doc-text | docbook-xsl-doc
docbook-xsl-saxon fop libsaxon-java libxalan2-java libxslthl-java xalan
gettext-doc libasprintf-dev libgettextpo-dev groff lrzip liblapack-doc
libice-doc cryptsetup-bin lm-sensors libsm-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk libx11-doc libxcb-doc libxext-doc libxt-doc
m4-doc apparmor less www-browser nfs-common libmail-box-perl python3-doc
python3-tk python3-venv python3.11-venv python3.11-doc binfmt-support
perlsgml w3-recs opensp dosfstools kbd util-linux-locales
Recommended packages:
xmlto curl | wget | lynx ca-certificates libarchive-cpio-perl publicsuffix
libltdl-dev uuid-runtime libmail-sendmail-perl psmisc
The following NEW packages will be installed:
asciidoc-base asciidoc-common autoconf automake autopoint autotools-dev
bsdextrautils cmake cmake-data debhelper dh-autoreconf
dh-strip-nondeterminism docbook-xml docbook-xsl dwz file freeglut3-dev
gemmi-dev gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libarchive13 libblas-dev libblas3 libbrotli1 libbsd0
libcurl4 libdebhelper-perl libdrm-amdgpu1 libdrm-common libdrm-nouveau2
libdrm-radeon1 libdrm2 libedit2 libegl-dev libegl-mesa0 libegl1 libelf1
libexpat1 libfile-stripnondeterminism-perl libgbm1 libgfortran5 libgl-dev
libgl1 libgl1-mesa-dev libgl1-mesa-dri libglapi-mesa libgles-dev libgles1
libgles2 libglu1-mesa libglu1-mesa-dev libglut-dev libglut3.12
libglvnd-core-dev libglvnd-dev libglvnd0 libglx-dev libglx-mesa0 libglx0
libice-dev libice6 libicu72 libjsoncpp25 liblapack-dev liblapack3 libllvm15
libmagic-mgc libmagic1 libnghttp2-14 libopengl-dev libopengl0 libopenmm-dev
libopenmm8.0 libpipeline1 libproc2-0 libpsl5 libpthread-stubs0-dev
libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librhash0
librtmp1 libsensors-config libsensors5 libseqan2-dev libsimbody-dev
libsimbody3.7 libsimtkmolmodel-dev libsimtkmolmodel-plugins
libsimtkmolmodel3.1 libsm-dev libsm6 libssh2-1 libstb-dev libstb0
libsub-override-perl libtool libuchardet0 libuv1 libwayland-client0
libwayland-server0 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev
libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0
libxcb-randr0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcb1-dev
libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes-dev libxfixes3
libxi-dev libxi6 libxml2 libxml2-utils libxmu-dev libxmu-headers libxmu6
libxshmfence1 libxslt1.1 libxt-dev libxt6 libxxf86vm1 libz3-4 m4 man-db
media-types po-debconf procps python3 python3-minimal python3.11
python3.11-minimal sbuild-build-depends-macromoleculebuilder-dummy sgml-data
tao-pegtl-dev x11-common x11proto-dev xml-core xorg-sgml-doctools xsltproc
xtrans-dev zlib1g-dev
The following packages will be upgraded:
bsdutils libblkid1 libmount1 libsmartcols1 libuuid1 mount util-linux
util-linux-extra
8 upgraded, 158 newly installed, 0 to remove and 32 not upgraded.
Need to get 97.3 MB of archives.
After this operation, 411 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-l0p8bh/apt_archive ./ sbuild-build-depends-macromoleculebuilder-dummy 0.invalid.0 [976 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf bsdutils armhf 1:2.39.2-6 [86.5 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf libsmartcols1 armhf 2.39.2-6 [102 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf util-linux-extra armhf 2.39.2-6 [135 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf util-linux armhf 2.39.2-6 [1110 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf mount armhf 2.39.2-6 [134 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-minimal armhf 3.11.6-3 [800 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-2 [76.8 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf python3.11-minimal armhf 3.11.6-3 [1674 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf python3-minimal armhf 3.11.4-5 [26.2 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf media-types all 10.1.0 [26.9 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf libuuid1 armhf 2.39.2-6 [28.1 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-stdlib armhf 3.11.6-3 [1679 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf python3.11 armhf 3.11.6-3 [586 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf libpython3-stdlib armhf 3.11.4-5 [9200 B]
Get:16 http://172.17.4.1/private trixie-staging/main armhf python3 armhf 3.11.4-5 [26.2 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf libblkid1 armhf 2.39.2-6 [145 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf libmount1 armhf 2.39.2-6 [167 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.2-6 [81.2 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-1 [1358 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf libproc2-0 armhf 2:4.0.4-2 [54.9 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf procps armhf 2:4.0.4-2 [848 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-13 [156 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf asciidoc-common all 10.2.0-2 [104 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf xml-core all 0.18+nmu1 [23.8 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf docbook-xsl all 1.79.2+dfsg-7 [1221 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libxml2-utils armhf 2.9.14+dfsg-1.3 [95.3 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf libxslt1.1 armhf 1.1.35-1 [221 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf xsltproc armhf 1.1.35-1 [126 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf asciidoc-base all 10.2.0-2 [85.3 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-13 [496 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf libarchive13 armhf 3.7.2-1 [294 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.1.0-2 [280 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.58.0-1 [61.7 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-2 [195 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf libcurl4 armhf 8.4.0-2+rpi1 [362 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf libjsoncpp25 armhf 1.9.5-6 [64.7 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf librhash0 armhf 1.4.3-3 [142 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf libuv1 armhf 1.46.0-2+rpi1 [128 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf cmake-data all 3.27.8-1 [2104 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf cmake armhf 3.27.8-1 [7635 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.8 [82.1 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:59 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:61 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:63 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:65 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-13 [1201 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:68 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.8 [956 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf sgml-data all 2.0.11+nmu1 [179 kB]
Get:70 http://172.17.4.1/private trixie-staging/main armhf docbook-xml all 4.5-12 [85.2 kB]
Get:71 http://172.17.4.1/private trixie-staging/main armhf libglvnd0 armhf 1.7.0-1 [49.4 kB]
Get:72 http://172.17.4.1/private trixie-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:73 http://172.17.4.1/private trixie-staging/main armhf libbsd0 armhf 0.11.7-4 [111 kB]
Get:74 http://172.17.4.1/private trixie-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:75 http://172.17.4.1/private trixie-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:76 http://172.17.4.1/private trixie-staging/main armhf libx11-data all 2:1.8.7-1 [328 kB]
Get:77 http://172.17.4.1/private trixie-staging/main armhf libx11-6 armhf 2:1.8.7-1 [729 kB]
Get:78 http://172.17.4.1/private trixie-staging/main armhf libdrm-common all 2.4.117-1+rpi1 [7468 B]
Get:79 http://172.17.4.1/private trixie-staging/main armhf libdrm2 armhf 2.4.117-1+rpi1 [33.3 kB]
Get:80 http://172.17.4.1/private trixie-staging/main armhf libglapi-mesa armhf 23.1.7-1+rpi1 [46.1 kB]
Get:81 http://172.17.4.1/private trixie-staging/main armhf libx11-xcb1 armhf 2:1.8.7-1 [231 kB]
Get:82 http://172.17.4.1/private trixie-staging/main armhf libxcb-dri2-0 armhf 1.15-1 [107 kB]
Get:83 http://172.17.4.1/private trixie-staging/main armhf libxcb-dri3-0 armhf 1.15-1 [107 kB]
Get:84 http://172.17.4.1/private trixie-staging/main armhf libxcb-glx0 armhf 1.15-1 [121 kB]
Get:85 http://172.17.4.1/private trixie-staging/main armhf libxcb-present0 armhf 1.15-1 [105 kB]
Get:86 http://172.17.4.1/private trixie-staging/main armhf libxcb-randr0 armhf 1.15-1 [116 kB]
Get:87 http://172.17.4.1/private trixie-staging/main armhf libxcb-shm0 armhf 1.15-1 [106 kB]
Get:88 http://172.17.4.1/private trixie-staging/main armhf libxcb-sync1 armhf 1.15-1 [108 kB]
Get:89 http://172.17.4.1/private trixie-staging/main armhf libxcb-xfixes0 armhf 1.15-1 [109 kB]
Get:90 http://172.17.4.1/private trixie-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:91 http://172.17.4.1/private trixie-staging/main armhf libxfixes3 armhf 1:6.0.0-2 [21.2 kB]
Get:92 http://172.17.4.1/private trixie-staging/main armhf libxshmfence1 armhf 1.3-1 [8636 B]
Get:93 http://172.17.4.1/private trixie-staging/main armhf libxxf86vm1 armhf 1:1.1.4-1+b2 [20.1 kB]
Get:94 http://172.17.4.1/private trixie-staging/main armhf libdrm-amdgpu1 armhf 2.4.117-1+rpi1 [19.8 kB]
Get:95 http://172.17.4.1/private trixie-staging/main armhf libdrm-nouveau2 armhf 2.4.117-1+rpi1 [17.1 kB]
Get:96 http://172.17.4.1/private trixie-staging/main armhf libdrm-radeon1 armhf 2.4.117-1+rpi1 [20.8 kB]
Get:97 http://172.17.4.1/private trixie-staging/main armhf libedit2 armhf 3.1-20230828-1 [76.0 kB]
Get:98 http://172.17.4.1/private trixie-staging/main armhf libz3-4 armhf 4.8.12-3.1 [5797 kB]
Get:99 http://172.17.4.1/private trixie-staging/main armhf libllvm15 armhf 1:15.0.7-10+rpi1 [20.7 MB]
Get:100 http://172.17.4.1/private trixie-staging/main armhf libsensors-config all 1:3.6.0-8 [14.4 kB]
Get:101 http://172.17.4.1/private trixie-staging/main armhf libsensors5 armhf 1:3.6.0-8 [31.7 kB]
Get:102 http://172.17.4.1/private trixie-staging/main armhf libgl1-mesa-dri armhf 23.1.7-1+rpi1 [5778 kB]
Get:103 http://172.17.4.1/private trixie-staging/main armhf libglx-mesa0 armhf 23.1.7-1+rpi1 [130 kB]
Get:104 http://172.17.4.1/private trixie-staging/main armhf libglx0 armhf 1.7.0-1 [32.2 kB]
Get:105 http://172.17.4.1/private trixie-staging/main armhf libgl1 armhf 1.7.0-1 [89.3 kB]
Get:106 http://172.17.4.1/private trixie-staging/main armhf libxi6 armhf 2:1.8-1 [78.1 kB]
Get:107 http://172.17.4.1/private trixie-staging/main armhf libglut3.12 armhf 3.4.0-1 [124 kB]
Get:108 http://172.17.4.1/private trixie-staging/main armhf xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get:109 http://172.17.4.1/private trixie-staging/main armhf x11proto-dev all 2023.2-1 [598 kB]
Get:110 http://172.17.4.1/private trixie-staging/main armhf libxau-dev armhf 1:1.0.9-1 [22.3 kB]
Get:111 http://172.17.4.1/private trixie-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:112 http://172.17.4.1/private trixie-staging/main armhf xtrans-dev all 1.4.0-1 [98.7 kB]
Get:113 http://172.17.4.1/private trixie-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:114 http://172.17.4.1/private trixie-staging/main armhf libxcb1-dev armhf 1.15-1 [175 kB]
Get:115 http://172.17.4.1/private trixie-staging/main armhf libx11-dev armhf 2:1.8.7-1 [807 kB]
Get:116 http://172.17.4.1/private trixie-staging/main armhf libglx-dev armhf 1.7.0-1 [15.5 kB]
Get:117 http://172.17.4.1/private trixie-staging/main armhf libgl-dev armhf 1.7.0-1 [100 kB]
Get:118 http://172.17.4.1/private trixie-staging/main armhf libglvnd-core-dev armhf 1.7.0-1 [13.1 kB]
Get:119 http://172.17.4.1/private trixie-staging/main armhf libwayland-server0 armhf 1.22.0-2.1 [26.0 kB]
Get:120 http://172.17.4.1/private trixie-staging/main armhf libgbm1 armhf 23.1.7-1+rpi1 [35.1 kB]
Get:121 http://172.17.4.1/private trixie-staging/main armhf libwayland-client0 armhf 1.22.0-2.1 [20.0 kB]
Get:122 http://172.17.4.1/private trixie-staging/main armhf libegl-mesa0 armhf 23.1.7-1+rpi1 [94.3 kB]
Get:123 http://172.17.4.1/private trixie-staging/main armhf libegl1 armhf 1.7.0-1 [28.4 kB]
Get:124 http://172.17.4.1/private trixie-staging/main armhf libegl-dev armhf 1.7.0-1 [19.2 kB]
Get:125 http://172.17.4.1/private trixie-staging/main armhf libgles1 armhf 1.7.0-1 [11.8 kB]
Get:126 http://172.17.4.1/private trixie-staging/main armhf libgles2 armhf 1.7.0-1 [17.3 kB]
Get:127 http://172.17.4.1/private trixie-staging/main armhf libgles-dev armhf 1.7.0-1 [50.5 kB]
Get:128 http://172.17.4.1/private trixie-staging/main armhf libopengl0 armhf 1.7.0-1 [31.8 kB]
Get:129 http://172.17.4.1/private trixie-staging/main armhf libopengl-dev armhf 1.7.0-1 [5104 B]
Get:130 http://172.17.4.1/private trixie-staging/main armhf libglvnd-dev armhf 1.7.0-1 [4868 B]
Get:131 http://172.17.4.1/private trixie-staging/main armhf libgl1-mesa-dev armhf 23.1.7-1+rpi1 [15.3 kB]
Get:132 http://172.17.4.1/private trixie-staging/main armhf libglu1-mesa armhf 9.0.2-1.1 [133 kB]
Get:133 http://172.17.4.1/private trixie-staging/main armhf libglu1-mesa-dev armhf 9.0.2-1.1 [175 kB]
Get:134 http://172.17.4.1/private trixie-staging/main armhf libxext-dev armhf 2:1.3.4-1 [102 kB]
Get:135 http://172.17.4.1/private trixie-staging/main armhf x11-common all 1:7.7+23 [252 kB]
Get:136 http://172.17.4.1/private trixie-staging/main armhf libice6 armhf 2:1.0.10-1 [51.7 kB]
Get:137 http://172.17.4.1/private trixie-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:138 http://172.17.4.1/private trixie-staging/main armhf libxt6 armhf 1:1.2.1-1.1 [155 kB]
Get:139 http://172.17.4.1/private trixie-staging/main armhf libice-dev armhf 2:1.0.10-1 [58.7 kB]
Get:140 http://172.17.4.1/private trixie-staging/main armhf libsm-dev armhf 2:1.2.3-1 [35.4 kB]
Get:141 http://172.17.4.1/private trixie-staging/main armhf libxt-dev armhf 1:1.2.1-1.1 [368 kB]
Get:142 http://172.17.4.1/private trixie-staging/main armhf libglut-dev armhf 3.4.0-1 [146 kB]
Get:143 http://172.17.4.1/private trixie-staging/main armhf freeglut3-dev armhf 3.4.0-1 [53.1 kB]
Get:144 http://172.17.4.1/private trixie-staging/main armhf gemmi-dev armhf 0.6.3+ds-1 [1046 kB]
Get:145 http://172.17.4.1/private trixie-staging/main armhf libblas3 armhf 3.11.0-2 [100.0 kB]
Get:146 http://172.17.4.1/private trixie-staging/main armhf libblas-dev armhf 3.11.0-2 [106 kB]
Get:147 http://172.17.4.1/private trixie-staging/main armhf libgfortran5 armhf 13.2.0-5+rpi1 [247 kB]
Get:148 http://172.17.4.1/private trixie-staging/main armhf liblapack3 armhf 3.11.0-2 [1624 kB]
Get:149 http://172.17.4.1/private trixie-staging/main armhf liblapack-dev armhf 3.11.0-2 [3007 kB]
Get:150 http://172.17.4.1/private trixie-staging/main armhf libopenmm8.0 armhf 8.0.0+dfsg-6 [834 kB]
Get:151 http://172.17.4.1/private trixie-staging/main armhf libopenmm-dev armhf 8.0.0+dfsg-6 [317 kB]
Get:152 http://172.17.4.1/private trixie-staging/main armhf libseqan2-dev all 2.4.0+dfsg-15 [1215 kB]
Get:153 http://172.17.4.1/private trixie-staging/main armhf libxfixes-dev armhf 1:6.0.0-2 [23.2 kB]
Get:154 http://172.17.4.1/private trixie-staging/main armhf libxi-dev armhf 2:1.8-1 [238 kB]
Get:155 http://172.17.4.1/private trixie-staging/main armhf libxmu6 armhf 2:1.1.3-3 [52.0 kB]
Get:156 http://172.17.4.1/private trixie-staging/main armhf libxmu-headers all 2:1.1.3-3 [68.5 kB]
Get:157 http://172.17.4.1/private trixie-staging/main armhf libxmu-dev armhf 2:1.1.3-3 [56.1 kB]
Get:158 http://172.17.4.1/private trixie-staging/main armhf libsimbody3.7 armhf 3.7+dfsg-3 [2610 kB]
Get:159 http://172.17.4.1/private trixie-staging/main armhf libsimbody-dev armhf 3.7+dfsg-3 [2727 kB]
Get:160 http://172.17.4.1/private trixie-staging/main armhf libsimtkmolmodel3.1 armhf 3.1.0-4 [583 kB]
Get:161 http://172.17.4.1/private trixie-staging/main armhf libsimtkmolmodel-dev armhf 3.1.0-4 [1863 kB]
Get:162 http://172.17.4.1/private trixie-staging/main armhf libsimtkmolmodel-plugins armhf 3.1.0-4 [16.1 kB]
Get:163 http://172.17.4.1/private trixie-staging/main armhf libstb0 armhf 0.0~git20230129.5736b15+ds-1 [175 kB]
Get:164 http://172.17.4.1/private trixie-staging/main armhf libstb-dev armhf 0.0~git20230129.5736b15+ds-1 [557 kB]
Get:165 http://172.17.4.1/private trixie-staging/main armhf tao-pegtl-dev all 3.2.7-1 [69.4 kB]
Get:166 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-3 [901 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up python3-minimal (3.11.4-5) ...
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Setting up libwayland-server0:armhf (1.22.0-2.1) ...
Setting up libxau6:armhf (1:1.0.9-1) ...
Setting up libpsl5:armhf (0.21.2-1+b1) ...
Setting up libicu72:armhf (72.1-4) ...
Setting up bsdextrautils (2.39.2-6) ...
Setting up libglvnd-core-dev:armhf (1.7.0-1) ...
Setting up libmagic-mgc (1:5.45-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglvnd0:armhf (1.7.0-1) ...
Setting up libpython3.11-stdlib:armhf (3.11.6-3) ...
Setting up libdebhelper-perl (13.11.8) ...
Setting up libbrotli1:armhf (1.1.0-2) ...
Setting up gemmi-dev (0.6.3+ds-1) ...
Setting up x11-common (1:7.7+23) ...
invoke-rc.d: could not determine current runlevel
invoke-rc.d: policy-rc.d denied execution of restart.
Setting up libsensors-config (1:3.6.0-8) ...
Setting up libnghttp2-14:armhf (1.58.0-1) ...
Setting up libmagic1:armhf (1:5.45-2) ...
Setting up gettext-base (0.21-13) ...
Setting up m4 (1.4.19-4) ...
Setting up file (1:5.45-2) ...
Setting up libpthread-stubs0-dev:armhf (0.4-1) ...
Setting up libopengl0:armhf (1.7.0-1) ...
Setting up libseqan2-dev (2.4.0+dfsg-15) ...
Setting up xtrans-dev (1.4.0-1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libz3-4:armhf (4.8.12-3.1) ...
Setting up libblas3:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libuv1:armhf (1.46.0-2+rpi1) ...
Setting up libgles2:armhf (1.7.0-1) ...
Setting up libx11-data (2:1.8.7-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libgles1:armhf (1.7.0-1) ...
Setting up libproc2-0:armhf (2:4.0.4-2) ...
Setting up libstb0:armhf (0.0~git20230129.5736b15+ds-1) ...
Setting up autopoint (0.21-13) ...
Setting up libjsoncpp25:armhf (1.9.5-6) ...
Setting up libsensors5:armhf (1:3.6.0-8) ...
Setting up libglapi-mesa:armhf (23.1.7-1+rpi1) ...
Setting up libgfortran5:armhf (13.2.0-5+rpi1) ...
Setting up autoconf (2.71-3) ...
Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-3) ...
Setting up libstb-dev:armhf (0.0~git20230129.5736b15+ds-1) ...
Setting up mount (2.39.2-6) ...
Setting up libxshmfence1:armhf (1.3-1) ...
Setting up librhash0:armhf (1.4.3-3) ...
Setting up xml-core (0.18+nmu1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up procps (2:4.0.4-2) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libssh2-1:armhf (1.11.0-2) ...
Setting up xorg-sgml-doctools (1:1.11-1.1) ...
Setting up cmake-data (3.27.8-1) ...
Setting up libglu1-mesa:armhf (9.0.2-1.1) ...
Setting up libopenmm8.0 (8.0.0+dfsg-6) ...
Setting up libopengl-dev:armhf (1.7.0-1) ...
Setting up libbsd0:armhf (0.11.7-4) ...
Setting up libdrm-common (2.4.117-1+rpi1) ...
Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
Setting up libblas-dev:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up tao-pegtl-dev (3.2.7-1) ...
Setting up util-linux-extra (2.39.2-6) ...
Setting up libpython3-stdlib:armhf (3.11.4-5) ...
Setting up libwayland-client0:armhf (1.22.0-2.1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up python3.11 (3.11.6-3) ...
Setting up libice6:armhf (2:1.0.10-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up liblapack3:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libxcb1:armhf (1.15-1) ...
Setting up gettext (0.21-13) ...
Setting up libxcb-xfixes0:armhf (1.15-1) ...
Setting up libtool (2.4.7-7) ...
Setting up libarchive13:armhf (3.7.2-1) ...
Setting up libxcb-glx0:armhf (1.15-1) ...
Setting up libedit2:armhf (3.1-20230828-1) ...
Setting up python3 (3.11.4-5) ...
Setting up libxcb-shm0:armhf (1.15-1) ...
Setting up libopenmm-dev (8.0.0+dfsg-6) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libxcb-present0:armhf (1.15-1) ...
Setting up dh-autoreconf (20) ...
Setting up asciidoc-common (10.2.0-2) ...
Setting up libxcb-sync1:armhf (1.15-1) ...
Setting up liblapack-dev:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libxcb-dri2-0:armhf (1.15-1) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up libdrm2:armhf (2.4.117-1+rpi1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.23.0-3) ...
Setting up libxcb-randr0:armhf (1.15-1) ...
Setting up libllvm15:armhf (1:15.0.7-10+rpi1) ...
Setting up libxslt1.1:armhf (1.1.35-1) ...
Setting up libcurl4:armhf (8.4.0-2+rpi1) ...
Setting up libx11-6:armhf (2:1.8.7-1) ...
Setting up libxml2-utils (2.9.14+dfsg-1.3) ...
Setting up libsm6:armhf (2:1.2.3-1) ...
Setting up libdrm-amdgpu1:armhf (2.4.117-1+rpi1) ...
Setting up libxcb-dri3-0:armhf (1.15-1) ...
Setting up libx11-xcb1:armhf (2:1.8.7-1) ...
Setting up libdrm-nouveau2:armhf (2.4.117-1+rpi1) ...
Setting up libgbm1:armhf (23.1.7-1+rpi1) ...
Setting up libdrm-radeon1:armhf (2.4.117-1+rpi1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libgl1-mesa-dri:armhf (23.1.7-1+rpi1) ...
Setting up xsltproc (1.1.35-1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up man-db (2.12.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxxf86vm1:armhf (1:1.1.4-1+b2) ...
Setting up libegl-mesa0:armhf (23.1.7-1+rpi1) ...
Setting up libxfixes3:armhf (1:6.0.0-2) ...
Setting up libxt6:armhf (1:1.2.1-1.1) ...
Setting up libegl1:armhf (1.7.0-1) ...
Setting up cmake (3.27.8-1) ...
Setting up libxmu6:armhf (2:1.1.3-3) ...
Setting up libglx-mesa0:armhf (23.1.7-1+rpi1) ...
Setting up libxi6:armhf (2:1.8-1) ...
Setting up libglx0:armhf (1.7.0-1) ...
Setting up debhelper (13.11.8) ...
Setting up libgl1:armhf (1.7.0-1) ...
Setting up libglut3.12:armhf (3.4.0-1) ...
Setting up libsimbody3.7:armhf (3.7+dfsg-3) ...
Setting up libsimtkmolmodel3.1:armhf (3.1.0-4) ...
Setting up libsimtkmolmodel-plugins (3.1.0-4) ...
Setting up libsimtkmolmodel-dev:armhf (3.1.0-4) ...
Processing triggers for libc-bin (2.37-12+rpi2) ...
Processing triggers for sgml-base (1.31) ...
Setting up sgml-data (2.0.11+nmu1) ...
Setting up x11proto-dev (2023.2-1) ...
Setting up libxau-dev:armhf (1:1.0.9-1) ...
Setting up libice-dev:armhf (2:1.0.10-1) ...
Setting up libsm-dev:armhf (2:1.2.3-1) ...
Setting up libxdmcp-dev:armhf (1:1.1.2-3) ...
Setting up docbook-xsl (1.79.2+dfsg-7) ...
Setting up libxcb1-dev:armhf (1.15-1) ...
Setting up libx11-dev:armhf (2:1.8.7-1) ...
Setting up libxfixes-dev:armhf (1:6.0.0-2) ...
Setting up asciidoc-base (10.2.0-2) ...
Setting up libxt-dev:armhf (1:1.2.1-1.1) ...
Setting up libxext-dev:armhf (2:1.3.4-1) ...
Setting up libglx-dev:armhf (1.7.0-1) ...
Setting up libxi-dev:armhf (2:1.8-1) ...
Setting up libgl-dev:armhf (1.7.0-1) ...
Setting up libxmu-headers (2:1.1.3-3) ...
Setting up libegl-dev:armhf (1.7.0-1) ...
Setting up libxmu-dev:armhf (2:1.1.3-3) ...
Setting up libglu1-mesa-dev:armhf (9.0.2-1.1) ...
Setting up libgles-dev:armhf (1.7.0-1) ...
Setting up libglvnd-dev:armhf (1.7.0-1) ...
Setting up libgl1-mesa-dev:armhf (23.1.7-1+rpi1) ...
Setting up libglut-dev:armhf (3.4.0-1) ...
Setting up freeglut3-dev:armhf (3.4.0-1) ...
Setting up libsimbody-dev:armhf (3.7+dfsg-3) ...
Processing triggers for sgml-base (1.31) ...
Setting up docbook-xml (4.5-12) ...
Processing triggers for sgml-base (1.31) ...
Setting up sbuild-build-depends-macromoleculebuilder-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc-12_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 libc6-dev_2.37-12+rpi2 libstdc++-12-dev_12.3.0-10+rpi1 libstdc++-13-dev_13.2.0-5+rpi1 libstdc++6_13.2.0-5+rpi1 linux-libc-dev_6.5.6-1+rpi1
Package versions: adduser_3.137 apt_2.7.6 asciidoc-base_10.2.0-2 asciidoc-common_10.2.0-2 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.2 bash_5.2.15-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.2-6 bsdutils_1:2.39.2-6 build-essential_12.10 bzip2_1.0.8-5+b2 cmake_3.27.8-1 cmake-data_3.27.8-1 coreutils_9.1-1 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-10+rpi1 cpp-13_13.2.0-5+rpi1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.8 debianutils_5.14 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 docbook-xml_4.5-12 docbook-xsl_1.79.2+dfsg-7 dpkg_1.22.1+rpi1 dpkg-dev_1.22.1+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.1-1 file_1:5.45-2 findutils_4.9.0-5 freeglut3-dev_3.4.0-1 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc_4:13.2.0-1+rpi1 gcc-12_12.3.0-10+rpi1 gcc-12-base_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 gcc-13-base_13.2.0-5+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gemmi-dev_0.6.3+ds-1 gettext_0.21-13 gettext-base_0.21-13 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-5 libacl1_2.3.1-3 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libarchive13_3.7.2-1 libasan8_13.2.0-5+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-5+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.41-6+rpi1 libblas-dev_3.11.0-2 libblas3_3.11.0-2 libblkid1_2.39.2-6 libbrotli1_1.1.0-2 libbsd0_0.11.7-4 libbz2-1.0_1.0.8-5+b2 libc-bin_2.37-12+rpi2 libc-dev-bin_2.37-12+rpi2 libc6_2.37-12+rpi2 libc6-dev_2.37-12+rpi2 libcap-ng0_0.8.3-1+b1 libcap2_1:2.66-4 libcap2-bin_1:2.66-4 libcc1-0_13.2.0-5+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libcurl4_8.4.0-2+rpi1 libdb5.3_5.3.28+dfsg2-2 libdebconfclient0_0.271 libdebhelper-perl_13.11.8 libdpkg-perl_1.22.1+rpi1 libdrm-amdgpu1_2.4.117-1+rpi1 libdrm-common_2.4.117-1+rpi1 libdrm-nouveau2_2.4.117-1+rpi1 libdrm-radeon1_2.4.117-1+rpi1 libdrm2_2.4.117-1+rpi1 libedit2_3.1-20230828-1 libegl-dev_1.7.0-1 libegl-mesa0_23.1.7-1+rpi1 libegl1_1.7.0-1 libelf1_0.188-2.1+rpi1 libexpat1_2.5.0-2 libext2fs2_1.47.0-2 libfakeroot_1.32.1-1 libffi8_3.4.4-1 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libgbm1_23.1.7-1+rpi1 libgcc-12-dev_12.3.0-10+rpi1 libgcc-13-dev_13.2.0-5+rpi1 libgcc-s1_13.2.0-5+rpi1 libgcrypt20_1.10.2-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_13.2.0-5+rpi1 libgl-dev_1.7.0-1 libgl1_1.7.0-1 libgl1-mesa-dev_23.1.7-1+rpi1 libgl1-mesa-dri_23.1.7-1+rpi1 libglapi-mesa_23.1.7-1+rpi1 libgles-dev_1.7.0-1 libgles1_1.7.0-1 libgles2_1.7.0-1 libglu1-mesa_9.0.2-1.1 libglu1-mesa-dev_9.0.2-1.1 libglut-dev_3.4.0-1 libglut3.12_3.4.0-1 libglvnd-core-dev_1.7.0-1 libglvnd-dev_1.7.0-1 libglvnd0_1.7.0-1 libglx-dev_1.7.0-1 libglx-mesa0_23.1.7-1+rpi1 libglx0_1.7.0-1 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.1-4 libgomp1_13.2.0-5+rpi1 libgpg-error0_1.47-2 libgssapi-krb5-2_1.20.1-5 libhogweed6_3.9.1-2 libice-dev_2:1.0.10-1 libice6_2:1.0.10-1 libicu72_72.1-4 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libjsoncpp25_1.9.5-6 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 libksba8_1.6.4-2 liblapack-dev_3.11.0-2 liblapack3_3.11.0-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 libllvm15_1:15.0.7-10+rpi1 liblz4-1_1.9.4-1+rpi1+b1 liblzma5_5.4.4-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.2-6 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20231016-1 libnettle8_3.9.1-2 libnghttp2-14_1.58.0-1 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| Build |
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Unpack source
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gpgv: Signature made Fri Jun 23 07:49:33 2023 UTC
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dpkg-buildpackage: info: source package macromoleculebuilder
dpkg-buildpackage: info: source version 4.0.0+dfsg-3
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cd obj-arm-linux-gnueabihf && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -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=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0" ..
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make[3]: Leaving directory '/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf'
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make[3]: Entering directory '/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf'
[ 3%] Building CXX object CMakeFiles/MMB.dir/src/Utils.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/Utils.cpp.o -MF CMakeFiles/MMB.dir/src/Utils.cpp.o.d -o CMakeFiles/MMB.dir/src/Utils.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Utils.cpp
[ 12%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o
[ 12%] Building CXX object CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o -MF CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o.d -o CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp
[ 12%] Building CXX object CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o -MF CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o.d -o CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/UnitCellParameters.cpp
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o -MF CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/Simbody.h:38,
from /usr/include/molmodel/SimTKmolmodel.h:47,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/UnitCellParameters.h:3,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/UnitCellParameters.cpp:4:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/SimTKsimbody.h:43,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:12:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/SimTKsimbody.h:43,
from /usr/include/molmodel/molmodel/internal/Compound.h:36,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:16,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:14:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/SimTKsimbody.h:43,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Utils.cpp:12:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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 /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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 /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'double AtomSpringContainer::calcRmsd(SimTK::State&, BiopolymerClassContainer&)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:65:12: warning: unused variable 'myExtension' [-Wunused-variable]
65 | double myExtension = 0.0;
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::deleteAtomSpring(int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
194 | if(id < 0 || id >= atomSpringVector.size()){
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateAtomSpring(int, const AtomSpring&, BiopolymerClassContainer&)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
201 | if(id < 0 || id >= atomSpringVector.size()){
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::deleteThreading(int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
260 | if(id < 0 || id >= threadingStructVector.size()){
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateThreading(int, const ThreadingStruct&, BiopolymerClassContainer&)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
268 | if(id < 0 || id >= threadingStructVector.size()){
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/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&)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
279 | if(id < 0 || id >= threadingStructVector.size()){
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::deleteGappedThreading(int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
441 | if(id < 0 || id >= gappedThreadingStructVector.size()){
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateGappedThreading(int, const ThreadingStruct&, BiopolymerClassContainer&)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
449 | if(id < 0 || id >= gappedThreadingStructVector.size()){
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::updateGappedThreading(int, SimTK::String, SimTK::String, double, bool, BiopolymerClassContainer&)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
458 | if(id < 0 || id >= gappedThreadingStructVector.size()){
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp: In member function 'void AtomSpringContainer::createSpringsFromGappedThreading(BiopolymerClassContainer&)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
488 | while ((aIndex < length(thread.updThreadingPartner(0).sequence)) &&
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
489 | (bIndex < length(thread.updThreadingPartner(1).sequence)))
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
| ~~^~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsPurine(char)':
/<<BUILDDIR>>/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';
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsRNA(char)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:57:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
57 | c == 'A' |
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:59:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
59 | c == 'G' |
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:60:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
60 | c == 'U'
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsDNA(char)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:67:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
67 | c == 'A' |
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:69:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
69 | c == 'G' |
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:70:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
70 | c == 'T'
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In function 'bool letterIsProtein(char)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:77:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
77 | c == 'C' |
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:79:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
79 | c == 'H' |
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:80:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
80 | c == 'I'
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:86:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
86 | c == 'M' |
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:88:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
88 | c == 'V' |
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:89:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
89 | c == 'A'
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:95:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
95 | c == 'G' |
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:97:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
97 | c == 'P' |
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:98:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
98 | c == 'T'
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:104:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
104 | c == 'R' |
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:106:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
106 | c == 'Y' |
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:107:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
107 | c == 'W'
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:113:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
113 | c == 'D' |
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:115:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
115 | c == 'E' |
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:116:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
116 | c == 'Q' |
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:117:11: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
117 | c == 'K'
| ~~^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::modifyResidue(BiopolymerModification, SimTK::Compound, SimTK::DuMMForceFieldSubsystem&)':
/<<BUILDDIR>>/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)));
| ^~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:135:29: warning: unused variable 'myOrdinality' [-Wunused-variable]
135 | Ordinality::Residue myOrdinality(SimTK::Ordinality::Any);
| ^~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:147:32: warning: unused variable 'myBondMobility' [-Wunused-variable]
147 | BondMobility::Mobility myBondMobility = stringToBondMobility("Rigid");
| ^~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'int BiopolymerClass::checkResidueNumbersAndInsertionCodes()':
/<<BUILDDIR>>/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();
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::setPdbResidueNumbersFromResidueIDVector()':
/<<BUILDDIR>>/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() ;
| ^~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:520:9: warning: unused variable 'numResidues' [-Wunused-variable]
520 | int numResidues = -1;
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClass::renumberPdbResidues(ResidueID)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:551:9: warning: unused variable 'myNewResidueNumberWithoutInsertionCode' [-Wunused-variable]
551 | int myNewResidueNumberWithoutInsertionCode = firstResidueID.getResidueNumber() ;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/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)':
/<<BUILDDIR>>/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();
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'bool BiopolymerClass::hasAtom(ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1053:9: warning: unused variable 'myResidueIndex' [-Wunused-variable]
1053 | int myResidueIndex = getResidueIndex(myResidueID);
| ^~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'SimTK::Vec3 BiopolymerClass::calcDefaultAtomLocationInGroundFrame(const ResidueID&, const SimTK::String&) const':
/<<BUILDDIR>>/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);
| ^~~~~~~~~~~
/<<BUILDDIR>>/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)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1437:12: warning: unused variable 'huntCrossleyDissipation' [-Wunused-variable]
1437 | double huntCrossleyDissipation =.0;
| ^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'ResidueID BiopolymerClass::sum(ResidueID, int) const':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
2172 | if ((newResidueIndex < 0) || (newResidueIndex >= residueIDVector.size())) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClassContainer::waterDropletAboutResidues(std::vector<WaterDropletAboutResidueStruct>, WaterDropletContainer&)':
/<<BUILDDIR>>/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
| ^~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClassContainer::substituteResidue(SimTK::String, ResidueID, SimTK::String, bool)':
/<<BUILDDIR>>/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();
| ^~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp: In member function 'void BiopolymerClassContainer::substituteResidue(Mutation, bool, bool, bool)':
/<<BUILDDIR>>/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();
| ^~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:16:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4682:61: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
283 | for (int i = 0; i < chainAtomInfoVector.size() ; i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
300 | for ( int j = 0 ; j < neighborList.size(); j++) {
| ~~^~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = MobilizerStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:2584:54: required from 'void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch&, ResidueStretchContainer<ResidueStretchType>&) [with ResidueStretchType = MobilizerStretch]'
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:2588:181: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
61 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
256 | const char* spaces = " \t";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'bool ResidueStretchContainer<ResidueStretchType>::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:320:27: required from 'void ResidueStretchContainer<ResidueStretchType>::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]'
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4682:61: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
104 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 15%] Building CXX object CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o -MF CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DisplacementContainer.cpp
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4827:54: required from 'void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer&, ResidueStretchContainer<ResidueStretchType>&) [with ResidueStretchType = DensityStretch]'
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4830:213: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
61 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/SimTKsimbody.h:43,
from /usr/include/molmodel/molmodel/internal/Compound.h:36,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:16,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DisplacementContainer.h:14,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DisplacementContainer.cpp:12:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93,
from /usr/include/simbody/SimTKcommon/Simmatrix.h:37:
In member function 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]',
inlined from 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
inlined from 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Mat<3, 3> [1]' [-Warray-bounds=]
784 | { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
| ~~~~~~~~~~~~^~~~
In file included from /usr/include/molmodel/molmodel/internal/Compound.h:41,
from /usr/include/molmodel/SimTKmolmodel.h:53,
from /<<BUILDDIR>>/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:201:24:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
784 | { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
| ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)':
/usr/include/molmodel/molmodel/internal/Superpose.h:201:33: note: object '<anonymous>' of size 72
201 | rotation = Rotation();
| ^
In member function 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]',
inlined from 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
inlined from 'SimTK::Rotation_<P>::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
inlined from 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:201:24:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
784 | { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
| ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)':
/usr/include/molmodel/molmodel/internal/Superpose.h:201:33: note: object '<anonymous>' of size 72
201 | rotation = Rotation();
| ^
In member function 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]',
inlined from 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
inlined from 'SimTK::Rotation_<P>::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
inlined from 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)' at /usr/include/molmodel/molmodel/internal/Superpose.h:201:24:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript 'SimTK::Vec<3, double, 4>[0]' is partly outside array bounds of 'SimTK::Rotation [1]' {aka 'SimTK::Rotation_<double> [1]'} [-Warray-bounds=]
784 | { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
| ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function 'static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)':
/usr/include/molmodel/molmodel/internal/Superpose.h:201:33: note: object '<anonymous>' of size 72
201 | rotation = Rotation();
| ^
In file included from /usr/include/c++/13/vector:72,
from /usr/include/simbody/SimTKcommon/internal/Array.h:39,
from /usr/include/simbody/SimTKcommon/basics.h:53,
from /usr/include/simbody/SimTKcommon.h:32:
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AtomSpring&}; _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<AtomSpring>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]',
inlined from 'void AtomSpringContainer::addAtomSpring(const AtomSpring&, BiopolymerClassContainer&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:190:31:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomSpring*, std::vector<AtomSpring> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/13/memory:69,
from /usr/include/simbody/SimTKcommon/internal/ClonePtr.h:29,
from /usr/include/simbody/SimTKcommon/basics.h:44:
/usr/include/c++/13/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]':
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]' at /usr/include/c++/13/bits/stl_vector.h:1619:35,
inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]' at /usr/include/c++/13/bits/vector.tcc:238:44:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]' at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from 'BiopolymerClass::BiopolymerClass(const BiopolymerClass&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:147:5:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]' at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from 'BiopolymerClass::BiopolymerClass(const BiopolymerClass&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:147:5:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/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 member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]',
inlined from 'void AtomSpringContainer::add(AtomSpring&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:41:102,
inlined from 'void AtomSpringContainer::createSpringsFromThreading(BiopolymerClassContainer&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:315:29:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomSpring*, std::vector<AtomSpring> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]',
inlined from 'void AtomSpringContainer::add(AtomSpring&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:41:102,
inlined from 'void AtomSpringContainer::createSpringsFromThreading(BiopolymerClassContainer&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:316:29:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomSpring*, std::vector<AtomSpring> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]',
inlined from 'void AtomSpringContainer::add(AtomSpring&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:41:102,
inlined from 'void AtomSpringContainer::createSpringsFromThreading(BiopolymerClassContainer&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:317:29:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomSpring*, std::vector<AtomSpring> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]',
inlined from 'void AtomSpringContainer::add(AtomSpring&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:41:102,
inlined from 'void AtomSpringContainer::createSpringsFromThreading(BiopolymerClassContainer&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:370:38:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomSpring*, std::vector<AtomSpring> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from /usr/include/simbody/SimTKcommon/internal/Array.h:39,
from /usr/include/simbody/SimTKcommon/basics.h:53,
from /usr/include/simbody/SimTKcommon.h:32:
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Interface&}; _Tp = Interface; _Alloc = std::allocator<Interface>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<Interface>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Interface; _Alloc = std::allocator<Interface>]',
inlined from 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, std::vector<SimTK::String>, double, SimTK::String)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Utils.cpp:759:30:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interface*, std::vector<Interface> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const TwoAtomClass&}; _Tp = TwoAtomClass; _Alloc = std::allocator<TwoAtomClass>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<TwoAtomClass>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = TwoAtomClass; _Alloc = std::allocator<TwoAtomClass>]',
inlined from 'std::vector<TwoAtomClass> InterfaceContainer::retrieveCloseContactPairs(std::vector<MMBAtomInfo>&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Utils.cpp:805:59:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TwoAtomClass*, std::vector<TwoAtomClass> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/13/set:62,
from /usr/include/simbody/simmath/internal/Contact.h:30,
from /usr/include/simbody/SimTKmath.h:46,
from /usr/include/simbody/SimTKsimbody.h:44:
/usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const SimTK::String&&>, std::tuple<>}; _Key = const SimTK::String; _Val = std::pair<const SimTK::String, double>; _KeyOfValue = std::_Select1st<std::pair<const SimTK::String, double> >; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]':
/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator' changed in GCC 7.1
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/map:63,
from /usr/include/simbody/simmath/internal/CollisionDetectionAlgorithm.h:32,
from /usr/include/simbody/SimTKmath.h:48:
/usr/include/c++/13/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const SimTK::String; _Tp = double; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]':
/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator' changed in GCC 7.1
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const SimTK::String; _Tp = double; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]',
inlined from 'myAtoI(std::map<const SimTK::String, double>, const char*)::<lambda()>' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Utils.cpp:1016:21,
inlined from 'constexpr _Res std::__invoke_impl(__invoke_other, _Fn&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Fn = myAtoI(std::map<const SimTK::String, double>, const char*)::<lambda()>&; _Args = {}]' at /usr/include/c++/13/bits/invoke.h:61:67,
inlined from 'constexpr std::enable_if_t<is_invocable_r_v<_Res, _Callable, _Args ...>, _Res> std::__invoke_r(_Callable&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Callable = myAtoI(std::map<const SimTK::String, double>, const char*)::<lambda()>&; _Args = {}]' at /usr/include/c++/13/bits/invoke.h:116:38,
inlined from 'static _Res std::_Function_handler<_Res(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Res = std::__cxx11::basic_ostringstream<char>; _Functor = myAtoI(std::map<const SimTK::String, double>, const char*)::<lambda()>; _ArgTypes = {}]' at /usr/include/c++/13/bits/std_function.h:291:44:
/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator' changed in GCC 7.1
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = ThreadingStruct; _Alloc = std::allocator<ThreadingStruct>]':
/usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector<ThreadingStruct>::iterator' changed in GCC 7.1
181 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = ThreadingStruct; _Alloc = std::allocator<ThreadingStruct>]',
inlined from 'void AtomSpringContainer::deleteGappedThreading(int)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:444:38:
/usr/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ThreadingStruct*, std::vector<ThreadingStruct> >' changed in GCC 7.1
1532 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = ThreadingStruct; _Alloc = std::allocator<ThreadingStruct>]',
inlined from 'void AtomSpringContainer::deleteThreading(int)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:263:32:
/usr/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ThreadingStruct*, std::vector<ThreadingStruct> >' changed in GCC 7.1
1532 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ThreadingStruct&}; _Tp = ThreadingStruct; _Alloc = std::allocator<ThreadingStruct>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<ThreadingStruct>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ThreadingStruct; _Alloc = std::allocator<ThreadingStruct>]',
inlined from 'void AtomSpringContainer::addGappedThreading(const ThreadingStruct&, BiopolymerClassContainer&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:426:42:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ThreadingStruct*, std::vector<ThreadingStruct> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ThreadingStruct; _Alloc = std::allocator<ThreadingStruct>]',
inlined from 'void AtomSpringContainer::addThreading(const ThreadingStruct&, BiopolymerClassContainer&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:248:36:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ThreadingStruct*, std::vector<ThreadingStruct> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 18%] Building CXX object CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o -MF CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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 member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]',
inlined from 'void AtomSpringContainer::add(AtomSpring&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:41:102,
inlined from 'void AtomSpringContainer::createSpringsFromGappedThreading(BiopolymerClassContainer&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/AtomSpringContainer.cpp:535:38:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomSpring*, std::vector<AtomSpring> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/SimTKsimbody.h:43,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
[ 21%] Building CXX object CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o -MF CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/MoleculeContainer.cpp
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/Simbody.h:38,
from /usr/include/molmodel/SimTKmolmodel.h:47,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/MoleculeContainer.h:6,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/MoleculeContainer.cpp:3:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
256 | const char* spaces = " \t";
| ^~~~~~
[ 25%] Building CXX object CMakeFiles/MMB.dir/src/DensityContainer.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DensityContainer.cpp.o -MF CMakeFiles/MMB.dir/src/DensityContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityContainer.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityContainer.cpp
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/SimTKsimbody.h:43,
from /usr/include/molmodel/molmodel/internal/Compound.h:36,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:16,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:4,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:14,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityContainer.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
| ~~^~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp:12:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp: In member function 'void MobilizerContainer::addMobilizerDomainsInterfacesToVector(const std::vector<MobilizerDomainsInterface>&, BiopolymerClassContainer&)':
/<<BUILDDIR>>/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)) ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
In file included from /usr/include/c++/13/memory:69,
from /usr/include/simbody/SimTKcommon/internal/ClonePtr.h:29,
from /usr/include/simbody/SimTKcommon/basics.h:44,
from /usr/include/simbody/SimTKcommon.h:32:
/usr/include/c++/13/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator<MMBAtomInfo*>; _ForwardIterator = MMBAtomInfo*]':
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type 'std::move_iterator<MMBAtomInfo*>' changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type 'std::move_iterator<MMBAtomInfo*>' changed in GCC 7.1
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ConstraintContainer.h:14,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/MoleculeContainer.h:8:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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); };
| ~~^~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/MoleculeContainer.cpp: In constructor 'CustomMolecule::CustomMolecule(std::vector<std::vector<SimTK::String> >, SimTK::DuMMForceFieldSubsystem&)':
/<<BUILDDIR>>/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
| ^~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/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 /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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); };
| ~~^~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityContainer.cpp: In member function 'void DensityContainer::updateDensityStretch(int, const DensityStretch&, BiopolymerClassContainer&)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
18 | if(id < 0 || id >= residueStretchVector.size()){
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
61 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
144 | if(id >= 0 && id < residueStretchVector.size())
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/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/c++/13/vector:72,
from /usr/include/simbody/SimTKcommon/internal/Array.h:39,
from /usr/include/simbody/SimTKcommon/basics.h:53,
from /usr/include/simbody/SimTKcommon.h:32:
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const MobilizerWithin&}; _Tp = MobilizerWithin; _Alloc = std::allocator<MobilizerWithin>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<MobilizerWithin>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MobilizerWithin; _Alloc = std::allocator<MobilizerWithin>]',
inlined from 'void MobilizerContainer::pushMobilizerWithin(MobilizerWithin, BiopolymerClassContainer&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp:287:36:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MobilizerWithin*, std::vector<MobilizerWithin> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MobilizerWithin; _Alloc = std::allocator<MobilizerWithin>]',
inlined from 'void MobilizerContainer::createMobilizersWithin(BiopolymerClassContainer&, SimTK::State&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp:268:79:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MobilizerWithin*, std::vector<MobilizerWithin> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/13/memory:69,
from /usr/include/simbody/SimTKcommon/internal/ClonePtr.h:29,
from /usr/include/simbody/SimTKcommon/basics.h:44:
/usr/include/c++/13/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]':
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]' at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from 'BiopolymerClass::BiopolymerClass(const BiopolymerClass&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:147:5,
inlined from 'void MobilizerContainer::addPhiPsiMobility(SimTK::String, BiopolymerClassContainer&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp:345:91:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]' at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from 'BiopolymerClass::BiopolymerClass(const BiopolymerClass&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:147:5,
inlined from 'void MobilizerContainer::addPhiPsiMobility(SimTK::String, BiopolymerClassContainer&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/MobilizerContainer.cpp:345:91:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 28%] Building CXX object CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o -MF CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BasePairContainer.cpp
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/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/c++/13/vector:72,
from /usr/include/simbody/SimTKcommon/internal/Array.h:39,
from /usr/include/simbody/SimTKcommon/basics.h:53:
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AllResiduesWithin&}; _Tp = AllResiduesWithin; _Alloc = std::allocator<AllResiduesWithin>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<AllResiduesWithin>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/Simbody.h:38,
from /usr/include/molmodel/SimTKmolmodel.h:47,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BasePairContainer.h:16,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BasePairContainer.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
[ 31%] Building CXX object CMakeFiles/MMB.dir/src/ContactContainer.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ContactContainer.cpp.o -MF CMakeFiles/MMB.dir/src/ContactContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/ContactContainer.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp
In file included from /usr/include/c++/13/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AllResiduesWithin; _Alloc = std::allocator<AllResiduesWithin>]',
inlined from 'void BiopolymerClass::physicsZone(std::vector<AllResiduesWithin>&, double, SimTK::SimbodyMatterSubsystem&, SimTK::State&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1735:59:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AllResiduesWithin*, std::vector<AllResiduesWithin> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/SimTKsimbody.h:43,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
[ 34%] Building CXX object CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o -MF CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BasePairContainer.h:17:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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); };
| ~~^~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93,
from /usr/include/simbody/SimTKcommon/Simmatrix.h:37:
In member function 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]',
inlined from 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
inlined from 'SimTK::Rotation_<P>::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
inlined from 'int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)' at /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/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&)':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/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&)':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/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&)':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/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&)':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/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&)':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/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&)':
/<<BUILDDIR>>/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/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/SimTKsimbody.h:43,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ConstraintContainer.h:14,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp:10:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
/usr/include/c++/13/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]':
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {MMBAtomInfo}; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<MMBAtomInfo>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {MMBAtomInfo}; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]',
inlined from 'void BiopolymerClass::initializeAtomInfoVector(SimTK::SimbodyMatterSubsystem&, const std::vector<AtomicPropertyOverrideStruct>&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1163:40:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {MMBAtomInfo}; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]',
inlined from 'void BiopolymerClass::initializeAtomInfoVector(SimTK::SimbodyMatterSubsystem&, SimTK::DuMMForceFieldSubsystem&, const std::vector<AtomicPropertyOverrideStruct>&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:1189:40:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const MMBAtomInfo&}; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<MMBAtomInfo>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/usr/include/c++/13/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]':
/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type 'std::vector<MMBAtomInfo>::iterator' changed in GCC 7.1
751 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<MMBAtomInfo*>; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator<MMBAtomInfo*>; _ForwardIterator = MMBAtomInfo*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = move_iterator<MMBAtomInfo*>; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from '_ForwardIterator std::__uninitialized_move_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = MMBAtomInfo*; _ForwardIterator = MMBAtomInfo*; _Allocator = allocator<MMBAtomInfo>]' at /usr/include/c++/13/bits/stl_uninitialized.h:384:41,
inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]' at /usr/include/c++/13/bits/vector.tcc:766:34:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type 'std::move_iterator<MMBAtomInfo*>' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]' at /usr/include/c++/13/bits/vector.tcc:781:34:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<MMBAtomInfo*>; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator<MMBAtomInfo*>; _ForwardIterator = MMBAtomInfo*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = move_iterator<MMBAtomInfo*>; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from '_ForwardIterator std::__uninitialized_move_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = MMBAtomInfo*; _ForwardIterator = MMBAtomInfo*; _Allocator = allocator<MMBAtomInfo>]' at /usr/include/c++/13/bits/stl_uninitialized.h:384:41,
inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]' at /usr/include/c++/13/bits/vector.tcc:786:34:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type 'std::move_iterator<MMBAtomInfo*>' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]' at /usr/include/c++/13/bits/vector.tcc:814:38:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >; <template-parameter-2-2> = void; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]',
inlined from 'std::vector<MMBAtomInfo> BiopolymerClassContainer::getConcatenatedAtomInfoVector(const SimTK::State&, bool)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4286:28:
/usr/include/c++/13/bits/stl_vector.h:1483:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
1483 | _M_range_insert(begin() + __offset, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1484 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_vector.h:1483:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >; <template-parameter-2-2> = void; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]',
inlined from 'std::vector<MMBAtomInfo> BiopolymerClassContainer::getConcatenatedAtomInfoVector(bool)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4262:28:
/usr/include/c++/13/bits/stl_vector.h:1483:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
1483 | _M_range_insert(begin() + __offset, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1484 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_vector.h:1483:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]',
inlined from 'void BiopolymerClassContainer::loadCysteineAtomInfoVector(std::vector<MMBAtomInfo>&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClass.cpp:4794:49:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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 /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:12:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::validateContact(ContactStretch, BiopolymerClassContainer&)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:26:10: warning: variable 'myEndCapsOn' set but not used [-Wunused-but-set-variable]
26 | bool myEndCapsOn;
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::deleteContactWithin(int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
70 | if(id < 0 || id >= contactWithinVector.size()){
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::updateContactWithin(int, SimTK::String, int, double, SimTK::String, BiopolymerClassContainer&)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
77 | if(id < 0 || id >= contactWithinVector.size()){
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::deleteContact(int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
275 | if(id < 0 || id >= residueStretchVector.size()){
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'void ContactContainer::updateContact(int, std::string, int, int, std::string, BiopolymerClassContainer&)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
283 | if(id < 0 || id >= residueStretchVector.size()){
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp: In member function 'bool ContactContainer::hasSharedContact(SimTK::String, ResidueID, ResidueID, SimTK::String)':
/<<BUILDDIR>>/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).
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
256 | const char* spaces = " \t";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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); };
| ~~^~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/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 /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp:11:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from /usr/include/simbody/SimTKcommon/internal/Array.h:39,
from /usr/include/simbody/SimTKcommon/basics.h:53,
from /usr/include/simbody/SimTKcommon.h:32:
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BaseInteraction&}; _Tp = BaseInteraction; _Alloc = std::allocator<BaseInteraction>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<BaseInteraction>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BaseInteraction; _Alloc = std::allocator<BaseInteraction>]',
inlined from 'void BasePairContainer::addBasePair(BiopolymerClassContainer&, const LeontisWesthofClass&, BaseInteraction, bool)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BasePairContainer.cpp:25:31:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BaseInteraction*, std::vector<BaseInteraction> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp: In member function 'void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
129 | if(index < 0 || index >= constraintClassVector.size())
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/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&)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
146 | if(index < 0 || index >= constraintClassVector.size())
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(iterator, _Arg&&) [with _Arg = BaseInteraction; _Tp = BaseInteraction; _Alloc = std::allocator<BaseInteraction>]':
/usr/include/c++/13/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<BaseInteraction>::iterator' changed in GCC 7.1
413 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = BaseInteraction; _Alloc = std::allocator<BaseInteraction>]':
/usr/include/c++/13/bits/vector.tcc:133:5: note: parameter passing for argument of type 'std::vector<BaseInteraction>::const_iterator' changed in GCC 7.1
133 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc:162:28: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<BaseInteraction*, std::vector<BaseInteraction> >' changed in GCC 7.1
162 | _M_insert_aux(__pos, std::move(__x_copy._M_val()));
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc:170:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BaseInteraction*, std::vector<BaseInteraction> >' changed in GCC 7.1
170 | _M_realloc_insert(begin() + (__position - cbegin()), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = BaseInteraction; _Alloc = std::allocator<BaseInteraction>]',
inlined from 'void BasePairContainer::updateBasePair(int, SimTK::String, int, SimTK::String, SimTK::String, int, SimTK::String, SimTK::String, BiopolymerClassContainer&, const LeontisWesthofClass&, bool)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BasePairContainer.cpp:63:32:
/usr/include/c++/13/bits/vector.tcc:162:28: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<BaseInteraction*, std::vector<BaseInteraction> >' changed in GCC 7.1
162 | _M_insert_aux(__pos, std::move(__x_copy._M_val()));
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc:170:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BaseInteraction*, std::vector<BaseInteraction> >' changed in GCC 7.1
170 | _M_realloc_insert(begin() + (__position - cbegin()), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/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)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BasePairContainer.cpp:69:32: note: parameter passing for argument of type 'std::vector<BaseInteraction>::const_iterator' changed in GCC 7.1
69 | myBasePairVector.insert(it, original);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/13/memory:69,
from /usr/include/simbody/SimTKcommon/internal/ClonePtr.h:29,
from /usr/include/simbody/SimTKcommon/basics.h:44:
/usr/include/c++/13/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]':
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]' at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from 'BiopolymerClass::BiopolymerClass(const BiopolymerClass&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:147:5:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]' at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from 'BiopolymerClass::BiopolymerClass(const BiopolymerClass&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:147:5:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 37%] Building CXX object CMakeFiles/MMB.dir/src/Repel.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/Repel.cpp.o -MF CMakeFiles/MMB.dir/src/Repel.cpp.o.d -o CMakeFiles/MMB.dir/src/Repel.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp
In file included from /usr/include/c++/13/vector:72,
from /usr/include/simbody/SimTKcommon/internal/Array.h:39,
from /usr/include/simbody/SimTKcommon/basics.h:53,
from /usr/include/simbody/SimTKcommon.h:32:
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ContactWithin&}; _Tp = ContactWithin; _Alloc = std::allocator<ContactWithin>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<ContactWithin>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ContactWithin; _Alloc = std::allocator<ContactWithin>]',
inlined from 'void ContactContainer::pushContactWithin(ContactWithin, BiopolymerClassContainer&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:66:34:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ContactWithin*, std::vector<ContactWithin> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 40%] Building CXX object CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o -MF CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o.d -o CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/MonoAtoms.cpp
In file included from /usr/include/c++/13/memory:69,
from /usr/include/simbody/SimTKcommon/internal/ClonePtr.h:29,
from /usr/include/simbody/SimTKcommon/basics.h:44:
/usr/include/c++/13/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]':
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]' at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from 'BiopolymerClass::BiopolymerClass(const BiopolymerClass&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:147:5:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]' at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from 'BiopolymerClass::BiopolymerClass(const BiopolymerClass&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:147:5:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, vector<LeontisWesthofBondRow> >; _ForwardIterator = LeontisWesthofBondRow*]':
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, std::vector<LeontisWesthofBondRow> >' changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, std::vector<LeontisWesthofBondRow> >' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, std::vector<LeontisWesthofBondRow> >; _ForwardIterator = LeontisWesthofBondRow*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, vector<LeontisWesthofBondRow> >; _ForwardIterator = LeontisWesthofBondRow*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, vector<LeontisWesthofBondRow> >; _ForwardIterator = LeontisWesthofBondRow*; _Tp = LeontisWesthofBondRow]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = LeontisWesthofBondRow; _Alloc = std::allocator<LeontisWesthofBondRow>]' at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from 'LeontisWesthofBondMatrix::LeontisWesthofBondMatrix(const LeontisWesthofBondMatrix&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BaseInteractionParameterReader.h:72:8,
inlined from 'LeontisWesthofClass::LeontisWesthofClass(const LeontisWesthofClass&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BaseInteractionParameterReader.h:75:7,
inlined from 'void ContactContainer::applyContactsToBiopolymers(BiopolymerClassContainer&, SimTK::GeneralContactSubsystem&, SimTK::GeneralForceSubsystem&, SimTK::SimbodyMatterSubsystem&, LeontisWesthofClass&, double, double)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ContactContainer.cpp:246:99:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, std::vector<LeontisWesthofBondRow> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/Simbody.h:38,
from /usr/include/molmodel/SimTKmolmodel.h:47,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:23,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:12:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/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/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/SimTKsimbody.h:43,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/MonoAtoms.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
[ 43%] Building CXX object CMakeFiles/MMB.dir/src/Spiral.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/Spiral.cpp.o -MF CMakeFiles/MMB.dir/src/Spiral.cpp.o.d -o CMakeFiles/MMB.dir/src/Spiral.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp
In file included from /usr/include/c++/13/vector:72,
from /usr/include/simbody/SimTKcommon/internal/Array.h:39,
from /usr/include/simbody/SimTKcommon/basics.h:53,
from /usr/include/simbody/SimTKcommon.h:32:
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ConstraintClass&}; _Tp = ConstraintClass; _Alloc = std::allocator<ConstraintClass>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<ConstraintClass>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ConstraintClass; _Alloc = std::allocator<ConstraintClass>]',
inlined from 'void ConstraintToGroundContainer::addConstraintClassToVector(ConstraintClass)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ConstraintContainer.cpp:75:37:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ConstraintClass*, std::vector<ConstraintClass> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/Simbody.h:38,
from /usr/include/molmodel/SimTKmolmodel.h:47,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Spiral.h:14,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
[ 46%] Building CXX object CMakeFiles/MMB.dir/src/ParameterReader.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ParameterReader.cpp.o -MF CMakeFiles/MMB.dir/src/ParameterReader.cpp.o.d -o CMakeFiles/MMB.dir/src/ParameterReader.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/SimTKsimbody.h:43,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:17:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/PeriodicScrubber.h:16,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:24:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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); };
| ~~^~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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 /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::constraintsAndRestraints(ParameterReader&, BiopolymerClassContainer&, SimTK::GeneralForceSubsystem&, SimTK::SimbodyMatterSubsystem&, SimTK::State&, SimTK::CompoundSystem&)':
/<<BUILDDIR>>/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();
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Repel.h: In constructor 'ConstrainedDynamics::ConstrainedDynamics(ParameterReader*)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:269:29: warning: 'ConstrainedDynamics::_parameterReader' will be initialized after [-Wreorder]
269 | ParameterReader * _parameterReader;
| ^~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:259:29: warning: 'SimTK::SimbodyMatterSubsystem ConstrainedDynamics::_matter' [-Wreorder]
259 | SimbodyMatterSubsystem _matter;
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:342:1: warning: when initialized here [-Wreorder]
342 | ConstrainedDynamics::ConstrainedDynamics(ParameterReader * myParameterReader) : _parameterReader(myParameterReader),
| ^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::initializeBiopolymer(SimTK::String, SimTK::String)':
/<<BUILDDIR>>/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;
| ^~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp: In member function 'void ConstrainedDynamics::runAllSteps()':
/<<BUILDDIR>>/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++){
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Spiral.h:16:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
61 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
144 | if(id >= 0 && id < residueStretchVector.size())
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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); };
| ~~^~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp: In member function 'void Spiral::clear()':
/<<BUILDDIR>>/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.
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp: In member function 'double Spiral::harmonicThetaAdjustment(double)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
124 | for (int i =0; i < frequencyPhaseAmplitudeVector.size(); i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp: In member function 'void Spiral::writeCylindricalSpiralCommandFile(MonoAtomsContainer&)':
/<<BUILDDIR>>/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 ;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp: In member function 'void Spiral::writeSphericalSpiralCommandFile(MonoAtomsContainer&)':
/<<BUILDDIR>>/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);
| ^~~~~~~~~~
/<<BUILDDIR>>/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
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
/<<BUILDDIR>>/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]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:210:4: required from 'void ResidueStretchContainer<ResidueStretchType>::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]'
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:470:84: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
232 | for (int i = 0; i < concatenatedAtomInfoVector.size() ; i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
244 | for ( int j = 0 ; j < neighborList.size(); j++) {
| ~~^~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/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]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:210:4: required from 'void ResidueStretchContainer<ResidueStretchType>::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]'
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:573:84: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
232 | for (int i = 0; i < concatenatedAtomInfoVector.size() ; i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
244 | for ( int j = 0 ; j < neighborList.size(); j++) {
| ~~^~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'bool ResidueStretchContainer<ResidueStretchType>::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = MobilizerStretch]':
/<<BUILDDIR>>/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]'
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:210:4: required from 'void ResidueStretchContainer<ResidueStretchType>::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]'
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:470:84: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
104 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'bool ResidueStretchContainer<ResidueStretchType>::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]':
/<<BUILDDIR>>/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]'
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h:210:4: required from 'void ResidueStretchContainer<ResidueStretchType>::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]'
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:573:84: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
256 | const char* spaces = " \t";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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 /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::removeNonPriorityBasePairs(int)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:727:9: warning: unused variable 'oldDutyCyclePriority' [-Wunused-variable]
727 | int oldDutyCyclePriority=0;
| ^~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::updateAllResiduesWithin(int, SimTK::String, int, double)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
776 | if(index < 0 || index >= includeAllResiduesWithinVector.size()){
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::deleteAllResiduesWithin(int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
785 | if(index < 0 || index >= includeAllResiduesWithinVector.size()){
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp: At global scope:
/<<BUILDDIR>>/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 ) {
| ^~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
256 | const char* spaces = " \t";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/<<BUILDDIR>>/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.
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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))
| ^
/<<BUILDDIR>>/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');
| ^~~~~~~~~~
/<<BUILDDIR>>/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');
| ^~~~~~~~~~
/<<BUILDDIR>>/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))
| ^
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
256 | const char* spaces = " \t";
| ^~~~~~
[ 50%] Building CXX object CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o -MF CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o.d -o CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BaseInteractionParameterReader.cpp
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
61 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
144 | if(id >= 0 && id < residueStretchVector.size())
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = SingleResidue]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:814:42: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/SimTKsimbody.h:43,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BaseInteractionParameterReader.cpp:17:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
In file included from /usr/include/c++/13/regex:59,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Spiral.h:13:
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const frequencyPhaseAmplitude&}; _Tp = frequencyPhaseAmplitude; _Alloc = std::allocator<frequencyPhaseAmplitude>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<frequencyPhaseAmplitude>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/regex:57:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = frequencyPhaseAmplitude; _Alloc = std::allocator<frequencyPhaseAmplitude>]',
inlined from 'void Spiral::parseInput(SimTK::String, double, double, double)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Spiral.cpp:449:41:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<frequencyPhaseAmplitude*, std::vector<frequencyPhaseAmplitude> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/13/regex:55:
/usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const SimTK::String&&>, std::tuple<>}; _Key = const SimTK::String; _Val = std::pair<const SimTK::String, double>; _KeyOfValue = std::_Select1st<std::pair<const SimTK::String, double> >; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]':
/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator' changed in GCC 7.1
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/regex:56:
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const SimTK::String; _Tp = double; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]',
inlined from 'double myAtoF(std::map<const SimTK::String, double>, const char*)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:180:77:
/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator' changed in GCC 7.1
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const SimTK::String; _Tp = double; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]',
inlined from 'myAtoF(std::map<const SimTK::String, double>, const char*)::<lambda()>' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:179:17,
inlined from 'constexpr _Res std::__invoke_impl(__invoke_other, _Fn&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Fn = myAtoF(std::map<const SimTK::String, double>, const char*)::<lambda()>&; _Args = {}]' at /usr/include/c++/13/bits/invoke.h:61:67,
inlined from 'constexpr std::enable_if_t<is_invocable_r_v<_Res, _Callable, _Args ...>, _Res> std::__invoke_r(_Callable&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Callable = myAtoF(std::map<const SimTK::String, double>, const char*)::<lambda()>&; _Args = {}]' at /usr/include/c++/13/bits/invoke.h:116:38,
inlined from 'static _Res std::_Function_handler<_Res(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Res = std::__cxx11::basic_ostringstream<char>; _Functor = myAtoF(std::map<const SimTK::String, double>, const char*)::<lambda()>; _ArgTypes = {}]' at /usr/include/c++/13/bits/std_function.h:291:44:
/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator' changed in GCC 7.1
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BaseInteractionParameterReader.h:22,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BaseInteractionParameterReader.cpp:18:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
1379 | for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);} myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
| ~~^~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/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/c++/13/vector:65,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Repel.h:18:
/usr/include/c++/13/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Displacement*, vector<Displacement> >; _ForwardIterator = Displacement*]':
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Displacement*, std::vector<Displacement> >' changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Displacement*, std::vector<Displacement> >' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Displacement*, std::vector<Displacement> >; _ForwardIterator = Displacement*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Displacement*, vector<Displacement> >; _ForwardIterator = Displacement*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Displacement*, vector<Displacement> >; _ForwardIterator = Displacement*; _Tp = Displacement]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Displacement; _Alloc = std::allocator<Displacement>]' at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from 'std::vector<Displacement> DisplacementContainer::getDisplacementVector()' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DisplacementContainer.h:31:63,
inlined from 'int ConstrainedDynamics::initializeBiopolymersAndCustomMolecules(SimTK::CompoundSystem&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:390:133:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Displacement*, std::vector<Displacement> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Displacement*, std::vector<Displacement> >; _ForwardIterator = Displacement*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Displacement*, vector<Displacement> >; _ForwardIterator = Displacement*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Displacement*, vector<Displacement> >; _ForwardIterator = Displacement*; _Tp = Displacement]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Displacement; _Alloc = std::allocator<Displacement>]' at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from 'std::vector<Displacement> DisplacementContainer::getDisplacementVector()' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DisplacementContainer.h:31:63,
inlined from 'void ConstrainedDynamics::initializeBiopolymer(SimTK::String, SimTK::String)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:418:132:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Displacement*, std::vector<Displacement> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const WaterDropletAboutResidueStruct*, vector<WaterDropletAboutResidueStruct> >; _ForwardIterator = WaterDropletAboutResidueStruct*]':
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const WaterDropletAboutResidueStruct*, std::vector<WaterDropletAboutResidueStruct> >' changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const WaterDropletAboutResidueStruct*, std::vector<WaterDropletAboutResidueStruct> >' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const WaterDropletAboutResidueStruct*, std::vector<WaterDropletAboutResidueStruct> >; _ForwardIterator = WaterDropletAboutResidueStruct*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const WaterDropletAboutResidueStruct*, vector<WaterDropletAboutResidueStruct> >; _ForwardIterator = WaterDropletAboutResidueStruct*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const WaterDropletAboutResidueStruct*, vector<WaterDropletAboutResidueStruct> >; _ForwardIterator = WaterDropletAboutResidueStruct*; _Tp = WaterDropletAboutResidueStruct]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = WaterDropletAboutResidueStruct; _Alloc = std::allocator<WaterDropletAboutResidueStruct>]' at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from 'void ConstrainedDynamics::initializeMoleculesAndBonds(SimTK::CompoundSystem&, SimTK::DuMMForceFieldSubsystem&, SimTK::SimbodyMatterSubsystem&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:432:140:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const WaterDropletAboutResidueStruct*, std::vector<WaterDropletAboutResidueStruct> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, vector<LeontisWesthofBondRow> >; _ForwardIterator = LeontisWesthofBondRow*]':
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, std::vector<LeontisWesthofBondRow> >' changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, std::vector<LeontisWesthofBondRow> >' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, std::vector<LeontisWesthofBondRow> >; _ForwardIterator = LeontisWesthofBondRow*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, vector<LeontisWesthofBondRow> >; _ForwardIterator = LeontisWesthofBondRow*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, vector<LeontisWesthofBondRow> >; _ForwardIterator = LeontisWesthofBondRow*; _Tp = LeontisWesthofBondRow]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = LeontisWesthofBondRow; _Alloc = std::allocator<LeontisWesthofBondRow>]' at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from 'LeontisWesthofBondMatrix::LeontisWesthofBondMatrix(const LeontisWesthofBondMatrix&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BaseInteractionParameterReader.h:72:8,
inlined from 'LeontisWesthofClass::LeontisWesthofClass(const LeontisWesthofClass&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BaseInteractionParameterReader.h:75:7,
inlined from 'void ConstrainedDynamics::initializeCustomForcesConstraints()' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/Repel.cpp:605:36:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const LeontisWesthofBondRow*, std::vector<LeontisWesthofBondRow> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 53%] Building CXX object CMakeFiles/MMB.dir/src/TetherForce.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/TetherForce.cpp.o -MF CMakeFiles/MMB.dir/src/TetherForce.cpp.o.d -o CMakeFiles/MMB.dir/src/TetherForce.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/TetherForce.cpp
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/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/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/Simbody.h:38,
from /usr/include/molmodel/SimTKmolmodel.h:47,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/TetherForce.h:18,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/TetherForce.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
[ 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/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o -MF CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o.d -o CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp
In file included from /usr/include/c++/13/vector:72,
from /usr/include/c++/13/functional:64,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/MMBLogger.h:6,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BaseInteractionParameterReader.cpp:11:
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {LeontisWesthofBondRow}; _Tp = LeontisWesthofBondRow; _Alloc = std::allocator<LeontisWesthofBondRow>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<LeontisWesthofBondRow>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {LeontisWesthofBondRow}; _Tp = LeontisWesthofBondRow; _Alloc = std::allocator<LeontisWesthofBondRow>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = LeontisWesthofBondRow; _Alloc = std::allocator<LeontisWesthofBondRow>]' at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from 'void LeontisWesthofClass::initialize(const SimTK::String&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BaseInteractionParameterReader.cpp:215:63:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LeontisWesthofBondRow*, std::vector<LeontisWesthofBondRow> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/Simbody.h:38,
from /usr/include/molmodel/SimTKmolmodel.h:47,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClassTwoTransformForces.h:16,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:10:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
[ 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/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o -MF CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o.d -o CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/WaterDroplet.cpp
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/Simbody.h:38,
from /usr/include/molmodel/SimTKmolmodel.h:47,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Water.h:1,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/WaterDroplet.h:15,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/WaterDroplet.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/TetherForce.h:19:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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 /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
61 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClassTwoTransformForces.h:17:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
144 | if(id >= 0 && id < residueStretchVector.size())
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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 /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const':
/<<BUILDDIR>>/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.
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:280:16: warning: variable 'scrubberPeriod' set but not used [-Wunused-but-set-variable]
280 | double scrubberPeriod;
| ^~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
61 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
144 | if(id >= 0 && id < residueStretchVector.size())
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/WaterDroplet.h:16:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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 /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/WaterDroplet.h:17:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
256 | const char* spaces = " \t";
| ^~~~~~
[ 62%] Building CXX object CMakeFiles/MMB.dir/src/DensityMap.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DensityMap.cpp.o -MF CMakeFiles/MMB.dir/src/DensityMap.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityMap.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/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/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/SimTKsimbody.h:43,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93,
from /usr/include/simbody/SimTKcommon/Simmatrix.h:37:
In member function 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]',
inlined from 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
inlined from 'SimTK::Rotation_<P>::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
inlined from 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const' at /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp: In member function 'virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object 'rotation2' of size 72
319 | Rotation rotation2;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/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 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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/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':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/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':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/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':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/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':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/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':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/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':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object 'rotation2' of size 72
116 | Rotation rotation2;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:254:29: warning: 'myFrcScalar' may be used uninitialized [-Wmaybe-uninitialized]
254 | myFrcScalar *= myParameterReader.twoTransformForceMultiplier;
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/BiopolymerClassTwoTransformForces.cpp:167:20: note: 'myFrcScalar' was declared here
167 | double myFrcScalar;
| ^~~~~~~~~~~
[ 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/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DensityForce.cpp.o -MF CMakeFiles/MMB.dir/src/DensityForce.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityForce.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityForce.cpp
In file included from /usr/include/c++/13/vector:72,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/WaterDroplet.h:13:
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const WaterDroplet&}; _Tp = WaterDroplet; _Alloc = std::allocator<WaterDroplet>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<WaterDroplet>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = WaterDroplet; _Alloc = std::allocator<WaterDroplet>]',
inlined from 'void WaterDropletContainer::add(WaterDroplet&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/WaterDroplet.cpp:70:33:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<WaterDroplet*, std::vector<WaterDroplet> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const MMBAtomInfo&}; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<MMBAtomInfo>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]',
inlined from 'void WaterDroplet::addWaterMolecules(SimTK::CompoundSystem&, SimTK::DuMMForceFieldSubsystem&, SimTK::SimbodyMatterSubsystem&, BiopolymerClassContainer&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/WaterDroplet.cpp:294:51:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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 /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/Simbody.h:38,
from /usr/include/molmodel/SimTKmolmodel.h:47,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityForce.h:19,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityForce.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AtomSpring&}; _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<AtomSpring>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]',
inlined from 'void AtomSpringContainer::add(AtomSpring&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:41:102,
inlined from 'void WaterDroplet::addTethers(AtomSpringContainer&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/WaterDroplet.cpp:164:32:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomSpring*, std::vector<AtomSpring> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::resizeVectorOfAmplitudeAndRandomPhases()':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
177 | if (vectorOfAmplitudeFrequencyAndRandomPhases.size() != (unitCellParameters.calcMaxFrequencyDoublingsZ()+1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
181 | if (vectorOfAmplitudeFrequencyAndRandomPhases[zIndex].size() != (unitCellParameters.calcMaxFrequencyDoublingsY()+1) ) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:185:90: warning: comparison of integer expressions of different signedness: 'std::vector<AmplitudeFrequencyAndRandomPhases>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
185 | if (vectorOfAmplitudeFrequencyAndRandomPhases[zIndex][yIndex].size() != (unitCellParameters.calcMaxFrequencyDoublingsX()+1 )) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::densityAutocorrelation(bool, bool) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:209:12: warning: unused variable 'ySquared' [-Wunused-variable]
209 | double ySquared = 0.;
| ^~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:210:12: warning: unused variable 'zSquared' [-Wunused-variable]
210 | double zSquared = 0.;
| ^~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::populateNoiseMap()':
/<<BUILDDIR>>/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;
| ^~~~~~~~~~~~~~~~
/<<BUILDDIR>>/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;
| ^~~~~~~~~~~~~~~~
/<<BUILDDIR>>/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;
| ^~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:311:12: warning: unused variable 'maxFrequencyX' [-Wunused-variable]
311 | double maxFrequencyX = 1/unitCellParameters.geta()/2;
| ^~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:312:12: warning: unused variable 'maxFrequencyY' [-Wunused-variable]
312 | double maxFrequencyY = 1/unitCellParameters.getb()/2;
| ^~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:313:12: warning: unused variable 'maxFrequencyZ' [-Wunused-variable]
313 | double maxFrequencyZ = 1/unitCellParameters.getc()/2;
| ^~~~~~~~~~~~~
/<<BUILDDIR>>/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.;
| ^~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/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.
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:18:
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const MMBAtomInfo&}; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<MMBAtomInfo>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
/usr/include/c++/13/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]':
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::loadParametersAndDensity_CCP4MAP()':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:543:13: warning: unused variable 'newU' [-Wunused-variable]
543 | int newU, newV, newW;
| ^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:543:19: warning: unused variable 'newV' [-Wunused-variable]
543 | int newU, newV, newW;
| ^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:543:25: warning: unused variable 'newW' [-Wunused-variable]
543 | int newU, newV, newW;
| ^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:507:9: warning: unused variable 'xGridInds' [-Wunused-variable]
507 | int xGridInds = xDimInds;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:508:9: warning: unused variable 'yGridInds' [-Wunused-variable]
508 | int yGridInds = yDimInds;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:509:9: warning: unused variable 'zGridInds' [-Wunused-variable]
509 | int zGridInds = zDimInds;
| ^~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AtomSpring&}; _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<AtomSpring>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp: In member function 'void DensityMap::writeDensityMapXplor(SimTK::String, bool, bool)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/DensityMap.cpp:689:13: warning: unused variable 'densitiesPerLine' [-Wunused-variable]
689 | int densitiesPerLine = 6;
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]':
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomSpring*, std::vector<AtomSpring> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomSpring; _Alloc = std::allocator<AtomSpring>]',
inlined from 'void AtomSpringContainer::add(AtomSpring&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:41:102,
inlined from 'void ParameterReader::addC1pSprings(LeontisWesthofClass)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:153:39:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomSpring*, std::vector<AtomSpring> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AllResiduesWithin&}; _Tp = AllResiduesWithin; _Alloc = std::allocator<AllResiduesWithin>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<AllResiduesWithin>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AllResiduesWithin; _Alloc = std::allocator<AllResiduesWithin>]':
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AllResiduesWithin*, std::vector<AllResiduesWithin> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AllResiduesWithin; _Alloc = std::allocator<AllResiduesWithin>]',
inlined from 'void ParameterReader::addAllResiduesWithin(SimTK::String, int, double)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:769:45:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AllResiduesWithin*, std::vector<AllResiduesWithin> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 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/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o -MF CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o.d -o CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ElectrostaticPotentialGridForce.cpp
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const CovalentBondClass&}; _Tp = CovalentBondClass; _Alloc = std::allocator<CovalentBondClass>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<CovalentBondClass>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = CovalentBondClass; _Alloc = std::allocator<CovalentBondClass>]':
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<CovalentBondClass*, std::vector<CovalentBondClass> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BasePair&}; _Tp = BasePair; _Alloc = std::allocator<BasePair>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<BasePair>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BasePair; _Alloc = std::allocator<BasePair>]':
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BasePair*, std::vector<BasePair> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const MobilizerDomainsInterface&}; _Tp = MobilizerDomainsInterface; _Alloc = std::allocator<MobilizerDomainsInterface>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<MobilizerDomainsInterface>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = MobilizerDomainsInterface; _Alloc = std::allocator<MobilizerDomainsInterface>]':
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MobilizerDomainsInterface*, std::vector<MobilizerDomainsInterface> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const AtomicPropertyOverrideStruct&}; _Tp = AtomicPropertyOverrideStruct; _Alloc = std::allocator<AtomicPropertyOverrideStruct>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<AtomicPropertyOverrideStruct>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = AtomicPropertyOverrideStruct; _Alloc = std::allocator<AtomicPropertyOverrideStruct>]':
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomicPropertyOverrideStruct*, std::vector<AtomicPropertyOverrideStruct> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const WaterDropletAboutResidueStruct&}; _Tp = WaterDropletAboutResidueStruct; _Alloc = std::allocator<WaterDropletAboutResidueStruct>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<WaterDropletAboutResidueStruct>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = WaterDropletAboutResidueStruct; _Alloc = std::allocator<WaterDropletAboutResidueStruct>]':
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<WaterDropletAboutResidueStruct*, std::vector<WaterDropletAboutResidueStruct> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const IncludeIntraChainInterface&}; _Tp = IncludeIntraChainInterface; _Alloc = std::allocator<IncludeIntraChainInterface>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<IncludeIntraChainInterface>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = IncludeIntraChainInterface; _Alloc = std::allocator<IncludeIntraChainInterface>]':
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<IncludeIntraChainInterface*, std::vector<IncludeIntraChainInterface> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/Simbody.h:38,
from /usr/include/molmodel/SimTKmolmodel.h:47,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ElectrostaticPotentialGridForce.h:18,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ElectrostaticPotentialGridForce.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
In file included from /usr/include/c++/13/set:62,
from /usr/include/simbody/simmath/internal/Contact.h:30,
from /usr/include/simbody/SimTKmath.h:46,
from /usr/include/simbody/SimTKsimbody.h:44:
/usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const SimTK::String&&>, std::tuple<>}; _Key = const SimTK::String; _Val = std::pair<const SimTK::String, double>; _KeyOfValue = std::_Select1st<std::pair<const SimTK::String, double> >; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]':
/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator' changed in GCC 7.1
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/map:63,
from /usr/include/simbody/simmath/internal/CollisionDetectionAlgorithm.h:32,
from /usr/include/simbody/SimTKmath.h:48:
/usr/include/c++/13/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const SimTK::String; _Tp = double; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]':
/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator' changed in GCC 7.1
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const SimTK::String; _Tp = double; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]',
inlined from 'ParameterReader::initializeFromFileOnly(const char*)::<lambda()>' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:4538:5,
inlined from 'constexpr _Res std::__invoke_impl(__invoke_other, _Fn&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Fn = ParameterReader::initializeFromFileOnly(const char*)::<lambda()>&; _Args = {}]' at /usr/include/c++/13/bits/invoke.h:61:67,
inlined from 'constexpr std::enable_if_t<is_invocable_r_v<_Res, _Callable, _Args ...>, _Res> std::__invoke_r(_Callable&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Callable = ParameterReader::initializeFromFileOnly(const char*)::<lambda()>&; _Args = {}]' at /usr/include/c++/13/bits/invoke.h:116:38,
inlined from 'static _Res std::_Function_handler<_Res(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Res = std::__cxx11::basic_ostringstream<char>; _Functor = ParameterReader::initializeFromFileOnly(const char*)::<lambda()>; _ArgTypes = {}]' at /usr/include/c++/13/bits/std_function.h:291:44:
/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator' changed in GCC 7.1
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const SimTK::String; _Tp = double; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]',
inlined from 'myAtoF(std::map<const SimTK::String, double>, const char*)::<lambda()>' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:179:17,
inlined from 'constexpr _Res std::__invoke_impl(__invoke_other, _Fn&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Fn = myAtoF(std::map<const SimTK::String, double>, const char*)::<lambda()>&; _Args = {}]' at /usr/include/c++/13/bits/invoke.h:61:67,
inlined from 'constexpr std::enable_if_t<is_invocable_r_v<_Res, _Callable, _Args ...>, _Res> std::__invoke_r(_Callable&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Callable = myAtoF(std::map<const SimTK::String, double>, const char*)::<lambda()>&; _Args = {}]' at /usr/include/c++/13/bits/invoke.h:116:38,
inlined from 'static _Res std::_Function_handler<_Res(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Res = std::__cxx11::basic_ostringstream<char>; _Functor = myAtoF(std::map<const SimTK::String, double>, const char*)::<lambda()>; _ArgTypes = {}]' at /usr/include/c++/13/bits/std_function.h:291:44:
/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator' changed in GCC 7.1
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = const SimTK::String; _Tp = double; _Compare = std::less<const SimTK::String>; _Alloc = std::allocator<std::pair<const SimTK::String, double> >]',
inlined from 'ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)::<lambda()>' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:3498:9,
inlined from 'constexpr _Res std::__invoke_impl(__invoke_other, _Fn&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Fn = ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)::<lambda()>&; _Args = {}]' at /usr/include/c++/13/bits/invoke.h:61:67,
inlined from 'constexpr std::enable_if_t<is_invocable_r_v<_Res, _Callable, _Args ...>, _Res> std::__invoke_r(_Callable&&, _Args&& ...) [with _Res = __cxx11::basic_ostringstream<char>; _Callable = ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)::<lambda()>&; _Args = {}]' at /usr/include/c++/13/bits/invoke.h:116:38,
inlined from 'static _Res std::_Function_handler<_Res(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Res = std::__cxx11::basic_ostringstream<char>; _Functor = ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)::<lambda()>; _ArgTypes = {}]' at /usr/include/c++/13/bits/std_function.h:291:44:
/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree<const SimTK::String, std::pair<const SimTK::String, double>, std::_Select1st<std::pair<const SimTK::String, double> >, std::less<const SimTK::String>, std::allocator<std::pair<const SimTK::String, double> > >::const_iterator' changed in GCC 7.1
532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
533 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:65:
/usr/include/c++/13/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]':
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, vector<MMBAtomInfo> >; _ForwardIterator = MMBAtomInfo*; _Tp = MMBAtomInfo]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >; _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]' at /usr/include/c++/13/bits/stl_vector.h:1619:35,
inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = MMBAtomInfo; _Alloc = std::allocator<MMBAtomInfo>]' at /usr/include/c++/13/bits/vector.tcc:238:44:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const MMBAtomInfo*, std::vector<MMBAtomInfo> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
256 | const char* spaces = " \t";
| ^~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Displacement&}; _Tp = Displacement; _Alloc = std::allocator<Displacement>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<Displacement>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Displacement; _Alloc = std::allocator<Displacement>]',
inlined from 'void DisplacementContainer::add(Displacement, BiopolymerClassContainer&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DisplacementContainer.h:25:181:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Displacement*, std::vector<Displacement> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityForce.h:20:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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 /usr/include/simbody/SimTKcommon/SmallMatrix.h:93,
from /usr/include/simbody/SimTKcommon/Simmatrix.h:37:
In member function 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]',
inlined from 'SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]' at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
inlined from 'SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]' at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
inlined from 'SimTK::Rotation_<P>::Rotation_() [with P = double]' at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
inlined from 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)' at /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/<<BUILDDIR>>/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 /<<BUILDDIR>>/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; }
| ~~~~~~~~~~~~^~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp: In member function 'void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ParameterReader.cpp:2209:26: note: object 'myRotation' of size 72
2209 | Rotation myRotation;
| ^~~~~~~~~~
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/set:62,
from /usr/include/simbody/simmath/internal/Contact.h:30,
from /usr/include/simbody/SimTKmath.h:46,
from /usr/include/simbody/SimTKsimbody.h:44:
/usr/include/c++/13/bits/stl_tree.h: In function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = double; _Val = std::pair<const double, DensityMap::densityAutocorrelation(bool, bool) const::autoCorrelationStruct>; _KeyOfValue = std::_Select1st<std::pair<const double, DensityMap::densityAutocorrelation(bool, bool) const::autoCorrelationStruct> >; _Compare = std::less<double>; _Alloc = std::allocator<std::pair<const double, DensityMap::densityAutocorrelation(bool, bool) const::autoCorrelationStruct> >]':
/usr/include/c++/13/bits/stl_tree.h:2210:5: note: parameter passing for argument of type 'std::_Rb_tree<double, std::pair<const double, DensityMap::densityAutocorrelation(bool, bool) const::autoCorrelationStruct>, std::_Select1st<std::pair<const double, DensityMap::densityAutocorrelation(bool, bool) const::autoCorrelationStruct> >, std::less<double>, std::allocator<std::pair<const double, DensityMap::densityAutocorrelation(bool, bool) const::autoCorrelationStruct> > >::const_iterator' changed in GCC 7.1
2210 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
61 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
144 | if(id >= 0 && id < residueStretchVector.size())
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ElectrostaticPotentialGridForce.h:19:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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 /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
61 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
144 | if(id >= 0 && id < residueStretchVector.size())
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
256 | const char* spaces = " \t";
| ^~~~~~
[ 71%] Building CXX object CMakeFiles/MMB.dir/src/MMBLogger.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/MMBLogger.cpp.o -MF CMakeFiles/MMB.dir/src/MMBLogger.cpp.o.d -o CMakeFiles/MMB.dir/src/MMBLogger.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/MMBLogger.cpp
[ 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/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -MF CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o.d -o CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
256 | const char* spaces = " \t";
| ^~~~~~
[ 78%] Building CXX object CMakeFiles/MMB.dir/src/CifOutput.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/CifOutput.cpp.o -MF CMakeFiles/MMB.dir/src/CifOutput.cpp.o.d -o CMakeFiles/MMB.dir/src/CifOutput.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/CifOutput.cpp
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/SimTKsimbody.h:43,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:22,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/PeriodicPdbAndEnergyWriter.h:13,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:18:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/SimTKsimbody.h:43,
from /usr/include/molmodel/molmodel/internal/Compound.h:36,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:16,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/CifOutput.h:5,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/CifOutput.cpp:1:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
[ 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/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o -MF CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o.d -o CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/ProgressWriter.cpp
[ 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/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o -MF CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o.d -o CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/NTC_PARAMETER_READER.cpp
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/SimTKsimbody.h:43,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/NTC_PARAMETER_READER.cpp:15:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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 /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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 /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp: In member function 'virtual void SimTK::PeriodicPdbAndEnergyWriter::handleEvent(SimTK::State&, SimTK::Real, bool&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:201:30: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
201 | if(myEnergies.size() > myParameterReader.convergenceTimeout) {
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:202:20: warning: unused variable 'lastEnergy' [-Wunused-variable]
202 | double lastEnergy = myEnergies.back();
| ^~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:49:9: warning: unused variable 'compoundNumber' [-Wunused-variable]
49 | int compoundNumber = 1;
| ^~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:50:9: warning: unused variable 'requiredPrecision' [-Wunused-variable]
50 | int requiredPrecision = 12;
| ^~~~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/PeriodicPdbAndEnergyWriter.h:13,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/CifOutput.h:12:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
61 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
144 | if(id >= 0 && id < residueStretchVector.size())
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
61 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
144 | if(id >= 0 && id < residueStretchVector.size())
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/NtC_Class_Container.h:14,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/NTC_PARAMETER_READER.cpp:16:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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 /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/NTC_FORCE_CLASS.h:4,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/NTC_PARAMETER_READER.cpp:17:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
256 | const char* spaces = " \t";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/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/c++/13/vector:72,
from /usr/include/c++/13/functional:64,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/MMBLogger.h:6,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:17:
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'virtual void SimTK::PeriodicPdbAndEnergyWriter::handleEvent(SimTK::State&, SimTK::Real, bool&) const' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:127:55:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'virtual void SimTK::PeriodicPdbAndEnergyWriter::handleEvent(SimTK::State&, SimTK::Real, bool&) const' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/PeriodicPdbAndEnergyWriter.cpp:175:33:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
256 | const char* spaces = " \t";
| ^~~~~~
[ 87%] Building CXX object CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o
/usr/bin/c++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o -MF CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/NtCClassContainer.cpp
In file included from /usr/include/c++/13/vector:72,
from /usr/include/c++/13/functional:64,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/MMBLogger.h:6,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/NTC_PARAMETER_READER.cpp:12:
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {NTC_PAR_BondRow}; _Tp = NTC_PAR_BondRow; _Alloc = std::allocator<NTC_PAR_BondRow>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<NTC_PAR_BondRow>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/SimTKsimbody.h:43,
from /usr/include/molmodel/molmodel/internal/Compound.h:36,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:16,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/NtCClassContainer.cpp:13:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {NTC_PAR_BondRow}; _Tp = NTC_PAR_BondRow; _Alloc = std::allocator<NTC_PAR_BondRow>]',
inlined from 'void NTC_PAR_Class::initialize(const SimTK::String&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/NTC_PARAMETER_READER.cpp:133:64:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NTC_PAR_BondRow*, std::vector<NTC_PAR_BondRow> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 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/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NtCForces.cpp.o -MF CMakeFiles/MMB.dir/src/NtCForces.cpp.o.d -o CMakeFiles/MMB.dir/src/NtCForces.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/NtCForces.cpp
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/Simbody.h:38,
from /usr/include/molmodel/SimTKmolmodel.h:47,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/NtCForces.h:12,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/NtCForces.cpp:11:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
In file included from /usr/include/c++/13/memory:69,
from /usr/include/simbody/SimTKcommon/internal/ClonePtr.h:29,
from /usr/include/simbody/SimTKcommon/basics.h:44,
from /usr/include/simbody/SimTKcommon.h:32:
/usr/include/c++/13/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gemmi::Atom*, vector<gemmi::Atom> >; _ForwardIterator = gemmi::Atom*]':
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gemmi::Atom*, std::vector<gemmi::Atom> >' changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gemmi::Atom*, std::vector<gemmi::Atom> >' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gemmi::Atom*, std::vector<gemmi::Atom> >; _ForwardIterator = gemmi::Atom*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gemmi::Atom*, vector<gemmi::Atom> >; _ForwardIterator = gemmi::Atom*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gemmi::Atom*, vector<gemmi::Atom> >; _ForwardIterator = gemmi::Atom*; _Tp = gemmi::Atom]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gemmi::Atom; _Alloc = std::allocator<gemmi::Atom>]' at /usr/include/c++/13/bits/stl_vector.h:603:31,
inlined from 'gemmi::Residue::Residue(const gemmi::Residue&)' at /usr/include/gemmi/model.hpp:175:8,
inlined from 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = gemmi::Residue; _Args = {const gemmi::Residue&}]' at /usr/include/c++/13/bits/stl_construct.h:119:7,
inlined from '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gemmi::Residue*, vector<gemmi::Residue, allocator<gemmi::Residue> > >; _ForwardIterator = gemmi::Residue*]' at /usr/include/c++/13/bits/stl_uninitialized.h:120:21:
/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gemmi::Atom*, std::vector<gemmi::Atom> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Mutation.h:4,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h:20:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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); };
| ~~^~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/NtCForces.h:13:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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 /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
61 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
144 | if(id >= 0 && id < residueStretchVector.size())
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:256:17: warning: '{anonymous}::spaces' defined but not used [-Wunused-variable]
256 | const char* spaces = " \t";
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/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/c++/13/vector:72,
from /usr/include/simbody/SimTKcommon/internal/Array.h:39,
from /usr/include/simbody/SimTKcommon/basics.h:53,
from /usr/include/simbody/SimTKcommon.h:32:
/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const NTC_Classes&}; _Tp = NTC_Classes; _Alloc = std::allocator<NTC_Classes>]':
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector<NTC_Classes>::iterator' changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = NTC_Classes; _Alloc = std::allocator<NTC_Classes>]',
inlined from 'void NTC_Class_Container::add_NTC_Class(BiopolymerClassContainer&, const NTC_PAR_Class&, NTC_Classes&)' at /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/NtCClassContainer.cpp:193:37:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NTC_Classes*, std::vector<NTC_Classes> >' changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 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=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -Wl,-z,relro -shared -Wl,-soname,libMMB.so.4.0 -o libMMB.so.4.0 CMakeFiles/MMB.dir/src/Utils.cpp.o CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o CMakeFiles/MMB.dir/src/DensityContainer.cpp.o CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o CMakeFiles/MMB.dir/src/ContactContainer.cpp.o CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o CMakeFiles/MMB.dir/src/Repel.cpp.o CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o CMakeFiles/MMB.dir/src/Spiral.cpp.o CMakeFiles/MMB.dir/src/ParameterReader.cpp.o CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o CMakeFiles/MMB.dir/src/TetherForce.cpp.o CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o CMakeFiles/MMB.dir/src/DensityMap.cpp.o CMakeFiles/MMB.dir/src/DensityForce.cpp.o CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o CMakeFiles/MMB.dir/src/MMBLogger.cpp.o CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o CMakeFiles/MMB.dir/src/CifOutput.cpp.o CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o CMakeFiles/MMB.dir/src/NtCForces.cpp.o -L/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/SYSTEM -Wl,-rpath,/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/SYSTEM: /usr/lib/arm-linux-gnueabihf/libSimTKmolmodel.so.3.1 /usr/lib/arm-linux-gnueabihf/libOpenMM.so /usr/lib/arm-linux-gnueabihf/libz.so -lgemmi_cpp /usr/lib/arm-linux-gnueabihf/libSimTKsimbody.so.3.7 /usr/lib/arm-linux-gnueabihf/libSimTKmath.so.3.7 /usr/lib/arm-linux-gnueabihf/libSimTKcommon.so.3.7 /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lrt -ldl -lm
/usr/bin/cmake -E cmake_symlink_library libMMB.so.4.0 libMMB.so.4.0 libMMB.so
make[3]: Leaving directory '/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf'
[ 93%] Built target MMB
make -f CMakeFiles/MMB_EXEC.dir/build.make CMakeFiles/MMB_EXEC.dir/depend
make[3]: Entering directory '/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/MMB_EXEC.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/MMB_EXEC.dir/build.make CMakeFiles/MMB_EXEC.dir/build
make[3]: Entering directory '/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf'
[ 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/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -I/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -MD -MT CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o -MF CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o.d -o CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o -c /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/RNABuilder.cpp
In file included from /usr/include/simbody/SimTKcommon/Simmatrix.h:36,
from /usr/include/simbody/SimTKcommon.h:35,
from /usr/include/simbody/Simbody.h:38,
from /usr/include/molmodel/SimTKmolmodel.h:47,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/RNABuilder.cpp:20:
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(double)':
/usr/include/simbody/SimTKcommon/Scalar.h:1169:43: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1169 | approxCompleteEllipticIntegralsKE(double m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::approxCompleteEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1177:42: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1177 | approxCompleteEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::approxCompleteEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1186:40: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1186 | approxCompleteEllipticIntegralsKE(int m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<float, float> SimTK::completeEllipticIntegralsKE(float)':
/usr/include/simbody/SimTKcommon/Scalar.h:1257:66: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1257 | inline std::pair<float,float> completeEllipticIntegralsKE(float m)
| ^
/usr/include/simbody/SimTKcommon/Scalar.h: In function 'std::pair<double, double> SimTK::completeEllipticIntegralsKE(int)':
/usr/include/simbody/SimTKcommon/Scalar.h:1265:66: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1265 | inline std::pair<double,double> completeEllipticIntegralsKE(int m)
| ^
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:14,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:20,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/src/RNABuilder.cpp:22:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:290:10: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
290 | if (derivComponents.size() == 1)
| ^~
/<<BUILDDIR>>/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;
| ^~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'ResidueID::ResidueID(SimTK::String)':
/<<BUILDDIR>>/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();
| ^~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const':
/<<BUILDDIR>>/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 'unsigned int'} and 'int' [-Wsign-compare]
386 | if ((myStringStream.str()).length() != (totalWidth - 1)) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void Interface::print()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
666 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
670 | for (int i = 0; i < Chains.size(); i ++) {
| ~~^~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1308:9: warning: when initialized here [-Wreorder]
1308 | MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In constructor 'MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1294:16: warning: 'MMBAtomInfo::chain' will be initialized after [-Wreorder]
1294 | String chain;
| ^~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:1292:19: warning: 'ResidueID MMBAtomInfo::residueID' [-Wreorder]
1292 | ResidueID residueID;
| ^~~~~~~~~
/<<BUILDDIR>>/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) :
| ^~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: In member function 'void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)':
/<<BUILDDIR>>/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 '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 /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h:2,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h:15:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/BiopolymerClass.h: In member function 'void BiopolymerClass::printAtomInfoVector()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
255 | void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
| ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'bool ThreadingStruct::hasResidue(ResidueID, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
71 | for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Threading.h: In member function 'void ThreadingStruct::supplementIncludedResidues(int, int)':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
78 | for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ; i++){
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/AtomSpringContainer.h: In member function 'void AtomSpringContainer::printAllAlignmentStats()':
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
73 | void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::approxCompleteEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1178:54: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1095:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
1095 | static inline std::pair<T,T> approxCompleteEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = double]':
/usr/include/simbody/SimTKcommon/Scalar.h:1249:49: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
1192 | static inline std::pair<T,T> completeEllipticIntegralsKE_T(T m) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/simbody/SimTKcommon/Scalar.h: In instantiation of 'std::pair<_FIter, _FIter> SimTK::completeEllipticIntegralsKE_T(T) [with T = float]':
/usr/include/simbody/SimTKcommon/Scalar.h:1258:48: required from here
/usr/include/simbody/SimTKcommon/Scalar.h:1192:30: note: parameter passing for argument of type 'std::pair<float, float>' when C++17 is enabled changed to match C++14 in GCC 10.1
In file included from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ContactContainer.h:15,
from /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ParameterReader.h:21:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:22:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
61 | for (int i = 0 ; i <residueStretchVector.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/ResidueStretchContainer.h: In instantiation of 'void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]':
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/DensityContainer.h:25:59: required from here
/<<BUILDDIR>>/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 'unsigned int'} [-Wsign-compare]
144 | if(id >= 0 && id < residueStretchVector.size())
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h: At global scope:
/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/include/Utils.h:257:17: warning: '{anonymous}::digits' defined but not used [-Wunused-variable]
257 | const char* digits = "0123456789";
| ^~~~~~
/<<BUILDDIR>>/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=/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -Wl,-z,relro CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o -o MMB -L/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/SYSTEM -Wl,-rpath,/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/SYSTEM:/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf: libMMB.so.4.0 /usr/lib/arm-linux-gnueabihf/libSimTKmolmodel.so.3.1 /usr/lib/arm-linux-gnueabihf/libSimTKsimbody.so.3.7 /usr/lib/arm-linux-gnueabihf/libSimTKmath.so.3.7 /usr/lib/arm-linux-gnueabihf/libSimTKcommon.so.3.7 /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lrt -ldl -lm
make[3]: Leaving directory '/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf'
[100%] Built target MMB_EXEC
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make[1]: Entering directory '/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg -B/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
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Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/AddBackboneOxygenForces.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/AddNASTForces.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/AtomSpringContainer.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/BaseInteractionParameterReader.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/BasePairContainer.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/BiopolymerClass.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/BiopolymerClassTwoTransformForces.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/CalcTransformCorrection.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/CenterOfMass.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/CifOutput.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Constexpr.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/ConstraintContainer.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/ContactContainer.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/DensityContainer.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/DensityForce.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/DensityMap.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/DisplacementContainer.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/ElectrostaticPotentialGridForce.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/ExportMacros.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/ExtraMath.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/GeometricCenter.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/HarmonicVelocityRescalingThermostat.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Impossible.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/KBBackboneTorsionForce.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Lepton.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/LigandDroplet.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Ligands.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Ligands.sam.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/MMBLogger.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/MobilizerContainer.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/MoleculeContainer.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/MonoAtoms.h
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-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/NTC_FORCE_CLASS.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/NTC_PARAMETER_READER.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/NtCBackboneTorsionForce.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/NtCForces.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/NtCInteractionParameterReader.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/NtC_Class_Container.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/ParameterReader.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/ParameterReader_wrapper.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/PeriodicParameterReaderUpdater.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/PeriodicPdbAndCOMWriter.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/PeriodicPdbAndEnergySingleFrameWriter.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/PeriodicPdbAndEnergyWriter.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/PeriodicPdbSingleFrameWriter.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/PeriodicScrubber.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/ProgressWriter.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/RandomizeRNACoordinates.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Repel.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/ResidueStretchContainer.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/RigidifyFormedHelices.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/SetChiMobility.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/SetSingleBondMobility.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Spiral.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/StackingForceSubsystem.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Sterics.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/TetherForce.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Threading.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/UnitCellParameters.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Utils.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/WadleyKeatingDuartePyleTorsionForce.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/Water.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/WaterDroplet.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/superimposer.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/include/MMB/MMB_config.h
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libMMB.so.4.0
-- Set runtime path of "/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libMMB.so.4.0" to ""
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libMMB.so
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/share/MMB/parameters.csv
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/bin/MMB
-- Set runtime path of "/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/bin/MMB" to ""
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/mmb/MmbConfigVersion.cmake
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/mmb/MmbTargets.cmake
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/mmb/MmbTargets-release.cmake
-- Installing: /<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/mmb.pc
make[1]: Leaving directory '/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg/obj-arm-linux-gnueabihf'
dh_install -a
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debian/rules override_dh_installman
make[1]: Entering directory '/<<BUILDDIR>>/macromoleculebuilder-4.0.0+dfsg'
a2x -d manpage -f manpage -D debian/tmp debian/MMB.1.asciidoc
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dh_perl -a
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dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mmb/usr/bin/MMB was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libmmb4.0/usr/lib/arm-linux-gnueabihf/libMMB.so.4.0 found in none of the libraries
dh_installdeb -a
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dpkg-deb: building package 'libmmb-dev' in '../libmmb-dev_4.0.0+dfsg-3_armhf.deb'.
dpkg-deb: building package 'libmmb4.0-dbgsym' in '../libmmb4.0-dbgsym_4.0.0+dfsg-3_armhf.deb'.
dpkg-deb: building package 'mmb-dbgsym' in '../mmb-dbgsym_4.0.0+dfsg-3_armhf.deb'.
dpkg-deb: building package 'libmmb4.0' in '../libmmb4.0_4.0.0+dfsg-3_armhf.deb'.
dpkg-deb: building package 'mmb' in '../mmb_4.0.0+dfsg-3_armhf.deb'.
dpkg-genbuildinfo --build=any -O../macromoleculebuilder_4.0.0+dfsg-3_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../macromoleculebuilder_4.0.0+dfsg-3_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2023-12-01T18:48:01Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
macromoleculebuilder_4.0.0+dfsg-3_armhf.changes:
------------------------------------------------
Format: 1.8
Date: Fri, 23 Jun 2023 01:37:57 -0400
Source: macromoleculebuilder
Binary: libmmb-dev libmmb4.0 libmmb4.0-dbgsym mmb mmb-dbgsym
Architecture: armhf
Version: 4.0.0+dfsg-3
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andrius Merkys <merkys@debian.org>
Description:
libmmb-dev - development files of MacroMoleculeBuilder
libmmb4.0 - shared library of MacroMoleculeBuilder
mmb - model the structure and dynamics of macromolecules
Closes: 1037463
Changes:
macromoleculebuilder (4.0.0+dfsg-3) unstable; urgency=medium
.
* Fix gemmi 0.6.2 support (Closes: #1037463)
* Update standards version to 4.6.2, no changes needed.
Checksums-Sha1:
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470aa41af349846a01b561e72be647c88089ff98 24500724 libmmb4.0-dbgsym_4.0.0+dfsg-3_armhf.deb
e34f3f1fa05514451ca2cf3f8251da30690bc1f9 1146120 libmmb4.0_4.0.0+dfsg-3_armhf.deb
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8cf306a9c297922265e081750b132c69adf98be2 1597132 mmb-dbgsym_4.0.0+dfsg-3_armhf.deb
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Files:
2a573fec78bf06d3007dc490f7552870 76320 libdevel optional libmmb-dev_4.0.0+dfsg-3_armhf.deb
11c9cb2dff0cef7009f7b23639161ec8 24500724 debug optional libmmb4.0-dbgsym_4.0.0+dfsg-3_armhf.deb
1dcae4106f95852e73928651dcc034ec 1146120 libs optional libmmb4.0_4.0.0+dfsg-3_armhf.deb
0a91a15e7e594e1efa045ac380731ff6 10202 science optional macromoleculebuilder_4.0.0+dfsg-3_armhf.buildinfo
ef01b517d980428e2e2e6c91e85cfe3b 1597132 debug optional mmb-dbgsym_4.0.0+dfsg-3_armhf.deb
b52bc0c1c72a10e3336041f5c8cd3ecc 25300 science optional mmb_4.0.0+dfsg-3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libmmb-dev_4.0.0+dfsg-3_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 76320 bytes: control archive=2896 bytes.
774 bytes, 20 lines control
5121 bytes, 72 lines md5sums
Package: libmmb-dev
Source: macromoleculebuilder
Version: 4.0.0+dfsg-3
Architecture: armhf
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Installed-Size: 559
Depends: libmmb4.0 (= 4.0.0+dfsg-3)
Breaks: libmmblib-dev (<< 4.0.0)
Replaces: libmmblib-dev (<< 4.0.0)
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: https://simtk.org/projects/rnatoolbox
Description: development files of MacroMoleculeBuilder
MacroMoleculeBuilder, previously known as RNABuilder, can be used for morphing,
homology modeling, folding (e.g. using base pairing contacts), redesigning
complexes, fitting to low-resolution density maps, predicting local
rearrangements upon mutation, and many other applications.
.
This package contains the development files.
drwxr-xr-x root/root 0 2023-06-23 05:37 ./
drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/
drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/include/
drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/include/MMB/
-rw-r--r-- root/root 8108 2022-11-29 12:01 ./usr/include/MMB/AddBackboneOxygenForces.h
-rw-r--r-- root/root 6293 2022-11-29 12:01 ./usr/include/MMB/AddNASTForces.h
-rw-r--r-- root/root 5724 2022-11-29 12:01 ./usr/include/MMB/AtomSpringContainer.h
-rw-r--r-- root/root 3559 2022-11-29 12:01 ./usr/include/MMB/BaseInteractionParameterReader.h
-rw-r--r-- root/root 3477 2022-11-29 12:01 ./usr/include/MMB/BasePairContainer.h
-rw-r--r-- root/root 42905 2022-11-29 12:01 ./usr/include/MMB/BiopolymerClass.h
-rw-r--r-- root/root 2644 2022-11-29 12:01 ./usr/include/MMB/BiopolymerClassTwoTransformForces.h
-rw-r--r-- root/root 19309 2022-11-29 12:01 ./usr/include/MMB/CalcTransformCorrection.h
-rw-r--r-- root/root 3188 2022-11-29 12:01 ./usr/include/MMB/CenterOfMass.h
-rw-r--r-- root/root 1328 2022-11-29 12:01 ./usr/include/MMB/CifOutput.h
-rw-r--r-- root/root 188 2022-11-29 12:01 ./usr/include/MMB/Constexpr.h
-rw-r--r-- root/root 3848 2022-11-29 12:01 ./usr/include/MMB/ConstraintContainer.h
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drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/lib/arm-linux-gnueabihf/cmake/
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-rw-r--r-- root/root 4458 2023-06-23 05:37 ./usr/lib/arm-linux-gnueabihf/cmake/mmb/MmbTargets.cmake
lrwxrwxrwx root/root 0 2023-06-23 05:37 ./usr/lib/arm-linux-gnueabihf/libMMB.so -> libMMB.so.4.0
drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 197 2023-06-23 05:37 ./usr/lib/arm-linux-gnueabihf/pkgconfig/mmb.pc
drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/share/
drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/share/doc/
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-rw-r--r-- root/root 1550 2023-06-23 05:37 ./usr/share/doc/libmmb-dev/copyright
libmmb4.0-dbgsym_4.0.0+dfsg-3_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 24500724 bytes: control archive=560 bytes.
400 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libmmb4.0-dbgsym
Source: macromoleculebuilder
Version: 4.0.0+dfsg-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Installed-Size: 25826
Depends: libmmb4.0 (= 4.0.0+dfsg-3)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libmmb4.0
Build-Ids: 2609a3035a414261f2ec2644b586e0ec528892e8
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drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/lib/debug/.build-id/
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drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/share/
drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/share/doc/
lrwxrwxrwx root/root 0 2023-06-23 05:37 ./usr/share/doc/libmmb4.0-dbgsym -> libmmb4.0
libmmb4.0_4.0.0+dfsg-3_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 1146120 bytes: control archive=1008 bytes.
839 bytes, 18 lines control
222 bytes, 3 lines md5sums
37 bytes, 1 lines shlibs
68 bytes, 2 lines triggers
Package: libmmb4.0
Source: macromoleculebuilder
Version: 4.0.0+dfsg-3
Architecture: armhf
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Installed-Size: 4376
Depends: libc6 (>= 2.33), libgcc-s1 (>= 3.5), libopenmm8.0 (>= 8.0.0+dfsg), libsimbody3.7 (>= 3.7+dfsg), libsimtkmolmodel3.1 (>= 3.1.0), libstdc++6 (>= 13.1), zlib1g (>= 1:1.2.6)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: https://simtk.org/projects/rnatoolbox
Description: shared library of MacroMoleculeBuilder
MacroMoleculeBuilder, previously known as RNABuilder, can be used for morphing,
homology modeling, folding (e.g. using base pairing contacts), redesigning
complexes, fitting to low-resolution density maps, predicting local
rearrangements upon mutation, and many other applications.
.
This package contains the shared library.
drwxr-xr-x root/root 0 2023-06-23 05:37 ./
drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/
drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/lib/
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-rw-r--r-- root/root 1550 2023-06-23 05:37 ./usr/share/doc/libmmb4.0/copyright
mmb-dbgsym_4.0.0+dfsg-3_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 1597132 bytes: control archive=540 bytes.
364 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: mmb-dbgsym
Source: macromoleculebuilder
Version: 4.0.0+dfsg-3
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Section: debug
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drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/lib/debug/
drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/lib/debug/.build-id/
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drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/share/
drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/share/doc/
lrwxrwxrwx root/root 0 2023-06-23 05:37 ./usr/share/doc/mmb-dbgsym -> mmb
mmb_4.0.0+dfsg-3_armhf.deb
--------------------------
new Debian package, version 2.0.
size 25300 bytes: control archive=884 bytes.
771 bytes, 15 lines control
242 bytes, 4 lines md5sums
Package: mmb
Source: macromoleculebuilder
Version: 4.0.0+dfsg-3
Architecture: armhf
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Installed-Size: 92
Depends: mmb-common, libc6 (>= 2.34), libgcc-s1 (>= 3.5), libmmb4.0 (>= 4.0.0+dfsg), libsimbody3.7 (>= 3.7+dfsg), libsimtkmolmodel3.1 (>= 3.1.0), libstdc++6 (>= 13.1)
Section: science
Priority: optional
Homepage: https://simtk.org/projects/rnatoolbox
Description: model the structure and dynamics of macromolecules
MacroMoleculeBuilder, previously known as RNABuilder, can be used for morphing,
homology modeling, folding (e.g. using base pairing contacts), redesigning
complexes, fitting to low-resolution density maps, predicting local
rearrangements upon mutation, and many other applications.
drwxr-xr-x root/root 0 2023-06-23 05:37 ./
drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/
drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/bin/
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drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/share/
drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/share/doc/
drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/share/doc/mmb/
-rw-r--r-- root/root 1185 2023-06-23 05:37 ./usr/share/doc/mmb/changelog.Debian.gz
-rw-r--r-- root/root 1550 2023-06-23 05:37 ./usr/share/doc/mmb/copyright
drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/share/man/
drwxr-xr-x root/root 0 2023-06-23 05:37 ./usr/share/man/man1/
-rw-r--r-- root/root 792 2023-06-23 05:37 ./usr/share/man/man1/MMB.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 564448
Build-Time: 693
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 687
Job: macromoleculebuilder_4.0.0+dfsg-3
Machine Architecture: armhf
Package: macromoleculebuilder
Package-Time: 1408
Source-Version: 4.0.0+dfsg-3
Space: 564448
Status: successful
Version: 4.0.0+dfsg-3
--------------------------------------------------------------------------------
Finished at 2023-12-01T18:48:01Z
Build needed 00:23:28, 564448k disk space