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

+==============================================================================+
| macromoleculebuilder 4.0.0+dfsg-5 (riscv64)  Mon, 06 Jan 2025 22:42:13 +0000 |
+==============================================================================+

Package: macromoleculebuilder
Version: 4.0.0+dfsg-5
Source Version: 4.0.0+dfsg-5
Distribution: unstable
Machine Architecture: amd64
Host Architecture: riscv64
Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-7db754d6-fd58-45a5-ae4c-2c5b547a7cfb' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-gNvqyC/resolver-zge6RF' with '<<RESOLVERDIR>>'

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

Get:1 http://localhost:3142/debian unstable InRelease [205 kB]
Get:2 http://localhost:3142/debian unstable/non-free-firmware Sources [6880 B]
Get:3 http://localhost:3142/debian unstable/contrib Sources [63.1 kB]
Get:4 http://localhost:3142/debian unstable/main Sources [10.8 MB]
Get:5 http://localhost:3142/debian unstable/non-free Sources [83.5 kB]
Get:6 http://localhost:3142/debian unstable/main amd64 Packages [9993 kB]
Get:7 http://localhost:3142/debian unstable/main riscv64 Packages [9633 kB]
Fetched 30.8 MB in 3s (11.7 MB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages were automatically installed and are no longer required:
  gpgv libffi8 libgcrypt20 libgnutls30t64 libgpg-error0 libidn2-0 libp11-kit0
  libtasn1-6 libunistring5
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sqv
The following packages will be upgraded:
  apt base-files base-passwd bash binutils binutils-common
  binutils-x86-64-linux-gnu bsdutils coreutils cpp-14 cpp-14-x86-64-linux-gnu
  dash debconf debianutils dpkg dpkg-dev e2fsprogs g++-14
  g++-14-x86-64-linux-gnu gcc-14 gcc-14-base gcc-14-x86-64-linux-gnu gpgv gzip
  init-system-helpers libacl1 libapt-pkg6.0t64 libasan8 libatomic1
  libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6
  libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libctf-nobfd0 libctf0
  libdebconfclient0 libdpkg-perl libext2fs2t64 libgcc-14-dev libgcc-s1
  libgcrypt20 libgmp10 libgnutls30t64 libgomp1 libgpg-error0 libgprofng0
  libhogweed6t64 libhwasan0 libidn2-0 libitm1 libjansson4 liblsan0 liblz4-1
  liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libnettle8t64 libp11-kit0
  libpam-modules libpam-modules-bin libpam0g libpcre2-8-0 libperl5.40
  libquadmath0 libseccomp2 libselinux1 libsemanage2 libsframe1 libsmartcols1
  libss2 libssl3t64 libstdc++-14-dev libstdc++6 libsystemd0 libtasn1-6
  libtinfo6 libtsan2 libubsan1 libudev1 libunistring5 libuuid1 libxxhash0
  libzstd1 linux-libc-dev login login.defs logsave make mount ncurses-bin
  openssl-provider-legacy passwd perl perl-base perl-modules-5.40
  sysvinit-utils tar tzdata util-linux xz-utils zlib1g
111 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 114 MB of archives.
After this operation, 2856 kB of additional disk space will be used.
Get:1 http://localhost:3142/debian unstable/main amd64 libc6-dev amd64 2.40-5 [1957 kB]
Get:2 http://localhost:3142/debian unstable/main amd64 libc-dev-bin amd64 2.40-5 [52.4 kB]
Get:3 http://localhost:3142/debian unstable/main amd64 linux-libc-dev all 6.12.8-1 [2484 kB]
Get:4 http://localhost:3142/debian unstable/main amd64 libcc1-0 amd64 14.2.0-12 [42.8 kB]
Get:5 http://localhost:3142/debian unstable/main amd64 gcc-14-base amd64 14.2.0-12 [48.3 kB]
Get:6 http://localhost:3142/debian unstable/main amd64 libgcc-s1 amd64 14.2.0-12 [72.7 kB]
Get:7 http://localhost:3142/debian unstable/main amd64 libgomp1 amd64 14.2.0-12 [137 kB]
Get:8 http://localhost:3142/debian unstable/main amd64 libitm1 amd64 14.2.0-12 [25.9 kB]
Get:9 http://localhost:3142/debian unstable/main amd64 libatomic1 amd64 14.2.0-12 [9300 B]
Get:10 http://localhost:3142/debian unstable/main amd64 libasan8 amd64 14.2.0-12 [2727 kB]
Get:11 http://localhost:3142/debian unstable/main amd64 liblsan0 amd64 14.2.0-12 [1205 kB]
Get:12 http://localhost:3142/debian unstable/main amd64 libtsan2 amd64 14.2.0-12 [2460 kB]
Get:13 http://localhost:3142/debian unstable/main amd64 libubsan1 amd64 14.2.0-12 [1075 kB]
Get:14 http://localhost:3142/debian unstable/main amd64 libhwasan0 amd64 14.2.0-12 [1489 kB]
Get:15 http://localhost:3142/debian unstable/main amd64 libquadmath0 amd64 14.2.0-12 [145 kB]
Get:16 http://localhost:3142/debian unstable/main amd64 gcc-14 amd64 14.2.0-12 [534 kB]
Get:17 http://localhost:3142/debian unstable/main amd64 g++-14 amd64 14.2.0-12 [20.5 kB]
Get:18 http://localhost:3142/debian unstable/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-12 [12.1 MB]
Get:19 http://localhost:3142/debian unstable/main amd64 libstdc++-14-dev amd64 14.2.0-12 [2372 kB]
Get:20 http://localhost:3142/debian unstable/main amd64 libgcc-14-dev amd64 14.2.0-12 [2673 kB]
Get:21 http://localhost:3142/debian unstable/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-12 [21.4 MB]
Get:22 http://localhost:3142/debian unstable/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-12 [11.0 MB]
Get:23 http://localhost:3142/debian unstable/main amd64 cpp-14 amd64 14.2.0-12 [1280 B]
Get:24 http://localhost:3142/debian unstable/main amd64 libstdc++6 amd64 14.2.0-12 [714 kB]
Get:25 http://localhost:3142/debian unstable/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1+b1 [88.9 kB]
Get:26 http://localhost:3142/debian unstable/main amd64 libgprofng0 amd64 2.43.50.20241230-1 [809 kB]
Get:27 http://localhost:3142/debian unstable/main amd64 libctf0 amd64 2.43.50.20241230-1 [88.5 kB]
Get:28 http://localhost:3142/debian unstable/main amd64 libctf-nobfd0 amd64 2.43.50.20241230-1 [155 kB]
Get:29 http://localhost:3142/debian unstable/main amd64 libjansson4 amd64 2.14-2+b3 [39.8 kB]
Get:30 http://localhost:3142/debian unstable/main amd64 libsframe1 amd64 2.43.50.20241230-1 [77.6 kB]
Get:31 http://localhost:3142/debian unstable/main amd64 libzstd1 amd64 1.5.6+dfsg-2 [300 kB]
Get:32 http://localhost:3142/debian unstable/main amd64 libbinutils amd64 2.43.50.20241230-1 [532 kB]
Get:33 http://localhost:3142/debian unstable/main amd64 binutils-common amd64 2.43.50.20241230-1 [2628 kB]
Get:34 http://localhost:3142/debian unstable/main amd64 binutils amd64 2.43.50.20241230-1 [68.4 kB]
Get:35 http://localhost:3142/debian unstable/main amd64 binutils-x86-64-linux-gnu amd64 2.43.50.20241230-1 [2274 kB]
Get:36 http://localhost:3142/debian unstable/main amd64 libgmp10 amd64 2:6.3.0+dfsg-3 [560 kB]
Get:37 http://localhost:3142/debian unstable/main amd64 libmpfr6 amd64 4.2.1-1+b2 [724 kB]
Get:38 http://localhost:3142/debian unstable/main amd64 libmpc3 amd64 1.3.1-1+b3 [52.2 kB]
Get:39 http://localhost:3142/debian unstable/main amd64 libc6 amd64 2.40-5 [2810 kB]
Get:40 http://localhost:3142/debian unstable/main amd64 base-files amd64 13.6 [72.8 kB]
Get:41 http://localhost:3142/debian unstable/main amd64 debianutils amd64 5.21 [92.1 kB]
Get:42 http://localhost:3142/debian unstable/main amd64 bash amd64 5.2.37-1 [1501 kB]
Get:43 http://localhost:3142/debian unstable/main amd64 bsdutils amd64 1:2.40.2-13 [106 kB]
Get:44 http://localhost:3142/debian unstable/main amd64 coreutils amd64 9.5-1+b1 [2922 kB]
Get:45 http://localhost:3142/debian unstable/main amd64 libperl5.40 amd64 5.40.0-8 [4320 kB]
Get:46 http://localhost:3142/debian unstable/main amd64 perl amd64 5.40.0-8 [267 kB]
Get:47 http://localhost:3142/debian unstable/main amd64 perl-base amd64 5.40.0-8 [1675 kB]
Get:48 http://localhost:3142/debian unstable/main amd64 perl-modules-5.40 all 5.40.0-8 [3015 kB]
Get:49 http://localhost:3142/debian unstable/main amd64 debconf all 1.5.89 [120 kB]
Get:50 http://localhost:3142/debian unstable/main amd64 dash amd64 0.5.12-10 [95.5 kB]
Get:51 http://localhost:3142/debian unstable/main amd64 libxxhash0 amd64 0.8.3-2 [27.1 kB]
Get:52 http://localhost:3142/debian unstable/main amd64 liblz4-1 amd64 1.9.4-4 [60.1 kB]
Get:53 http://localhost:3142/debian unstable/main amd64 liblzma5 amd64 5.6.3-1+b1 [272 kB]
Get:54 http://localhost:3142/debian unstable/main amd64 openssl-provider-legacy amd64 3.4.0-2 [301 kB]
Get:55 http://localhost:3142/debian unstable/main amd64 libssl3t64 amd64 3.4.0-2 [2302 kB]
Get:56 http://localhost:3142/debian unstable/main amd64 libcap2 amd64 1:2.66-5+b1 [27.8 kB]
Get:57 http://localhost:3142/debian unstable/main amd64 libsystemd0 amd64 257.1-7 [449 kB]
Get:58 http://localhost:3142/debian unstable/main amd64 libudev1 amd64 257.1-7 [148 kB]
Get:59 http://localhost:3142/debian unstable/main amd64 libapt-pkg6.0t64 amd64 2.9.21 [1115 kB]
Get:60 http://localhost:3142/debian unstable/main amd64 tar amd64 1.35+dfsg-3.1 [815 kB]
Get:61 http://localhost:3142/debian unstable/main amd64 dpkg amd64 1.22.13 [1534 kB]
Get:62 http://localhost:3142/debian unstable/main amd64 gzip amd64 1.12-1.2 [134 kB]
Get:63 http://localhost:3142/debian unstable/main amd64 ncurses-bin amd64 6.5-2+b1 [434 kB]
Get:64 http://localhost:3142/debian unstable/main amd64 libuuid1 amd64 2.40.2-13 [36.1 kB]
Get:65 http://localhost:3142/debian unstable/main amd64 libblkid1 amd64 2.40.2-13 [168 kB]
Get:66 http://localhost:3142/debian unstable/main amd64 libmount1 amd64 2.40.2-13 [199 kB]
Get:67 http://localhost:3142/debian unstable/main amd64 libsmartcols1 amd64 2.40.2-13 [139 kB]
Get:68 http://localhost:3142/debian unstable/main amd64 util-linux amd64 2.40.2-13 [1209 kB]
Get:69 http://localhost:3142/debian unstable/main amd64 mount amd64 2.40.2-13 [155 kB]
Get:70 http://localhost:3142/debian unstable/main amd64 libpcre2-8-0 amd64 10.44-5 [275 kB]
Get:71 http://localhost:3142/debian unstable/main amd64 libselinux1 amd64 3.7-3+b1 [77.0 kB]
Get:72 http://localhost:3142/debian unstable/main amd64 libnettle8t64 amd64 3.10-1+b1 [305 kB]
Get:73 http://localhost:3142/debian unstable/main amd64 libhogweed6t64 amd64 3.10-1+b1 [335 kB]
Get:74 http://localhost:3142/debian unstable/main amd64 sqv amd64 1.2.1-5 [615 kB]
Get:75 http://localhost:3142/debian unstable/main amd64 libdebconfclient0 amd64 0.277 [10.4 kB]
Get:76 http://localhost:3142/debian unstable/main amd64 base-passwd amd64 3.6.6 [53.1 kB]
Get:77 http://localhost:3142/debian unstable/main amd64 libseccomp2 amd64 2.5.5-2 [47.8 kB]
Get:78 http://localhost:3142/debian unstable/main amd64 apt amd64 2.9.21 [1390 kB]
Get:79 http://localhost:3142/debian unstable/main amd64 init-system-helpers all 1.68 [38.7 kB]
Get:80 http://localhost:3142/debian unstable/main amd64 libc-bin amd64 2.40-5 [627 kB]
Get:81 http://localhost:3142/debian unstable/main amd64 sysvinit-utils amd64 3.11-1 [33.1 kB]
Get:82 http://localhost:3142/debian unstable/main amd64 libaudit-common all 1:4.0.2-2 [12.7 kB]
Get:83 http://localhost:3142/debian unstable/main amd64 libcap-ng0 amd64 0.8.5-4 [17.3 kB]
Get:84 http://localhost:3142/debian unstable/main amd64 libaudit1 amd64 1:4.0.2-2 [54.9 kB]
Get:85 http://localhost:3142/debian unstable/main amd64 libpam0g amd64 1.5.3-7+b1 [68.3 kB]
Get:86 http://localhost:3142/debian unstable/main amd64 libpam-modules-bin amd64 1.5.3-7+b1 [54.1 kB]
Get:87 http://localhost:3142/debian unstable/main amd64 libpam-modules amd64 1.5.3-7+b1 [267 kB]
Get:88 http://localhost:3142/debian unstable/main amd64 logsave amd64 1.47.2-1 [23.9 kB]
Get:89 http://localhost:3142/debian unstable/main amd64 libext2fs2t64 amd64 1.47.2-1 [212 kB]
Get:90 http://localhost:3142/debian unstable/main amd64 e2fsprogs amd64 1.47.2-1 [590 kB]
Get:91 http://localhost:3142/debian unstable/main amd64 login amd64 1:4.16.0-2+really2.40.2-13 [81.9 kB]
Get:92 http://localhost:3142/debian unstable/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB]
Get:93 http://localhost:3142/debian unstable/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB]
Get:94 http://localhost:3142/debian unstable/main amd64 gpgv amd64 2.2.45-2 [219 kB]
Get:95 http://localhost:3142/debian unstable/main amd64 libacl1 amd64 2.3.2-2+b1 [32.9 kB]
Get:96 http://localhost:3142/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get:97 http://localhost:3142/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB]
Get:98 http://localhost:3142/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get:99 http://localhost:3142/debian unstable/main amd64 libtasn1-6 amd64 4.19.0-3+b3 [49.5 kB]
Get:100 http://localhost:3142/debian unstable/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB]
Get:101 http://localhost:3142/debian unstable/main amd64 libmd0 amd64 1.1.0-2+b1 [36.3 kB]
Get:102 http://localhost:3142/debian unstable/main amd64 libtinfo6 amd64 6.5-2+b1 [344 kB]
Get:103 http://localhost:3142/debian unstable/main amd64 login.defs all 1:4.16.0-7 [185 kB]
Get:104 http://localhost:3142/debian unstable/main amd64 libsemanage2 amd64 3.7-2+b1 [91.2 kB]
Get:105 http://localhost:3142/debian unstable/main amd64 passwd amd64 1:4.16.0-7 [1233 kB]
Get:106 http://localhost:3142/debian unstable/main amd64 tzdata all 2024b-4 [256 kB]
Get:107 http://localhost:3142/debian unstable/main amd64 xz-utils amd64 5.6.3-1+b1 [542 kB]
Get:108 http://localhost:3142/debian unstable/main amd64 dpkg-dev all 1.22.13 [1334 kB]
Get:109 http://localhost:3142/debian unstable/main amd64 libdpkg-perl all 1.22.13 [642 kB]
Get:110 http://localhost:3142/debian unstable/main amd64 make amd64 4.4.1-1 [463 kB]
Get:111 http://localhost:3142/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get:112 http://localhost:3142/debian unstable/main amd64 libss2 amd64 1.47.2-1 [28.7 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libsframe1:amd64 (2.43.50.20241230-1) ...
Setting up libjansson4:amd64 (2.14-2+b3) ...
Setting up tzdata (2024b-4) ...

Current default time zone: 'Etc/UTC'
Local time is now:      Mon Jan  6 22:42:30 UTC 2025.
Universal Time is now:  Mon Jan  6 22:42:30 UTC 2025.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

Setting up make (4.4.1-1) ...
Setting up libmpfr6:amd64 (4.2.1-1+b2) ...
Setting up xz-utils (5.6.3-1+b1) ...
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Setting up cpp-14 (14.2.0-12) ...
Setting up libubsan1:amd64 (14.2.0-12) ...
Setting up mount (2.40.2-13) ...
Setting up perl-modules-5.40 (5.40.0-8) ...
Setting up libhwasan0:amd64 (14.2.0-12) ...
Setting up libasan8:amd64 (14.2.0-12) ...
Setting up libsemanage2:amd64 (3.7-2+b1) ...
Setting up libtsan2:amd64 (14.2.0-12) ...
Setting up libbinutils:amd64 (2.43.50.20241230-1) ...
Setting up libc-dev-bin (2.40-5) ...
Setting up libcc1-0:amd64 (14.2.0-12) ...
Setting up liblsan0:amd64 (14.2.0-12) ...
Setting up libitm1:amd64 (14.2.0-12) ...
Setting up login (1:4.16.0-2+really2.40.2-13) ...
Setting up libctf0:amd64 (2.43.50.20241230-1) ...
Setting up e2fsprogs (1.47.2-1) ...
Setting up libperl5.40:amd64 (5.40.0-8) ...
Setting up perl (5.40.0-8) ...
Setting up libgprofng0:amd64 (2.43.50.20241230-1) ...
Setting up libdpkg-perl (1.22.13) ...
Setting up passwd (1:4.16.0-7) ...
Setting up libc6-dev:amd64 (2.40-5) ...
Setting up libgcc-14-dev:amd64 (14.2.0-12) ...
Setting up libstdc++-14-dev:amd64 (14.2.0-12) ...
Setting up binutils-x86-64-linux-gnu (2.43.50.20241230-1) ...
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Setting up dpkg-dev (1.22.13) ...
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Setting up g++-14 (14.2.0-12) ...
Processing triggers for debianutils (5.21) ...
Processing triggers for libc-bin (2.40-5) ...

+------------------------------------------------------------------------------+
| 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 2576 kB of source archives.
Get:1 http://localhost:3142/debian unstable/main macromoleculebuilder 4.0.0+dfsg-5 (dsc) [2491 B]
Get:2 http://localhost:3142/debian unstable/main macromoleculebuilder 4.0.0+dfsg-5 (tar) [2567 kB]
Get:3 http://localhost:3142/debian unstable/main macromoleculebuilder 4.0.0+dfsg-5 (diff) [5964 B]
Fetched 2576 kB in 1s (1753 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-gNvqyC/macromoleculebuilder-4.0.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/macromoleculebuilder-gNvqyC' with '<<BUILDDIR>>'

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


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

Merged Build-Depends: architecture-is-64-bit, asciidoc-base, cmake, debhelper-compat (= 13), docbook-xml, dpkg-dev (>= 1.22.5), gemmi-dev (>= 0.6.2+ds-2), libopenmm-dev, libseqan2-dev, libsimbody-dev, libsimtkmolmodel-dev (>= 3.1.0), libsimtkmolmodel-plugins, libstb-dev, tao-pegtl-dev, zlib1g-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-riscv64:amd64, libc-dev:riscv64, libstdc++-dev:riscv64
Filtered Build-Depends: architecture-is-64-bit, asciidoc-base, cmake, debhelper-compat (= 13), docbook-xml, dpkg-dev (>= 1.22.5), gemmi-dev (>= 0.6.2+ds-2), libopenmm-dev, libseqan2-dev, libsimbody-dev, libsimtkmolmodel-dev (>= 3.1.0), libsimtkmolmodel-plugins, libstb-dev, tao-pegtl-dev, zlib1g-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-riscv64:amd64, libc-dev:riscv64, libstdc++-dev:riscv64
dpkg-deb: warning: root directory /<<RESOLVERDIR>>/sbuild-build-depends-main-dummy has unusual owner or group 1000:119
dpkg-deb: Hint: you might need to pass --root-owner-group, see <https://wiki.debian.org/Teams/Dpkg/RootlessBuilds> for further details
dpkg-deb: warning: ignoring 1 warning about the control file(s)
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [612 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [972 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [1018 B]
Fetched 2602 B in 0s (0 B/s)
Reading package lists...
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
Execute external solver...
The following package was automatically installed and is no longer required:
  gpgv
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
  architecture-properties:riscv64 asciidoc-base asciidoc-common autoconf
  automake autopoint autotools-dev binutils-riscv64-linux-gnu bsdextrautils
  cmake cmake-data cpp-14-riscv64-linux-gnu cpp-riscv64-linux-gnu
  crossbuild-essential-riscv64 debhelper dh-autoreconf dh-strip-nondeterminism
  docbook-xml docbook-xsl dwz fakeroot file freeglut3-dev:riscv64
  g++-14-riscv64-linux-gnu g++-riscv64-linux-gnu gcc-14-base:riscv64
  gcc-14-cross-base gcc-14-riscv64-linux-gnu gcc-14-riscv64-linux-gnu-base
  gcc-riscv64-linux-gnu gemmi-dev:riscv64 gettext gettext-base groff-base
  intltool-debian libarchive-zip-perl libarchive13t64 libasan8:riscv64
  libasan8-riscv64-cross libatomic1:riscv64 libatomic1-riscv64-cross
  libblas-dev:riscv64 libblas3:riscv64 libbrotli1 libbsd0:riscv64
  libc6:riscv64 libc6-dev:riscv64 libc6-dev-riscv64-cross libc6-riscv64-cross
  libcrypt-dev:riscv64 libcrypt1:riscv64 libcurl4t64 libdebhelper-perl
  libdrm-amdgpu1:riscv64 libdrm-common libdrm-radeon1:riscv64 libdrm2:riscv64
  libedit2:riscv64 libelf1t64 libelf1t64:riscv64 libexpat1 libexpat1:riscv64
  libfakeroot libffi8:riscv64 libfile-stripnondeterminism-perl libgbm1:riscv64
  libgcc-14-dev:riscv64 libgcc-14-dev-riscv64-cross libgcc-s1:riscv64
  libgcc-s1-riscv64-cross libgfortran5:riscv64 libgl-dev:riscv64
  libgl1:riscv64 libgl1-mesa-dri:riscv64 libglapi-mesa:riscv64
  libglu1-mesa:riscv64 libglu1-mesa-dev:riscv64 libglut-dev:riscv64
  libglut3.12:riscv64 libglvnd0:riscv64 libglx-dev:riscv64
  libglx-mesa0:riscv64 libglx0:riscv64 libgomp1:riscv64 libgomp1-riscv64-cross
  libgssapi-krb5-2 libice-dev:riscv64 libice6:riscv64 libicu72
  libicu72:riscv64 libitm1:riscv64 libitm1-riscv64-cross libjsoncpp26
  libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev:riscv64
  liblapack3:riscv64 libldap-2.5-0 libllvm19:riscv64 liblsan0:riscv64
  liblsan0-riscv64-cross liblzma5:riscv64 libmagic-mgc libmagic1t64
  libmd0:riscv64 libncursesw6 libnghttp2-14 libnsl2 libopengl-dev:riscv64
  libopengl0:riscv64 libopenmm-dev:riscv64 libopenmm8.1:riscv64 libpipeline1
  libproc2-0 libpsl5t64 libpython3-stdlib libpython3.12-minimal
  libpython3.12-stdlib libreadline8t64 librhash1 librtmp1 libsasl2-2
  libsasl2-modules-db libsensors-config libsensors5:riscv64 libseqan2-dev
  libsimbody-dev:riscv64 libsimbody3.7:riscv64 libsimtkmolmodel-dev:riscv64
  libsimtkmolmodel-plugins:riscv64 libsimtkmolmodel3.1t64:riscv64
  libsm-dev:riscv64 libsm6:riscv64 libsqlite3-0 libssh2-1t64
  libstb-dev:riscv64 libstb0t64:riscv64 libstdc++-14-dev:riscv64
  libstdc++-14-dev-riscv64-cross libstdc++6:riscv64 libstdc++6-riscv64-cross
  libtinfo6:riscv64 libtirpc-common libtirpc3t64 libtool libtsan2:riscv64
  libtsan2-riscv64-cross libubsan1:riscv64 libubsan1-riscv64-cross
  libuchardet0 libuuid1:riscv64 libuv1t64 libvulkan1:riscv64
  libwayland-server0:riscv64 libx11-6 libx11-6:riscv64 libx11-data libx11-dev
  libx11-dev:riscv64 libx11-xcb1:riscv64 libxau-dev libxau-dev:riscv64 libxau6
  libxau6:riscv64 libxcb-dri2-0:riscv64 libxcb-dri3-0:riscv64
  libxcb-glx0:riscv64 libxcb-present0:riscv64 libxcb-randr0:riscv64
  libxcb-shm0:riscv64 libxcb-sync1:riscv64 libxcb-xfixes0:riscv64 libxcb1
  libxcb1:riscv64 libxcb1-dev libxcb1-dev:riscv64 libxdmcp-dev
  libxdmcp-dev:riscv64 libxdmcp6 libxdmcp6:riscv64 libxext-dev:riscv64
  libxext6:riscv64 libxfixes-dev:riscv64 libxfixes3:riscv64 libxi-dev:riscv64
  libxi6:riscv64 libxml2 libxml2:riscv64 libxml2-utils libxmu-dev:riscv64
  libxmu-headers libxmu6:riscv64 libxshmfence1:riscv64 libxslt1.1
  libxt-dev:riscv64 libxt6t64:riscv64 libxxf86vm1:riscv64 libz3-4:riscv64
  libzstd1:riscv64 linux-libc-dev-riscv64-cross m4 man-db media-types
  mesa-libgallium:riscv64 netbase po-debconf procps python3 python3-minimal
  python3.12 python3.12-minimal readline-common sensible-utils sgml-base
  sgml-data tao-pegtl-dev uuid-dev:riscv64 x11-common x11proto-dev xml-core
  xorg-sgml-doctools xsltproc xtrans-dev zlib1g:riscv64 zlib1g-dev:riscv64
Suggested packages:
  asciidoc-doc docbook-utils source-highlight autoconf-archive gnu-standards
  autoconf-doc binutils-doc cmake-doc cmake-format elpa-cmake-mode ninja-build
  gcc-14-locales cpp-14-doc cpp-doc dh-make docbook docbook-defguide
  docbook-dsssl dbtoepub docbook-xsl-doc-html | docbook-xsl-doc-pdf
  | docbook-xsl-doc-text | docbook-xsl-doc docbook-xsl-saxon fop libsaxon-java
  libxalan2-java libxslthl-java xalan gcc-14-doc manpages-dev flex bison
  gdb-riscv64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev
  groff lrzip liblapack-doc:riscv64 glibc-doc:riscv64 libc-l10n:riscv64
  locales:riscv64 libnss-nis:riscv64 libnss-nisplus:riscv64
  manpages-dev:riscv64 krb5-doc krb5-user libice-doc:riscv64 lm-sensors
  lm-sensors:riscv64 libsm-doc:riscv64 libstdc++-14-doc:riscv64 libtool-doc
  gfortran | fortran95-compiler gcj-jdk uuid-runtime:riscv64 libx11-doc
  libx11-doc:riscv64 libxcb-doc libxcb-doc:riscv64 libxext-doc:riscv64
  libxt-doc:riscv64 m4-doc apparmor less www-browser libmail-box-perl
  python3-doc python3-tk python3-venv python3.12-venv python3.12-doc
  binfmt-support readline-doc sgml-base-doc perlsgml w3-recs opensp
Recommended packages:
  xmlto curl | wget | lynx libidn2-0:riscv64 ca-certificates
  libarchive-cpio-perl krb5-locales libldap-common libgpm2 publicsuffix
  libsasl2-modules libltdl-dev mesa-vulkan-drivers:riscv64
  | vulkan-icd:riscv64 libmail-sendmail-perl psmisc linux-sysctl-defaults
The following NEW packages will be installed:
  architecture-properties:riscv64 asciidoc-base asciidoc-common autoconf
  automake autopoint autotools-dev binutils-riscv64-linux-gnu bsdextrautils
  cmake cmake-data cpp-14-riscv64-linux-gnu cpp-riscv64-linux-gnu
  crossbuild-essential-riscv64 debhelper dh-autoreconf dh-strip-nondeterminism
  docbook-xml docbook-xsl dwz fakeroot file freeglut3-dev:riscv64
  g++-14-riscv64-linux-gnu g++-riscv64-linux-gnu gcc-14-base:riscv64
  gcc-14-cross-base gcc-14-riscv64-linux-gnu gcc-14-riscv64-linux-gnu-base
  gcc-riscv64-linux-gnu gemmi-dev:riscv64 gettext gettext-base groff-base
  intltool-debian libarchive-zip-perl libarchive13t64 libasan8:riscv64
  libasan8-riscv64-cross libatomic1:riscv64 libatomic1-riscv64-cross
  libblas-dev:riscv64 libblas3:riscv64 libbrotli1 libbsd0:riscv64
  libc6:riscv64 libc6-dev:riscv64 libc6-dev-riscv64-cross libc6-riscv64-cross
  libcrypt-dev:riscv64 libcrypt1:riscv64 libcurl4t64 libdebhelper-perl
  libdrm-amdgpu1:riscv64 libdrm-common libdrm-radeon1:riscv64 libdrm2:riscv64
  libedit2:riscv64 libelf1t64 libelf1t64:riscv64 libexpat1 libexpat1:riscv64
  libfakeroot libffi8:riscv64 libfile-stripnondeterminism-perl libgbm1:riscv64
  libgcc-14-dev:riscv64 libgcc-14-dev-riscv64-cross libgcc-s1:riscv64
  libgcc-s1-riscv64-cross libgfortran5:riscv64 libgl-dev:riscv64
  libgl1:riscv64 libgl1-mesa-dri:riscv64 libglapi-mesa:riscv64
  libglu1-mesa:riscv64 libglu1-mesa-dev:riscv64 libglut-dev:riscv64
  libglut3.12:riscv64 libglvnd0:riscv64 libglx-dev:riscv64
  libglx-mesa0:riscv64 libglx0:riscv64 libgomp1:riscv64 libgomp1-riscv64-cross
  libgssapi-krb5-2 libice-dev:riscv64 libice6:riscv64 libicu72
  libicu72:riscv64 libitm1:riscv64 libitm1-riscv64-cross libjsoncpp26
  libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev:riscv64
  liblapack3:riscv64 libldap-2.5-0 libllvm19:riscv64 liblsan0:riscv64
  liblsan0-riscv64-cross liblzma5:riscv64 libmagic-mgc libmagic1t64
  libmd0:riscv64 libncursesw6 libnghttp2-14 libnsl2 libopengl-dev:riscv64
  libopengl0:riscv64 libopenmm-dev:riscv64 libopenmm8.1:riscv64 libpipeline1
  libproc2-0 libpsl5t64 libpython3-stdlib libpython3.12-minimal
  libpython3.12-stdlib libreadline8t64 librhash1 librtmp1 libsasl2-2
  libsasl2-modules-db libsensors-config libsensors5:riscv64 libseqan2-dev
  libsimbody-dev:riscv64 libsimbody3.7:riscv64 libsimtkmolmodel-dev:riscv64
  libsimtkmolmodel-plugins:riscv64 libsimtkmolmodel3.1t64:riscv64
  libsm-dev:riscv64 libsm6:riscv64 libsqlite3-0 libssh2-1t64
  libstb-dev:riscv64 libstb0t64:riscv64 libstdc++-14-dev:riscv64
  libstdc++-14-dev-riscv64-cross libstdc++6:riscv64 libstdc++6-riscv64-cross
  libtinfo6:riscv64 libtirpc-common libtirpc3t64 libtool libtsan2:riscv64
  libtsan2-riscv64-cross libubsan1:riscv64 libubsan1-riscv64-cross
  libuchardet0 libuuid1:riscv64 libuv1t64 libvulkan1:riscv64
  libwayland-server0:riscv64 libx11-6 libx11-6:riscv64 libx11-data libx11-dev
  libx11-dev:riscv64 libx11-xcb1:riscv64 libxau-dev libxau-dev:riscv64 libxau6
  libxau6:riscv64 libxcb-dri2-0:riscv64 libxcb-dri3-0:riscv64
  libxcb-glx0:riscv64 libxcb-present0:riscv64 libxcb-randr0:riscv64
  libxcb-shm0:riscv64 libxcb-sync1:riscv64 libxcb-xfixes0:riscv64 libxcb1
  libxcb1:riscv64 libxcb1-dev libxcb1-dev:riscv64 libxdmcp-dev
  libxdmcp-dev:riscv64 libxdmcp6 libxdmcp6:riscv64 libxext-dev:riscv64
  libxext6:riscv64 libxfixes-dev:riscv64 libxfixes3:riscv64 libxi-dev:riscv64
  libxi6:riscv64 libxml2 libxml2:riscv64 libxml2-utils libxmu-dev:riscv64
  libxmu-headers libxmu6:riscv64 libxshmfence1:riscv64 libxslt1.1
  libxt-dev:riscv64 libxt6t64:riscv64 libxxf86vm1:riscv64 libz3-4:riscv64
  libzstd1:riscv64 linux-libc-dev-riscv64-cross m4 man-db media-types
  mesa-libgallium:riscv64 netbase po-debconf procps python3 python3-minimal
  python3.12 python3.12-minimal readline-common
  sbuild-build-depends-main-dummy:riscv64 sensible-utils sgml-base sgml-data
  tao-pegtl-dev uuid-dev:riscv64 x11-common x11proto-dev xml-core
  xorg-sgml-doctools xsltproc xtrans-dev zlib1g:riscv64 zlib1g-dev:riscv64
0 upgraded, 228 newly installed, 0 to remove and 0 not upgraded.
Need to get 244 MB of archives.
After this operation, 1199 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1048 B]
Get:2 http://localhost:3142/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.8-3 [817 kB]
Get:3 http://localhost:3142/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get:4 http://localhost:3142/debian unstable/main amd64 python3.12-minimal amd64 3.12.8-3 [2162 kB]
Get:5 http://localhost:3142/debian unstable/main amd64 python3-minimal amd64 3.12.8-1 [26.9 kB]
Get:6 http://localhost:3142/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB]
Get:7 http://localhost:3142/debian unstable/main amd64 netbase all 6.4 [12.8 kB]
Get:8 http://localhost:3142/debian unstable/main amd64 libncursesw6 amd64 6.5-2+b1 [136 kB]
Get:9 http://localhost:3142/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB]
Get:10 http://localhost:3142/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB]
Get:11 http://localhost:3142/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get:12 http://localhost:3142/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB]
Get:13 http://localhost:3142/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB]
Get:14 http://localhost:3142/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get:15 http://localhost:3142/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB]
Get:16 http://localhost:3142/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB]
Get:17 http://localhost:3142/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB]
Get:18 http://localhost:3142/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get:19 http://localhost:3142/debian unstable/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB]
Get:20 http://localhost:3142/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.8-3 [1969 kB]
Get:21 http://localhost:3142/debian unstable/main amd64 python3.12 amd64 3.12.8-3 [677 kB]
Get:22 http://localhost:3142/debian unstable/main amd64 libpython3-stdlib amd64 3.12.8-1 [9788 B]
Get:23 http://localhost:3142/debian unstable/main amd64 python3 amd64 3.12.8-1 [27.9 kB]
Get:24 http://localhost:3142/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB]
Get:25 http://localhost:3142/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB]
Get:26 http://localhost:3142/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB]
Get:27 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get:28 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get:29 http://localhost:3142/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get:30 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get:31 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.22.5-4 [200 kB]
Get:32 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get:33 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get:34 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.40.2-13 [91.9 kB]
Get:35 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get:36 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get:37 http://localhost:3142/debian unstable/main riscv64 architecture-properties riscv64 0.2.3 [2184 B]
Get:38 http://localhost:3142/debian unstable/main amd64 asciidoc-common all 10.2.1-1 [104 kB]
Get:39 http://localhost:3142/debian unstable/main amd64 xml-core all 0.19 [20.1 kB]
Get:40 http://localhost:3142/debian unstable/main amd64 docbook-xsl all 1.79.2+dfsg-7 [1221 kB]
Get:41 http://localhost:3142/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB]
Get:42 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
Get:43 http://localhost:3142/debian unstable/main amd64 libxml2-utils amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [99.4 kB]
Get:44 http://localhost:3142/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB]
Get:45 http://localhost:3142/debian unstable/main amd64 xsltproc amd64 1.1.35-1.1+b1 [115 kB]
Get:46 http://localhost:3142/debian unstable/main amd64 asciidoc-base all 10.2.1-1 [84.9 kB]
Get:47 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB]
Get:48 http://localhost:3142/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get:49 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get:50 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get:51 http://localhost:3142/debian unstable/main amd64 autopoint all 0.22.5-4 [723 kB]
Get:52 http://localhost:3142/debian unstable/main amd64 binutils-riscv64-linux-gnu amd64 2.43.50.20241230-1 [1428 kB]
Get:53 http://localhost:3142/debian unstable/main amd64 cmake-data all 3.31.3-1 [2268 kB]
Get:54 http://localhost:3142/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB]
Get:55 http://localhost:3142/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB]
Get:56 http://localhost:3142/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB]
Get:57 http://localhost:3142/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB]
Get:58 http://localhost:3142/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.19+dfsg-1 [187 kB]
Get:59 http://localhost:3142/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get:60 http://localhost:3142/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get:61 http://localhost:3142/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get:62 http://localhost:3142/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get:63 http://localhost:3142/debian unstable/main amd64 libcurl4t64 amd64 8.11.1-1 [351 kB]
Get:64 http://localhost:3142/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB]
Get:65 http://localhost:3142/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB]
Get:66 http://localhost:3142/debian unstable/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB]
Get:67 http://localhost:3142/debian unstable/main amd64 cmake amd64 3.31.3-1 [11.9 MB]
Get:68 http://localhost:3142/debian unstable/main amd64 gcc-14-riscv64-linux-gnu-base amd64 14.2.0-12cross1 [48.5 kB]
Get:69 http://localhost:3142/debian unstable/main amd64 cpp-14-riscv64-linux-gnu amd64 14.2.0-12cross1 [13.3 MB]
Get:70 http://localhost:3142/debian unstable/main amd64 cpp-riscv64-linux-gnu amd64 4:14.2.0-1 [4848 B]
Get:71 http://localhost:3142/debian unstable/main amd64 gcc-14-cross-base all 14.2.0-12cross1 [43.7 kB]
Get:72 http://localhost:3142/debian unstable/main amd64 libc6-riscv64-cross all 2.40-4cross1 [1142 kB]
Get:73 http://localhost:3142/debian unstable/main amd64 libgcc-s1-riscv64-cross all 14.2.0-12cross1 [56.7 kB]
Get:74 http://localhost:3142/debian unstable/main amd64 libgomp1-riscv64-cross all 14.2.0-12cross1 [129 kB]
Get:75 http://localhost:3142/debian unstable/main amd64 libitm1-riscv64-cross all 14.2.0-12cross1 [25.2 kB]
Get:76 http://localhost:3142/debian unstable/main amd64 libatomic1-riscv64-cross all 14.2.0-12cross1 [8336 B]
Get:77 http://localhost:3142/debian unstable/main amd64 libasan8-riscv64-cross all 14.2.0-12cross1 [2355 kB]
Get:78 http://localhost:3142/debian unstable/main amd64 liblsan0-riscv64-cross all 14.2.0-12cross1 [1077 kB]
Get:79 http://localhost:3142/debian unstable/main amd64 libtsan2-riscv64-cross all 14.2.0-12cross1 [2231 kB]
Get:80 http://localhost:3142/debian unstable/main amd64 libstdc++6-riscv64-cross all 14.2.0-12cross1 [660 kB]
Get:81 http://localhost:3142/debian unstable/main amd64 libubsan1-riscv64-cross all 14.2.0-12cross1 [979 kB]
Get:82 http://localhost:3142/debian unstable/main amd64 libgcc-14-dev-riscv64-cross all 14.2.0-12cross1 [5173 kB]
Get:83 http://localhost:3142/debian unstable/main amd64 gcc-14-riscv64-linux-gnu amd64 14.2.0-12cross1 [25.7 MB]
Get:84 http://localhost:3142/debian unstable/main amd64 gcc-riscv64-linux-gnu amd64 4:14.2.0-1 [1444 B]
Get:85 http://localhost:3142/debian unstable/main amd64 linux-libc-dev-riscv64-cross all 6.12.6-1cross1 [2291 kB]
Get:86 http://localhost:3142/debian unstable/main amd64 libc6-dev-riscv64-cross all 2.40-4cross1 [3088 kB]
Get:87 http://localhost:3142/debian unstable/main amd64 libstdc++-14-dev-riscv64-cross all 14.2.0-12cross1 [4949 kB]
Get:88 http://localhost:3142/debian unstable/main amd64 g++-14-riscv64-linux-gnu amd64 14.2.0-12cross1 [14.2 MB]
Get:89 http://localhost:3142/debian unstable/main amd64 g++-riscv64-linux-gnu amd64 4:14.2.0-1 [1200 B]
Get:90 http://localhost:3142/debian unstable/main amd64 crossbuild-essential-riscv64 all 12.12 [3544 B]
Get:91 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.23 [90.6 kB]
Get:92 http://localhost:3142/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB]
Get:93 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get:94 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:95 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get:96 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get:97 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get:98 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get:99 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.22.5-4 [1600 kB]
Get:100 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:101 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:102 http://localhost:3142/debian unstable/main amd64 debhelper all 13.23 [919 kB]
Get:103 http://localhost:3142/debian unstable/main amd64 sgml-data all 2.0.11+nmu1 [179 kB]
Get:104 http://localhost:3142/debian unstable/main amd64 docbook-xml all 4.5-13 [77.4 kB]
Get:105 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.36.2-1 [29.6 kB]
Get:106 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.36.2-1 [75.4 kB]
Get:107 http://localhost:3142/debian unstable/main riscv64 gcc-14-base riscv64 14.2.0-12 [48.3 kB]
Get:108 http://localhost:3142/debian unstable/main riscv64 libgcc-s1 riscv64 14.2.0-12 [56.6 kB]
Get:109 http://localhost:3142/debian unstable/main riscv64 libc6 riscv64 2.40-5 [2440 kB]
Get:110 http://localhost:3142/debian unstable/main riscv64 libglvnd0 riscv64 1.7.0-1+b2 [62.6 kB]
Get:111 http://localhost:3142/debian unstable/main riscv64 libxau6 riscv64 1:1.0.11-1 [20.5 kB]
Get:112 http://localhost:3142/debian unstable/main riscv64 libxdmcp6 riscv64 1:1.1.5-1 [28.0 kB]
Get:113 http://localhost:3142/debian unstable/main riscv64 libxcb1 riscv64 1.17.0-2+b1 [145 kB]
Get:114 http://localhost:3142/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB]
Get:115 http://localhost:3142/debian unstable/main riscv64 libx11-6 riscv64 2:1.8.10-2 [812 kB]
Get:116 http://localhost:3142/debian unstable/main amd64 libdrm-common all 2.4.123-1 [8084 B]
Get:117 http://localhost:3142/debian unstable/main riscv64 libdrm2 riscv64 2.4.123-1 [39.8 kB]
Get:118 http://localhost:3142/debian unstable/main riscv64 libexpat1 riscv64 2.6.4-1 [99.3 kB]
Get:119 http://localhost:3142/debian unstable/main riscv64 libglapi-mesa riscv64 24.2.8-1 [50.4 kB]
Get:120 http://localhost:3142/debian unstable/main riscv64 libx11-xcb1 riscv64 2:1.8.10-2 [241 kB]
Get:121 http://localhost:3142/debian unstable/main riscv64 libxcb-dri2-0 riscv64 1.17.0-2+b1 [107 kB]
Get:122 http://localhost:3142/debian unstable/main riscv64 libxcb-dri3-0 riscv64 1.17.0-2+b1 [107 kB]
Get:123 http://localhost:3142/debian unstable/main riscv64 libxcb-glx0 riscv64 1.17.0-2+b1 [123 kB]
Get:124 http://localhost:3142/debian unstable/main riscv64 libxcb-present0 riscv64 1.17.0-2+b1 [105 kB]
Get:125 http://localhost:3142/debian unstable/main riscv64 libxcb-randr0 riscv64 1.17.0-2+b1 [117 kB]
Get:126 http://localhost:3142/debian unstable/main riscv64 libxcb-shm0 riscv64 1.17.0-2+b1 [105 kB]
Get:127 http://localhost:3142/debian unstable/main riscv64 libxcb-sync1 riscv64 1.17.0-2+b1 [109 kB]
Get:128 http://localhost:3142/debian unstable/main riscv64 libxcb-xfixes0 riscv64 1.17.0-2+b1 [109 kB]
Get:129 http://localhost:3142/debian unstable/main riscv64 libxext6 riscv64 2:1.3.4-1+b3 [51.7 kB]
Get:130 http://localhost:3142/debian unstable/main riscv64 libxfixes3 riscv64 1:6.0.0-2+b3 [20.3 kB]
Get:131 http://localhost:3142/debian unstable/main riscv64 libxshmfence1 riscv64 1.3-1+b3 [8832 B]
Get:132 http://localhost:3142/debian unstable/main riscv64 libxxf86vm1 riscv64 1:1.1.4-1+b4 [19.8 kB]
Get:133 http://localhost:3142/debian unstable/main riscv64 libdrm-amdgpu1 riscv64 2.4.123-1 [22.1 kB]
Get:134 http://localhost:3142/debian unstable/main riscv64 libdrm-radeon1 riscv64 2.4.123-1 [23.5 kB]
Get:135 http://localhost:3142/debian unstable/main riscv64 libzstd1 riscv64 1.5.6+dfsg-2 [355 kB]
Get:136 http://localhost:3142/debian unstable/main riscv64 zlib1g riscv64 1:1.3.dfsg+really1.3.1-1+b1 [85.7 kB]
Get:137 http://localhost:3142/debian unstable/main riscv64 libelf1t64 riscv64 0.192-4 [194 kB]
Get:138 http://localhost:3142/debian unstable/main riscv64 libatomic1 riscv64 14.2.0-12 [8676 B]
Get:139 http://localhost:3142/debian unstable/main riscv64 libmd0 riscv64 1.1.0-2+b1 [37.6 kB]
Get:140 http://localhost:3142/debian unstable/main riscv64 libbsd0 riscv64 0.12.2-2 [132 kB]
Get:141 http://localhost:3142/debian unstable/main riscv64 libtinfo6 riscv64 6.5-2+b1 [343 kB]
Get:142 http://localhost:3142/debian unstable/main riscv64 libedit2 riscv64 3.1-20240808-1 [92.5 kB]
Get:143 http://localhost:3142/debian unstable/main riscv64 libffi8 riscv64 3.4.6-1 [21.4 kB]
Get:144 http://localhost:3142/debian unstable/main riscv64 libstdc++6 riscv64 14.2.0-12 [708 kB]
Get:145 http://localhost:3142/debian unstable/main riscv64 libicu72 riscv64 72.1-5+b1 [9391 kB]
Get:146 http://localhost:3142/debian unstable/main riscv64 liblzma5 riscv64 5.6.3-1+b1 [277 kB]
Get:147 http://localhost:3142/debian unstable/main riscv64 libxml2 riscv64 2.12.7+dfsg+really2.9.14-0.2+b1 [709 kB]
Get:148 http://localhost:3142/debian unstable/main riscv64 libz3-4 riscv64 4.13.3-1 [8514 kB]
Get:149 http://localhost:3142/debian unstable/main riscv64 libllvm19 riscv64 1:19.1.6-1 [24.9 MB]
Get:150 http://localhost:3142/debian unstable/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB]
Get:151 http://localhost:3142/debian unstable/main riscv64 libsensors5 riscv64 1:3.6.0-10+b1 [34.7 kB]
Get:152 http://localhost:3142/debian unstable/main riscv64 mesa-libgallium riscv64 24.2.8-1 [6974 kB]
Get:153 http://localhost:3142/debian unstable/main riscv64 libvulkan1 riscv64 1.3.296.0-1 [123 kB]
Get:154 http://localhost:3142/debian unstable/main riscv64 libwayland-server0 riscv64 1.23.0-1+b1 [34.4 kB]
Get:155 http://localhost:3142/debian unstable/main riscv64 libgbm1 riscv64 24.2.8-1 [44.2 kB]
Get:156 http://localhost:3142/debian unstable/main riscv64 libgl1-mesa-dri riscv64 24.2.8-1 [42.6 kB]
Get:157 http://localhost:3142/debian unstable/main riscv64 libglx-mesa0 riscv64 24.2.8-1 [175 kB]
Get:158 http://localhost:3142/debian unstable/main riscv64 libglx0 riscv64 1.7.0-1+b2 [30.8 kB]
Get:159 http://localhost:3142/debian unstable/main riscv64 libgl1 riscv64 1.7.0-1+b2 [115 kB]
Get:160 http://localhost:3142/debian unstable/main riscv64 libxi6 riscv64 2:1.8.2-1 [80.2 kB]
Get:161 http://localhost:3142/debian unstable/main riscv64 libglut3.12 riscv64 3.4.0-4 [136 kB]
Get:162 http://localhost:3142/debian unstable/main riscv64 libopengl0 riscv64 1.7.0-1+b2 [40.4 kB]
Get:163 http://localhost:3142/debian unstable/main riscv64 libglu1-mesa riscv64 9.0.2-1.1+b3 [180 kB]
Get:164 http://localhost:3142/debian unstable/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get:165 http://localhost:3142/debian unstable/main amd64 x11proto-dev all 2024.1-1 [603 kB]
Get:166 http://localhost:3142/debian unstable/main riscv64 libxau-dev riscv64 1:1.0.11-1 [27.6 kB]
Get:167 http://localhost:3142/debian unstable/main riscv64 libxdmcp-dev riscv64 1:1.1.5-1 [52.9 kB]
Get:168 http://localhost:3142/debian unstable/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB]
Get:169 http://localhost:3142/debian unstable/main riscv64 libxcb1-dev riscv64 1.17.0-2+b1 [241 kB]
Get:170 http://localhost:3142/debian unstable/main riscv64 libx11-dev riscv64 2:1.8.10-2 [1406 kB]
Get:171 http://localhost:3142/debian unstable/main riscv64 libglx-dev riscv64 1.7.0-1+b2 [15.8 kB]
Get:172 http://localhost:3142/debian unstable/main riscv64 libgl-dev riscv64 1.7.0-1+b2 [101 kB]
Get:173 http://localhost:3142/debian unstable/main riscv64 libopengl-dev riscv64 1.7.0-1+b2 [5372 B]
Get:174 http://localhost:3142/debian unstable/main riscv64 libglu1-mesa-dev riscv64 9.0.2-1.1+b3 [546 kB]
Get:175 http://localhost:3142/debian unstable/main riscv64 libxext-dev riscv64 2:1.3.4-1+b3 [147 kB]
Get:176 http://localhost:3142/debian unstable/main amd64 x11-common all 1:7.7+23.1 [216 kB]
Get:177 http://localhost:3142/debian unstable/main riscv64 libice6 riscv64 2:1.1.1-1 [64.8 kB]
Get:178 http://localhost:3142/debian unstable/main riscv64 libuuid1 riscv64 2.40.2-13 [38.2 kB]
Get:179 http://localhost:3142/debian unstable/main riscv64 libsm6 riscv64 2:1.2.4-1 [35.2 kB]
Get:180 http://localhost:3142/debian unstable/main riscv64 libxt6t64 riscv64 1:1.2.1-1.2+b2 [183 kB]
Get:181 http://localhost:3142/debian unstable/main riscv64 libice-dev riscv64 2:1.1.1-1 [130 kB]
Get:182 http://localhost:3142/debian unstable/main riscv64 libcrypt1 riscv64 1:4.4.36-5 [105 kB]
Get:183 http://localhost:3142/debian unstable/main riscv64 libcrypt-dev riscv64 1:4.4.36-5 [221 kB]
Get:184 http://localhost:3142/debian unstable/main riscv64 libc6-dev riscv64 2.40-5 [3092 kB]
Get:185 http://localhost:3142/debian unstable/main riscv64 uuid-dev riscv64 2.40.2-13 [62.5 kB]
Get:186 http://localhost:3142/debian unstable/main riscv64 libsm-dev riscv64 2:1.2.4-1 [56.6 kB]
Get:187 http://localhost:3142/debian unstable/main riscv64 libxt-dev riscv64 1:1.2.1-1.2+b2 [624 kB]
Get:188 http://localhost:3142/debian unstable/main riscv64 libglut-dev riscv64 3.4.0-4 [247 kB]
Get:189 http://localhost:3142/debian unstable/main riscv64 freeglut3-dev riscv64 3.4.0-4 [53.4 kB]
Get:190 http://localhost:3142/debian unstable/main amd64 tao-pegtl-dev all 3.2.7-1 [69.4 kB]
Get:191 http://localhost:3142/debian unstable/main riscv64 gemmi-dev riscv64 0.6.5+ds-2 [3535 kB]
Get:192 http://localhost:3142/debian unstable/main riscv64 libasan8 riscv64 14.2.0-12 [2366 kB]
Get:193 http://localhost:3142/debian unstable/main riscv64 libblas3 riscv64 3.12.0-4 [117 kB]
Get:194 http://localhost:3142/debian unstable/main riscv64 libblas-dev riscv64 3.12.0-4 [260 kB]
Get:195 http://localhost:3142/debian unstable/main riscv64 libgomp1 riscv64 14.2.0-12 [131 kB]
Get:196 http://localhost:3142/debian unstable/main riscv64 libitm1 riscv64 14.2.0-12 [25.7 kB]
Get:197 http://localhost:3142/debian unstable/main riscv64 liblsan0 riscv64 14.2.0-12 [1078 kB]
Get:198 http://localhost:3142/debian unstable/main riscv64 libtsan2 riscv64 14.2.0-12 [2242 kB]
Get:199 http://localhost:3142/debian unstable/main riscv64 libubsan1 riscv64 14.2.0-12 [979 kB]
Get:200 http://localhost:3142/debian unstable/main riscv64 libgcc-14-dev riscv64 14.2.0-12 [5197 kB]
Get:201 http://localhost:3142/debian unstable/main riscv64 libgfortran5 riscv64 14.2.0-12 [398 kB]
Get:202 http://localhost:3142/debian unstable/main riscv64 liblapack3 riscv64 3.12.0-4 [1979 kB]
Get:203 http://localhost:3142/debian unstable/main riscv64 liblapack-dev riscv64 3.12.0-4 [11.5 MB]
Get:204 http://localhost:3142/debian unstable/main riscv64 libopenmm8.1 riscv64 8.1.2+dfsg-2 [808 kB]
Get:205 http://localhost:3142/debian unstable/main riscv64 libopenmm-dev riscv64 8.1.2+dfsg-2 [338 kB]
Get:206 http://localhost:3142/debian unstable/main amd64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB]
Get:207 http://localhost:3142/debian unstable/main riscv64 libxfixes-dev riscv64 1:6.0.0-2+b3 [31.7 kB]
Get:208 http://localhost:3142/debian unstable/main riscv64 libxi-dev riscv64 2:1.8.2-1 [282 kB]
Get:209 http://localhost:3142/debian unstable/main riscv64 libxmu6 riscv64 2:1.1.3-3+b4 [58.0 kB]
Get:210 http://localhost:3142/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get:211 http://localhost:3142/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get:212 http://localhost:3142/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get:213 http://localhost:3142/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB]
Get:214 http://localhost:3142/debian unstable/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB]
Get:215 http://localhost:3142/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.5-1 [44.3 kB]
Get:216 http://localhost:3142/debian unstable/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB]
Get:217 http://localhost:3142/debian unstable/main amd64 libx11-dev amd64 2:1.8.10-2 [891 kB]
Get:218 http://localhost:3142/debian unstable/main amd64 libxmu-headers all 2:1.1.3-3 [68.5 kB]
Get:219 http://localhost:3142/debian unstable/main riscv64 libxmu-dev riscv64 2:1.1.3-3+b4 [124 kB]
Get:220 http://localhost:3142/debian unstable/main riscv64 libsimbody3.7 riscv64 3.7+dfsg-3 [3171 kB]
Get:221 http://localhost:3142/debian unstable/main riscv64 libsimbody-dev riscv64 3.7+dfsg-3 [2727 kB]
Get:222 http://localhost:3142/debian unstable/main riscv64 libsimtkmolmodel3.1t64 riscv64 3.1.0-4.1 [653 kB]
Get:223 http://localhost:3142/debian unstable/main riscv64 libsimtkmolmodel-dev riscv64 3.1.0-4.1 [1863 kB]
Get:224 http://localhost:3142/debian unstable/main riscv64 libsimtkmolmodel-plugins riscv64 3.1.0-4.1 [17.2 kB]
Get:225 http://localhost:3142/debian unstable/main riscv64 libstb0t64 riscv64 0.0~git20240715.f7f20f39fe4f+ds-1 [221 kB]
Get:226 http://localhost:3142/debian unstable/main riscv64 libstb-dev riscv64 0.0~git20240715.f7f20f39fe4f+ds-1 [950 kB]
Get:227 http://localhost:3142/debian unstable/main riscv64 libstdc++-14-dev riscv64 14.2.0-12 [5278 kB]
Get:228 http://localhost:3142/debian unstable/main riscv64 zlib1g-dev riscv64 1:1.3.dfsg+really1.3.1-1+b1 [978 kB]
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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
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Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
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invoke-rc.d: could not determine current runlevel
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Setting up libxext-dev:riscv64 (2:1.3.4-1+b3) ...
Setting up zlib1g-dev:riscv64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up libllvm19:riscv64 (1:19.1.6-1) ...
Setting up mesa-libgallium:riscv64 (24.2.8-1) ...
Setting up libxmu6:riscv64 (2:1.1.3-3+b4) ...
Setting up libxi6:riscv64 (2:1.8.2-1) ...
Setting up libgbm1:riscv64 (24.2.8-1) ...
Setting up libsm-dev:riscv64 (2:1.2.4-1) ...
Setting up libgl1-mesa-dri:riscv64 (24.2.8-1) ...
Setting up libxfixes-dev:riscv64 (1:6.0.0-2+b3) ...
Setting up libxt-dev:riscv64 (1:1.2.1-1.2+b2) ...
Setting up libxi-dev:riscv64 (2:1.8.2-1) ...
Setting up libglx-mesa0:riscv64 (24.2.8-1) ...
Setting up libglx0:riscv64 (1.7.0-1+b2) ...
Setting up libxmu-dev:riscv64 (2:1.1.3-3+b4) ...
Setting up libgl1:riscv64 (1.7.0-1+b2) ...
Setting up libglut3.12:riscv64 (3.4.0-4) ...
Setting up libsimbody3.7:riscv64 (3.7+dfsg-3) ...
Setting up libglx-dev:riscv64 (1.7.0-1+b2) ...
Setting up libgl-dev:riscv64 (1.7.0-1+b2) ...
Setting up libsimtkmolmodel3.1t64:riscv64 (3.1.0-4.1) ...
Setting up libglu1-mesa-dev:riscv64 (9.0.2-1.1+b3) ...
Setting up libglut-dev:riscv64 (3.4.0-4) ...
Setting up libsimtkmolmodel-plugins:riscv64 (3.1.0-4.1) ...
Setting up libsimtkmolmodel-dev:riscv64 (3.1.0-4.1) ...
Setting up freeglut3-dev:riscv64 (3.4.0-4) ...
Setting up libsimbody-dev:riscv64 (3.7+dfsg-3) ...
Processing triggers for libc-bin (2.40-5) ...
Processing triggers for sgml-base (1.31) ...
Setting up docbook-xsl (1.79.2+dfsg-7) ...
Setting up sgml-data (2.0.11+nmu1) ...
Setting up asciidoc-base (10.2.1-1) ...
Processing triggers for sgml-base (1.31) ...
Setting up docbook-xml (4.5-13) ...
Processing triggers for sgml-base (1.31) ...
Setting up sbuild-build-depends-main-dummy:riscv64 (0.invalid.0) ...

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

Arch check ok (riscv64 included in any all)

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

Kernel: Linux 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) amd64 (x86_64)
Toolchain package versions: binutils_2.43.50.20241230-1 dpkg-dev_1.22.13 g++-14_14.2.0-12 gcc-14_14.2.0-12 libc6-dev_2.40-5 libstdc++-14-dev_14.2.0-12 libstdc++-14-dev-riscv64-cross_14.2.0-12cross1 libstdc++6_14.2.0-12 libstdc++6-riscv64-cross_14.2.0-12cross1 linux-libc-dev_6.12.8-1
Package versions: apt_2.9.21 architecture-properties_0.2.3 asciidoc-base_10.2.1-1 asciidoc-common_10.2.1-1 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-4 autotools-dev_20220109.1 base-files_13.6 base-passwd_3.6.6 bash_5.2.37-1 binutils_2.43.50.20241230-1 binutils-common_2.43.50.20241230-1 binutils-riscv64-linux-gnu_2.43.50.20241230-1 binutils-x86-64-linux-gnu_2.43.50.20241230-1 bsdextrautils_2.40.2-13 bsdutils_1:2.40.2-13 build-essential_12.12 bzip2_1.0.8-6 cmake_3.31.3-1 cmake-data_3.31.3-1 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-14_14.2.0-12 cpp-14-riscv64-linux-gnu_14.2.0-12cross1 cpp-14-x86-64-linux-gnu_14.2.0-12 cpp-riscv64-linux-gnu_4:14.2.0-1 cpp-x86-64-linux-gnu_4:14.2.0-1 crossbuild-essential-riscv64_12.12 dash_0.5.12-10 debconf_1.5.89 debhelper_13.23 debian-archive-keyring_2023.4 debianutils_5.21 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 docbook-xml_4.5-13 docbook-xsl_1.79.2+dfsg-7 dpkg_1.22.13 dpkg-dev_1.22.13 dwz_0.15-1+b1 e2fsprogs_1.47.2-1 fakeroot_1.36.2-1 file_1:5.45-3+b1 findutils_4.10.0-3 freeglut3-dev_3.4.0-4 g++_4:14.2.0-1 g++-14_14.2.0-12 g++-14-riscv64-linux-gnu_14.2.0-12cross1 g++-14-x86-64-linux-gnu_14.2.0-12 g++-riscv64-linux-gnu_4:14.2.0-1 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.2.0-12 gcc-14-base_14.2.0-12 gcc-14-cross-base_14.2.0-12cross1 gcc-14-riscv64-linux-gnu_14.2.0-12cross1 gcc-14-riscv64-linux-gnu-base_14.2.0-12cross1 gcc-14-x86-64-linux-gnu_14.2.0-12 gcc-riscv64-linux-gnu_4:14.2.0-1 gcc-x86-64-linux-gnu_4:14.2.0-1 gemmi-dev_0.6.5+ds-2 gettext_0.22.5-4 gettext-base_0.22.5-4 gpgv_2.2.45-2 grep_3.11-4 groff-base_1.23.0-7 gzip_1.12-1.2 hostname_3.25 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libapt-pkg6.0t64_2.9.21 libarchive-zip-perl_1.68-1 libarchive13t64_3.7.4-1.1 libasan8_14.2.0-12 libasan8-riscv64-cross_14.2.0-12cross1 libatomic1_14.2.0-12 libatomic1-riscv64-cross_14.2.0-12cross1 libattr1_1:2.5.2-2 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2 libbinutils_2.43.50.20241230-1 libblas-dev_3.12.0-4 libblas3_3.12.0-4 libblkid1_2.40.2-13 libbrotli1_1.1.0-2+b6 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.40-5 libc-dev-bin_2.40-5 libc6_2.40-5 libc6-dev_2.40-5 libc6-dev-riscv64-cross_2.40-4cross1 libc6-riscv64-cross_2.40-4cross1 libcap-ng0_0.8.5-4 libcap2_1:2.66-5+b1 libcc1-0_14.2.0-12 libcom-err2_1.47.2-1 libcrypt-dev_1:4.4.36-5 libcrypt1_1:4.4.36-5 libctf-nobfd0_2.43.50.20241230-1 libctf0_2.43.50.20241230-1 libcurl4t64_8.11.1-1 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.277 libdebhelper-perl_13.23 libdpkg-perl_1.22.13 libdrm-amdgpu1_2.4.123-1 libdrm-common_2.4.123-1 libdrm-radeon1_2.4.123-1 libdrm2_2.4.123-1 libedit2_3.1-20240808-1 libelf1t64_0.192-4 libexpat1_2.6.4-1 libext2fs2t64_1.47.2-1 libfakeroot_1.36.2-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgbm1_24.2.8-1 libgcc-14-dev_14.2.0-12 libgcc-14-dev-riscv64-cross_14.2.0-12cross1 libgcc-s1_14.2.0-12 libgcc-s1-riscv64-cross_14.2.0-12cross1 libgcrypt20_1.11.0-7 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgfortran5_14.2.0-12 libgl-dev_1.7.0-1+b2 libgl1_1.7.0-1+b2 libgl1-mesa-dri_24.2.8-1 libglapi-mesa_24.2.8-1 libglu1-mesa_9.0.2-1.1+b3 libglu1-mesa-dev_9.0.2-1.1+b3 libglut-dev_3.4.0-4 libglut3.12_3.4.0-4 libglvnd0_1.7.0-1+b2 libglx-dev_1.7.0-1+b2 libglx-mesa0_24.2.8-1 libglx0_1.7.0-1+b2 libgmp10_2:6.3.0+dfsg-3 libgnutls30t64_3.8.8-2 libgomp1_14.2.0-12 libgomp1-riscv64-cross_14.2.0-12cross1 libgpg-error0_1.51-3 libgprofng0_2.43.50.20241230-1 libgssapi-krb5-2_1.21.3-3 libhogweed6t64_3.10-1+b1 libhwasan0_14.2.0-12 libice-dev_2:1.1.1-1 libice6_2:1.1.1-1 libicu72_72.1-5+b1 libidn2-0_2.3.7-2+b1 libisl23_0.27-1 libitm1_14.2.0-12 libitm1-riscv64-cross_14.2.0-12cross1 libjansson4_2.14-2+b3 libjsoncpp26_1.9.6-3 libk5crypto3_1.21.3-3 libkeyutils1_1.6.3-4 libkrb5-3_1.21.3-3 libkrb5support0_1.21.3-3 liblapack-dev_3.12.0-4 liblapack3_3.12.0-4 libldap-2.5-0_2.5.19+dfsg-1 libllvm19_1:19.1.6-1 liblsan0_14.2.0-12 liblsan0-riscv64-cross_14.2.0-12cross1 liblz4-1_1.9.4-4 liblzma5_5.6.3-1+b1 libmagic-mgc_1:5.45-3+b1 libmagic1t64_1:5.45-3+b1 libmd0_1.1.0-2+b1 libmount1_2.40.2-13 libmpc3_1.3.1-1+b3 libmpfr6_4.2.1-1+b2 libncursesw6_6.5-2+b1 libnettle8t64_3.10-1+b1 libnghttp2-14_1.64.0-1 libnsl2_1.3.0-3+b3 libopengl-dev_1.7.0-1+b2 libopengl0_1.7.0-1+b2 libopenmm-dev_8.1.2+dfsg-2 libopenmm8.1_8.1.2+dfsg-2 libp11-kit0_0.25.5-3 libpam-modules_1.5.3-7+b1 libpam-modules-bin_1.5.3-7+b1 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7+b1 libpcre2-8-0_10.44-5 libperl5.40_5.40.0-8 libpipeline1_1.5.8-1 libproc2-0_2:4.0.4-6 libpsl5t64_0.21.2-1.1+b1 libpython3-stdlib_3.12.8-1 libpython3.12-minimal_3.12.8-3 libpython3.12-stdlib_3.12.8-3 libquadmath0_14.2.0-12 libreadline8t64_8.2-6 librhash1_1.4.5-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b5 libsasl2-2_2.1.28+dfsg1-8 libsasl2-modules-db_2.1.28+dfsg1-8 libseccomp2_2.5.5-2 libselinux1_3.7-3+b1 libsemanage-common_3.7-2 libsemanage2_3.7-2+b1 libsensors-config_1:3.6.0-10 libsensors5_1:3.6.0-10+b1 libsepol2_3.7-1 libseqan2-dev_2.4.0+dfsg-16 libsframe1_2.43.50.20241230-1 libsimbody-dev_3.7+dfsg-3 libsimbody3.7_3.7+dfsg-3 libsimtkmolmodel-dev_3.1.0-4.1 libsimtkmolmodel-plugins_3.1.0-4.1 libsimtkmolmodel3.1t64_3.1.0-4.1 libsm-dev_2:1.2.4-1 libsm6_2:1.2.4-1 libsmartcols1_2.40.2-13 libsqlite3-0_3.46.1-1 libss2_1.47.2-1 libssh2-1t64_1.11.1-1 libssl3t64_3.4.0-2 libstb-dev_0.0~git20240715.f7f20f39fe4f+ds-1 libstb0t64_0.0~git20240715.f7f20f39fe4f+ds-1 libstdc++-14-dev_14.2.0-12 libstdc++-14-dev-riscv64-cross_14.2.0-12cross1 libstdc++6_14.2.0-12 libstdc++6-riscv64-cross_14.2.0-12cross1 libsystemd0_257.1-7 libtasn1-6_4.19.0-3+b3 libtinfo6_6.5-2+b1 libtirpc-common_1.3.4+ds-1.3 libtirpc3t64_1.3.4+ds-1.3+b1 libtool_2.5.4-2 libtsan2_14.2.0-12 libtsan2-riscv64-cross_14.2.0-12cross1 libubsan1_14.2.0-12 libubsan1-riscv64-cross_14.2.0-12cross1 libuchardet0_0.0.8-1+b2 libudev1_257.1-7 libunistring5_1.3-1 libuuid1_2.40.2-13 libuv1t64_1.48.0-7 libvulkan1_1.3.296.0-1 libwayland-server0_1.23.0-1+b1 libx11-6_2:1.8.10-2 libx11-data_2:1.8.10-2 libx11-dev_2:1.8.10-2 libx11-xcb1_2:1.8.10-2 libxau-dev_1:1.0.11-1 libxau6_1:1.0.11-1 libxcb-dri2-0_1.17.0-2+b1 libxcb-dri3-0_1.17.0-2+b1 libxcb-glx0_1.17.0-2+b1 libxcb-present0_1.17.0-2+b1 libxcb-randr0_1.17.0-2+b1 libxcb-shm0_1.17.0-2+b1 libxcb-sync1_1.17.0-2+b1 libxcb-xfixes0_1.17.0-2+b1 libxcb1_1.17.0-2+b1 libxcb1-dev_1.17.0-2+b1 libxdmcp-dev_1:1.1.5-1 libxdmcp6_1:1.1.5-1 libxext-dev_2:1.3.4-1+b3 libxext6_2:1.3.4-1+b3 libxfixes-dev_1:6.0.0-2+b3 libxfixes3_1:6.0.0-2+b3 libxi-dev_2:1.8.2-1 libxi6_2:1.8.2-1 libxml2_2.12.7+dfsg+really2.9.14-0.2+b1 libxml2-utils_2.12.7+dfsg+really2.9.14-0.2+b1 libxmu-dev_2:1.1.3-3+b4 libxmu-headers_2:1.1.3-3 libxmu6_2:1.1.3-3+b4 libxshmfence1_1.3-1+b3 libxslt1.1_1.1.35-1.1+b1 libxt-dev_1:1.2.1-1.2+b2 libxt6t64_1:1.2.1-1.2+b2 libxxf86vm1_1:1.1.4-1+b4 libxxhash0_0.8.3-2 libz3-4_4.13.3-1 libzstd1_1.5.6+dfsg-2 linux-libc-dev_6.12.8-1 linux-libc-dev-riscv64-cross_6.12.6-1cross1 login_1:4.16.0-2+really2.40.2-13 login.defs_1:4.16.0-7 logsave_1.47.2-1 m4_1.4.19-4 make_4.4.1-1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 media-types_10.1.0 mesa-libgallium_24.2.8-1 mount_2.40.2-13 ncurses-base_6.5-2 ncurses-bin_6.5-2+b1 netbase_6.4 openssl-provider-legacy_3.4.0-2 passwd_1:4.16.0-7 patch_2.7.6-7 perl_5.40.0-8 perl-base_5.40.0-8 perl-modules-5.40_5.40.0-8 po-debconf_1.0.21+nmu1 procps_2:4.0.4-6 python3_3.12.8-1 python3-minimal_3.12.8-1 python3.12_3.12.8-3 python3.12-minimal_3.12.8-3 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sgml-base_1.31 sgml-data_2.0.11+nmu1 sqv_1.2.1-5 sysvinit-utils_3.11-1 tao-pegtl-dev_3.2.7-1 tar_1.35+dfsg-3.1 tzdata_2024b-4 util-linux_2.40.2-13 uuid-dev_2.40.2-13 x11-common_1:7.7+23.1 x11proto-dev_2024.1-1 xml-core_0.19 xorg-sgml-doctools_1:1.11-1.1 xsltproc_1.1.35-1.1+b1 xtrans-dev_1.4.0-1 xz-utils_5.6.3-1+b1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1

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


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

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

Format: 3.0 (quilt)
Source: macromoleculebuilder
Binary: libmmb-dev, libmmb4.0t64, mmb, mmb-common
Architecture: any all
Version: 4.0.0+dfsg-5
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Uploaders:  Andrius Merkys <merkys@debian.org>,
Homepage: https://simtk.org/projects/rnatoolbox
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/debichem-team/macromoleculebuilder
Vcs-Git: https://salsa.debian.org/debichem-team/macromoleculebuilder.git
Build-Depends: architecture-is-64-bit, asciidoc-base, cmake, debhelper-compat (= 13), docbook-xml, dpkg-dev (>= 1.22.5), gemmi-dev (>= 0.6.2+ds-2), libopenmm-dev, libseqan2-dev, libsimbody-dev, libsimtkmolmodel-dev (>= 3.1.0), libsimtkmolmodel-plugins, libstb-dev, tao-pegtl-dev, zlib1g-dev
Package-List:
 libmmb-dev deb libdevel optional arch=any
 libmmb4.0t64 deb libs optional arch=any
 mmb deb science optional arch=any
 mmb-common deb science optional arch=all
Checksums-Sha1:
 c37eccceb961f3e78d5b7145faf79ce425cf104e 2567256 macromoleculebuilder_4.0.0+dfsg.orig.tar.xz
 92ca5482b680f90676592a9fd69ec77274b4269d 5964 macromoleculebuilder_4.0.0+dfsg-5.debian.tar.xz
Checksums-Sha256:
 2f50d11c886c36fd18476f942d7521536ded599584e0d83462a63ba5f9ccc449 2567256 macromoleculebuilder_4.0.0+dfsg.orig.tar.xz
 139eb1301e44a6b967bb990e97300618befc1784e04c2b62bf399c8b835f4afd 5964 macromoleculebuilder_4.0.0+dfsg-5.debian.tar.xz
Files:
 951370d06adf03fb858edccdee43c075 2567256 macromoleculebuilder_4.0.0+dfsg.orig.tar.xz
 69bbd609e8a36fbef46bcfbf9328d2c5 5964 macromoleculebuilder_4.0.0+dfsg-5.debian.tar.xz

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gpgv: Signature made Wed Nov 27 07:10:58 2024 UTC
gpgv:                using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287
gpgv:                issuer "merkys@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./macromoleculebuilder_4.0.0+dfsg-5.dsc: no acceptable signature found
dpkg-source: info: extracting macromoleculebuilder in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking macromoleculebuilder_4.0.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking macromoleculebuilder_4.0.0+dfsg-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying drop-CMAKE_CXX_STANDARD.patch
dpkg-source: info: applying 96da444290ab1af4385013c566079d381d8051b4.patch
dpkg-source: info: applying bf1ab1ebf49bb9e48f4f133e155f9315cc37079d.patch
dpkg-source: info: applying 27.patch

Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
CONFIG_SITE=/etc/dpkg-cross/cross-config.riscv64
DEB_BUILD_OPTIONS=nocheck
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LOGNAME=crossqa
OLDPWD=/home/crossqa
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SBUILD_CONFIG=/tmp/tmp.DxpiAFp9EP/sbuild.conf
SCHROOT_ALIAS_NAME=unstable-amd64-sbuild
SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=crossqa
SCHROOT_SESSION_ID=sid-amd64-sbuild-7db754d6-fd58-45a5-ae4c-2c5b547a7cfb
SCHROOT_UID=1000
SCHROOT_USER=crossqa
SHELL=/bin/sh
USER=crossqa

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

Command: dpkg-buildpackage --sanitize-env -ariscv64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1
dpkg-buildpackage: info: source package macromoleculebuilder
dpkg-buildpackage: info: source version 4.0.0+dfsg-5
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andrius Merkys <merkys@debian.org>
dpkg-architecture: warning: specified GNU system type riscv64-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture riscv64
 debian/rules clean
dh clean
   dh_clean
 debian/rules binary-arch
dh binary-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- \
	-DCMAKE_BUILD_TYPE=Release \
	-DENABLE_LEPTON=OFF \
	-DGEMMI_DIR=/usr \
	-DOpenMM_INCLUDE_DIR=/usr/include \
	-DSimTKmolmodel=/usr \
	-DCMAKE_CXX_FLAGS="-D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0"
	cd obj-riscv64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/riscv64-linux-gnu-pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_SYSTEM_NAME=Linux -DCMAKE_SYSTEM_PROCESSOR=riscv64 -DCMAKE_C_COMPILER=riscv64-linux-gnu-gcc -DCMAKE_CXX_COMPILER=riscv64-linux-gnu-g\+\+ -DPKG_CONFIG_EXECUTABLE=/usr/bin/riscv64-linux-gnu-pkg-config -DPKGCONFIG_EXECUTABLE=/usr/bin/riscv64-linux-gnu-pkg-config -DQMAKE_EXECUTABLE=/usr/bin/riscv64-linux-gnu-qmake -DCMAKE_INSTALL_LIBDIR=lib/riscv64-linux-gnu -DBUILD_TESTING:BOOL=OFF -DCMAKE_BUILD_TYPE=Release -DENABLE_LEPTON=OFF -DGEMMI_DIR=/usr -DOpenMM_INCLUDE_DIR=/usr/include -DSimTKmolmodel=/usr "-DCMAKE_CXX_FLAGS=-D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0" ..
-- The CXX compiler identification is GNU 14.2.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/riscv64-linux-gnu-g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMM: /usr/include
-- Found ZLIB: /usr/lib/riscv64-linux-gnu/libz.so (found version "1.3.1")
-- Found gemmi version 0.6.5
-- Looking for copy_file_range
-- Looking for copy_file_range - found
-- Looking for sendfile
-- Looking for sendfile - found
-- Configuring done (0.5s)
-- Generating done (0.0s)
CMake Warning:
  Manually-specified variables were not used by the project:

    BUILD_TESTING
    CMAKE_C_COMPILER
    CMAKE_EXPORT_NO_PACKAGE_REGISTRY
    CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
    FETCHCONTENT_FULLY_DISCONNECTED
    PKGCONFIG_EXECUTABLE
    PKG_CONFIG_EXECUTABLE
    QMAKE_EXECUTABLE
    SimTKmolmodel


-- Build files have been written to: /<<PKGBUILDDIR>>/obj-riscv64-linux-gnu
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	cd obj-riscv64-linux-gnu && make -j1 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu'
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cd /<<PKGBUILDDIR>>/obj-riscv64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-riscv64-linux-gnu /<<PKGBUILDDIR>>/obj-riscv64-linux-gnu /<<PKGBUILDDIR>>/obj-riscv64-linux-gnu/CMakeFiles/MMB.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu'
make  -f CMakeFiles/MMB.dir/build.make CMakeFiles/MMB.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu'
[  3%] Building CXX object CMakeFiles/MMB.dir/src/Utils.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/Utils.cpp.o -MF CMakeFiles/MMB.dir/src/Utils.cpp.o.d -o CMakeFiles/MMB.dir/src/Utils.cpp.o -c /<<PKGBUILDDIR>>/src/Utils.cpp
In file included from /<<PKGBUILDDIR>>/src/Utils.cpp:12:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
[  6%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o -MF CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o.d -o CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o -c /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20,
                 from /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:14:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In function ‘bool letterIsPurine(char)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:51:14: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   51 |     return c == 'A' | c == 'G';
      |            ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In function ‘bool letterIsRNA(char)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:57:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   57 |         c == 'A' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:59:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   59 |         c == 'G' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:60:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   60 |         c == 'U'
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In function ‘bool letterIsDNA(char)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:67:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   67 |         c == 'A' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:69:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   69 |         c == 'G' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:70:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   70 |         c == 'T'
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In function ‘bool letterIsProtein(char)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:77:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   77 |         c == 'C' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:79:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   79 |         c == 'H' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:80:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   80 |         c == 'I'
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:86:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   86 |         c == 'M' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:88:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   88 |         c == 'V' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:89:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   89 |         c == 'A'
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:95:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   95 |         c == 'G' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:97:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   97 |         c == 'P' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:98:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
   98 |         c == 'T'
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:104:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  104 |         c == 'R' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:106:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  106 |         c == 'Y' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:107:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  107 |         c == 'W'
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:113:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  113 |         c == 'D' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:115:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  115 |         c == 'E' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:116:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  116 |         c == 'Q' |
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:117:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  117 |         c == 'K'
      |         ~~^~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClass::modifyResidue(BiopolymerModification, SimTK::Compound, SimTK::DuMMForceFieldSubsystem&)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:127:41: warning: variable ‘myChargedAtomTypeIndex’ set but not used [-Wunused-but-set-variable]
  127 |         DuMM::ChargedAtomTypeIndex      myChargedAtomTypeIndex = dumm.getBiotypeChargedAtomType( compoundToAdd.getAtomBiotypeIndex(Compound::AtomIndex( 0)));
      |                                         ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:135:29: warning: unused variable ‘myOrdinality’ [-Wunused-variable]
  135 |         Ordinality::Residue myOrdinality(SimTK::Ordinality::Any);
      |                             ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:147:32: warning: unused variable ‘myBondMobility’ [-Wunused-variable]
  147 |         BondMobility::Mobility myBondMobility = stringToBondMobility("Rigid");
      |                                ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::checkResidueNumbersAndInsertionCodes()’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:244:15: warning: variable ‘myResidueID’ set but not used [-Wunused-but-set-variable]
  244 |     ResidueID myResidueID = getFirstResidueID();
      |               ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClass::setPdbResidueNumbersFromResidueIDVector()’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:518:15: warning: variable ‘myFirstResidueID’ set but not used [-Wunused-but-set-variable]
  518 |     ResidueID myFirstResidueID = getFirstResidueID() ;
      |               ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:520:9: warning: unused variable ‘numResidues’ [-Wunused-variable]
  520 |     int numResidues = -1;
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClass::renumberPdbResidues(ResidueID)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:551:9: warning: unused variable ‘myNewResidueNumberWithoutInsertionCode’ [-Wunused-variable]
  551 |     int myNewResidueNumberWithoutInsertionCode = firstResidueID.getResidueNumber() ;
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::matchCoordinates(const SimTK::PdbStructure&, bool, bool, bool, bool, bool, bool, double, double)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:669:45: warning: variable ‘biopolymerAtomTargetsIterator’ set but not used [-Wunused-but-set-variable]
  669 |     Compound::AtomTargetLocations::iterator biopolymerAtomTargetsIterator = biopolymerAtomTargets.begin();
      |                                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘bool BiopolymerClass::hasAtom(ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:1053:9: warning: unused variable ‘myResidueIndex’ [-Wunused-variable]
 1053 |     int myResidueIndex = getResidueIndex(myResidueID);
      |         ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘SimTK::Vec3 BiopolymerClass::calcDefaultAtomLocationInGroundFrame(const ResidueID&, const SimTK::String&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:1316:25: warning: variable ‘myAtomIndex’ set but not used [-Wunused-but-set-variable]
 1316 |     Compound::AtomIndex myAtomIndex = atomIndex(myResidueID,atomName);
      |                         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClass::addGeneralSterics(SimTK::GeneralContactSubsystem&, SimTK::ContactSetIndex, SimTK::HuntCrossleyForce&, SimTK::SimbodyMatterSubsystem&, double, double, ResidueID, ResidueID, bool, bool)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:1437:12: warning: unused variable ‘huntCrossleyDissipation’ [-Wunused-variable]
 1437 |     double huntCrossleyDissipation  =.0;
      |            ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘ResidueID BiopolymerClass::sum(ResidueID, int) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:2172:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 2172 |         if ((newResidueIndex < 0) || (newResidueIndex >= residueIDVector.size())) {
      |                                       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClassContainer::waterDropletAboutResidues(std::vector<WaterDropletAboutResidueStruct>, WaterDropletContainer&)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:3577:23: warning: variable ‘myLocation’ set but not used [-Wunused-but-set-variable]
 3577 |                  Vec3 myLocation = (primaryBiopolymerClass.calcDefaultAtomLocationInGroundFrame(waterDropletAboutResidueVector[i].residue, primaryBiopolymerClass.getRepresentativeAtomName()))*(1.0); // used to convert to Å, now using nm
      |                       ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClassContainer::substituteResidue(SimTK::String, ResidueID, SimTK::String, bool)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:4130:15: warning: variable ‘myFirstResidueNumber’ set but not used [-Wunused-but-set-variable]
 4130 |     ResidueID myFirstResidueNumber = myOldBiopolymerClass.getFirstResidueID();
      |               ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘void BiopolymerClassContainer::substituteResidue(Mutation, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:4519:15: warning: variable ‘myFirstResidueNumber’ set but not used [-Wunused-but-set-variable]
 4519 |     ResidueID myFirstResidueNumber = myOldBiopolymerClass.getFirstResidueID();
      |               ^~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:16:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:4682:61:   required from here
 4682 |     myResidueStretchContainer.addIntraChainInterfaceResidues( radius, chain, *this );
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:283:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  283 |             for (int i = 0; i < chainAtomInfoVector.size() ; i++) {
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:300:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<unsigned int, unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  300 |             for ( int j = 0 ; j < neighborList.size(); j++) {
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = MobilizerStretch]’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:2584:54:   required from ‘void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch&, ResidueStretchContainer<ResidueStretchType>&) [with ResidueStretchType = MobilizerStretch]’
 2584 |     residueStretchContainer.printResidueStretchVector();
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:2588:181:   required from here
 2588 | template void BiopolymerClass::selectivelyRemoveResidueStretchFromContainer(const ResidueStretch &residueStretch, ResidueStretchContainer<MobilizerStretch> &residueStretchContainer);
      |                                                                                                                                                                                     ^
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MobilizerStretch>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘bool ResidueStretchContainer<ResidueStretchType>::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]’:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:320:27:   required from ‘void ResidueStretchContainer<ResidueStretchType>::addIntraChainInterfaceResidues(double, SimTK::String, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’
  320 |                     if (!(vectorHasResidueStretch(myResidueStretch1))) {addResidueStretchToVector(myResidueStretch1);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:4682:61:   required from here
 4682 |     myResidueStretchContainer.addIntraChainInterfaceResidues( radius, chain, *this );
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:104:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SingleResidue>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  104 |                 for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:4827:54:   required from ‘void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer&, ResidueStretchContainer<ResidueStretchType>&) [with ResidueStretchType = DensityStretch]’
 4827 |     residueStretchContainer.printResidueStretchVector();
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:4830:213:   required from here
 4830 | template void BiopolymerClassContainer::selectivelyRemoveRigidMobilizerStretchesFromResidueStretchContainer(MobilizerContainer &mobilizerContainer, ResidueStretchContainer<DensityStretch> &residueStretchContainer);
      |                                                                                                                                                                                                                     ^
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93,
                 from /usr/include/simbody/SimTKcommon/Simmatrix.h:37,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /usr/include/molmodel/molmodel/internal/Compound.h:36,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:16:
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’ at /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:875:14:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72
  875 |     Rotation myRotation;
      |              ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’ at /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:875:14:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72
  875 |     Rotation myRotation;
      |              ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’ at /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:875:14:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72
  875 |     Rotation myRotation;
      |              ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70,
    inlined from ‘SimTK::Rotation_<P>& SimTK::Rotation_<P>::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20,
    inlined from ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’ at /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:876:44:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72
  875 |     Rotation myRotation;
      |              ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70,
    inlined from ‘SimTK::Rotation_<P>& SimTK::Rotation_<P>::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20,
    inlined from ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’ at /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:876:44:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72
  875 |     Rotation myRotation;
      |              ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70,
    inlined from ‘SimTK::Rotation_<P>& SimTK::Rotation_<P>::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20,
    inlined from ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’ at /<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:876:44:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp: In member function ‘int BiopolymerClass::initializeBiopolymer(SimTK::CompoundSystem&, bool, bool, bool, bool, bool, bool, bool, int, double, const std::vector<Displacement>&, double, double, const std::vector<SecondaryStructureStretch>&, PdbStructureMapType&)’:
/<<PKGBUILDDIR>>/src/BiopolymerClass.cpp:875:14: note: object ‘myRotation’ of size 72
  875 |     Rotation myRotation;
      |              ^~~~~~~~~~
[  9%] Building CXX object CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o -MF CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o.d -o CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o -c /<<PKGBUILDDIR>>/src/UnitCellParameters.cpp
[ 12%] Building CXX object CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o -MF CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o -c /<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:12:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘double AtomSpringContainer::calcRmsd(SimTK::State&, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:65:12: warning: unused variable ‘myExtension’ [-Wunused-variable]
   65 |     double myExtension = 0.0;
      |            ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::deleteAtomSpring(int)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:194:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<AtomSpring>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  194 |     if(id < 0 || id >= atomSpringVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateAtomSpring(int, const AtomSpring&, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:201:21: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::vector<AtomSpring>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  201 |     if(id < 0 || id >= atomSpringVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::deleteThreading(int)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:260:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  260 |     if(id < 0 || id >= threadingStructVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateThreading(int, const ThreadingStruct&, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:268:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  268 |     if(id < 0 || id >= threadingStructVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateThreading(int, SimTK::String, ResidueID, ResidueID, SimTK::String, ResidueID, ResidueID, double, bool, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:279:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  279 |     if(id < 0 || id >= threadingStructVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::deleteGappedThreading(int)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:441:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  441 |     if(id < 0 || id >= gappedThreadingStructVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateGappedThreading(int, const ThreadingStruct&, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:449:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  449 |     if(id < 0 || id >= gappedThreadingStructVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::updateGappedThreading(int, SimTK::String, SimTK::String, double, bool, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:458:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  458 |     if(id < 0 || id >= gappedThreadingStructVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp: In member function ‘void AtomSpringContainer::createSpringsFromGappedThreading(BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:488:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘seqan::Size<seqan::String<char, seqan::Alloc<> > >::Type’ {aka ‘long unsigned int’} [-Wsign-compare]
  488 |         while ((aIndex < length(thread.updThreadingPartner(0).sequence)) &&
      |                 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/AtomSpringContainer.cpp:489:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘seqan::Size<seqan::String<char, seqan::Alloc<> > >::Type’ {aka ‘long unsigned int’} [-Wsign-compare]
  489 |                (bIndex < length(thread.updThreadingPartner(1).sequence)))
      |                 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93,
                 from /usr/include/simbody/SimTKcommon/Simmatrix.h:37,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /<<PKGBUILDDIR>>/include/Utils.h:22:
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Mat<3, 3> [1]’ [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
In file included from /usr/include/molmodel/molmodel/internal/Compound.h:41,
                 from /usr/include/molmodel/SimTKmolmodel.h:53,
                 from /<<PKGBUILDDIR>>/include/Utils.h:23:
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’:
/usr/include/molmodel/molmodel/internal/Superpose.h:107:18: note: object ‘R’ of size 72
  107 |         Mat<3,3> R(0.0);
      |                  ^
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Mat<3, 3> [1]’ [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’:
/usr/include/molmodel/molmodel/internal/Superpose.h:107:18: note: object ‘R’ of size 72
  107 |         Mat<3,3> R(0.0);
      |                  ^
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:107:23:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Mat<3, 3> [1]’ [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’:
/usr/include/molmodel/molmodel/internal/Superpose.h:107:18: note: object ‘R’ of size 72
  107 |         Mat<3,3> R(0.0);
      |                  ^
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:183:23:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Mat<3, 3> [1]’ [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’:
/usr/include/molmodel/molmodel/internal/Superpose.h:183:18: note: object ‘U’ of size 72
  183 |         Mat<3,3> U(0.0);   // initialize 2-d array
      |                  ^
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:183:23:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Mat<3, 3> [1]’ [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’:
/usr/include/molmodel/molmodel/internal/Superpose.h:183:18: note: object ‘U’ of size 72
  183 |         Mat<3,3> U(0.0);   // initialize 2-d array
      |                  ^
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:183:23:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Mat<3, 3> [1]’ [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’:
/usr/include/molmodel/molmodel/internal/Superpose.h:183:18: note: object ‘U’ of size 72
  183 |         Mat<3,3> U(0.0);   // initialize 2-d array
      |                  ^
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:201:33:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’:
/usr/include/molmodel/molmodel/internal/Superpose.h:201:33: note: object ‘<anonymous>’ of size 72
  201 |             rotation = Rotation();
      |                                 ^
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:201:33:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’:
/usr/include/molmodel/molmodel/internal/Superpose.h:201:33: note: object ‘<anonymous>’ of size 72
  201 |             rotation = Rotation();
      |                                 ^
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’ at /usr/include/molmodel/molmodel/internal/Superpose.h:201:33:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/usr/include/molmodel/molmodel/internal/Superpose.h: In static member function ‘static SimTK::TransformAndResidual SimTK::Kabsch78::superpose(const VectorSet&)’:
/usr/include/molmodel/molmodel/internal/Superpose.h:201:33: note: object ‘<anonymous>’ of size 72
  201 |             rotation = Rotation();
      |                                 ^
[ 15%] Building CXX object CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o -MF CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o -c /<<PKGBUILDDIR>>/src/DisplacementContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20,
                 from /<<PKGBUILDDIR>>/include/DisplacementContainer.h:14,
                 from /<<PKGBUILDDIR>>/src/DisplacementContainer.cpp:12:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 18%] Building CXX object CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o -MF CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o -c /<<PKGBUILDDIR>>/src/MobilizerContainer.cpp
In file included from /<<PKGBUILDDIR>>/src/MobilizerContainer.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/MobilizerContainer.cpp:12:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/MobilizerContainer.cpp: In member function ‘void MobilizerContainer::addMobilizerDomainsInterfacesToVector(const std::vector<MobilizerDomainsInterface>&, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/MobilizerContainer.cpp:190:37: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  190 |             if( (dist <= it->range) &&
      |                 ~~~~~~~~~~~~~~~~~~~~^~
  191 |                 (it->domain1.contains(chain1, res1) && it->domain2.contains(chain2, res2)) ||
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 21%] Building CXX object CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o -MF CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o -c /<<PKGBUILDDIR>>/src/MoleculeContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/ConstraintContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/MoleculeContainer.h:8,
                 from /<<PKGBUILDDIR>>/src/MoleculeContainer.cpp:3:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/MoleculeContainer.cpp: In constructor ‘CustomMolecule::CustomMolecule(std::vector<std::vector<SimTK::String> >, SimTK::DuMMForceFieldSubsystem&)’:
/<<PKGBUILDDIR>>/src/MoleculeContainer.cpp:324:15: warning: unused variable ‘myAngle1’ [-Wunused-variable]
  324 |         Angle myAngle1 = 180*Deg2Rad; // this is a bond angle
      |               ^~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 25%] Building CXX object CMakeFiles/MMB.dir/src/DensityContainer.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DensityContainer.cpp.o -MF CMakeFiles/MMB.dir/src/DensityContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityContainer.cpp.o -c /<<PKGBUILDDIR>>/src/DensityContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20,
                 from /<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:4,
                 from /<<PKGBUILDDIR>>/include/DensityContainer.h:14,
                 from /<<PKGBUILDDIR>>/src/DensityContainer.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityContainer.cpp: In member function ‘void DensityContainer::updateDensityStretch(int, const DensityStretch&, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/DensityContainer.cpp:18:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   18 |     if(id < 0 || id >= residueStretchVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 28%] Building CXX object CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o -MF CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o -c /<<PKGBUILDDIR>>/src/BasePairContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20,
                 from /<<PKGBUILDDIR>>/include/BasePairContainer.h:17,
                 from /<<PKGBUILDDIR>>/src/BasePairContainer.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BasePairContainer.cpp: In member function ‘void BasePairContainer::updateBasePair(int, SimTK::String, int, SimTK::String, SimTK::String, int, SimTK::String, SimTK::String, BiopolymerClassContainer&, const LeontisWesthofClass&, bool)’:
/<<PKGBUILDDIR>>/src/BasePairContainer.cpp:44:28: warning: ignoring return value of ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::at(size_type) [with _Tp = BaseInteraction; _Alloc = std::allocator<BaseInteraction>; reference = BaseInteraction&; size_type = long unsigned int]’, declared with attribute ‘nodiscard’ [-Wunused-result]
   44 |         myBasePairVector.at(index);
      |         ~~~~~~~~~~~~~~~~~~~^~~~~~~
In file included from /usr/riscv64-linux-gnu/include/c++/14/vector:66,
                 from /usr/include/simbody/SimTKcommon/internal/Array.h:39,
                 from /usr/include/simbody/SimTKcommon/basics.h:53,
                 from /usr/include/simbody/SimTKcommon.h:32,
                 from /usr/include/simbody/Simbody.h:38,
                 from /usr/include/molmodel/SimTKmolmodel.h:47,
                 from /<<PKGBUILDDIR>>/include/BasePairContainer.h:16:
/usr/riscv64-linux-gnu/include/c++/14/bits/stl_vector.h:1180:7: note: declared here
 1180 |       at(size_type __n)
      |       ^~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 31%] Building CXX object CMakeFiles/MMB.dir/src/ContactContainer.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ContactContainer.cpp.o -MF CMakeFiles/MMB.dir/src/ContactContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/ContactContainer.cpp.o -c /<<PKGBUILDDIR>>/src/ContactContainer.cpp
In file included from /<<PKGBUILDDIR>>/src/ContactContainer.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/ContactContainer.cpp:12:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ContactContainer.cpp: In member function ‘void ContactContainer::validateContact(ContactStretch, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/ContactContainer.cpp:26:10: warning: variable ‘myEndCapsOn’ set but not used [-Wunused-but-set-variable]
   26 |     bool myEndCapsOn;
      |          ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ContactContainer.cpp: In member function ‘void ContactContainer::deleteContactWithin(int)’:
/<<PKGBUILDDIR>>/src/ContactContainer.cpp:70:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ContactWithin>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   70 |     if(id < 0 || id >= contactWithinVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ContactContainer.cpp: In member function ‘void ContactContainer::updateContactWithin(int, SimTK::String, int, double, SimTK::String, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/ContactContainer.cpp:77:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ContactWithin>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   77 |     if(id < 0 || id >= contactWithinVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ContactContainer.cpp: In member function ‘void ContactContainer::deleteContact(int)’:
/<<PKGBUILDDIR>>/src/ContactContainer.cpp:275:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ContactStretch, std::allocator<ContactStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  275 |     if(id < 0 || id >= residueStretchVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ContactContainer.cpp: In member function ‘void ContactContainer::updateContact(int, std::string, int, int, std::string, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/ContactContainer.cpp:283:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ContactStretch, std::allocator<ContactStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  283 |     if(id < 0 || id >= residueStretchVector.size()){
      |                  ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ContactContainer.cpp: In member function ‘bool ContactContainer::hasSharedContact(SimTK::String, ResidueID, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/src/ContactContainer.cpp:313:71: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  313 |             ((tempContactStretch.getStartResidue() <= endResidueID)   && (tempContactStretch.getEndResidue() >= endResidueID) ||   // the supplied end residue is in the range of this ContactStretch (with index $i).
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 34%] Building CXX object CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o -MF CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o -c /<<PKGBUILDDIR>>/src/ConstraintContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/ConstraintContainer.h:14,
                 from /<<PKGBUILDDIR>>/src/ConstraintContainer.cpp:10:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/ConstraintContainer.cpp:11:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ConstraintContainer.cpp: In member function ‘void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/ConstraintContainer.cpp:129:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ConstraintClass>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  129 |     if(index < 0 || index >= constraintClassVector.size())
      |                     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ConstraintContainer.cpp: In member function ‘void ConstraintToGroundContainer::updateConstraintToVector(int, SimTK::String, ResidueID, SimTK::String, SimTK::String, ResidueID, SimTK::String, BiopolymerClassContainer&)’:
/<<PKGBUILDDIR>>/src/ConstraintContainer.cpp:146:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ConstraintClass>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  146 |     if(index < 0 || index >= constraintClassVector.size())
      |                     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 37%] Building CXX object CMakeFiles/MMB.dir/src/Repel.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/Repel.cpp.o -MF CMakeFiles/MMB.dir/src/Repel.cpp.o.d -o CMakeFiles/MMB.dir/src/Repel.cpp.o -c /<<PKGBUILDDIR>>/src/Repel.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/PeriodicScrubber.h:16,
                 from /<<PKGBUILDDIR>>/include/Repel.h:24,
                 from /<<PKGBUILDDIR>>/src/Repel.cpp:12:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Repel.cpp: In member function ‘void ConstrainedDynamics::constraintsAndRestraints(ParameterReader&, BiopolymerClassContainer&, SimTK::GeneralForceSubsystem&, SimTK::SimbodyMatterSubsystem&, SimTK::State&, SimTK::CompoundSystem&)’:
/<<PKGBUILDDIR>>/src/Repel.cpp:172:31: warning: variable ‘myResidueID’ set but not used [-Wunused-but-set-variable]
  172 |                     ResidueID myResidueID = myConstraintClass.getResidueID1();
      |                               ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Repel.h: In constructor ‘ConstrainedDynamics::ConstrainedDynamics(ParameterReader*)’:
/<<PKGBUILDDIR>>/include/Repel.h:269:29: warning: ‘ConstrainedDynamics::_parameterReader’ will be initialized after [-Wreorder]
  269 |     ParameterReader *       _parameterReader;
      |                             ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Repel.h:259:29: warning:   ‘SimTK::SimbodyMatterSubsystem ConstrainedDynamics::_matter’ [-Wreorder]
  259 |     SimbodyMatterSubsystem  _matter;
      |                             ^~~~~~~
/<<PKGBUILDDIR>>/src/Repel.cpp:342:1: warning:   when initialized here [-Wreorder]
  342 | ConstrainedDynamics::ConstrainedDynamics(ParameterReader * myParameterReader) : _parameterReader(myParameterReader),
      | ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Repel.cpp: In member function ‘void ConstrainedDynamics::initializeBiopolymer(SimTK::String, SimTK::String)’:
/<<PKGBUILDDIR>>/src/Repel.cpp:405:10: warning: variable ‘readFromFile’ set but not used [-Wunused-but-set-variable]
  405 |     bool readFromFile = false;
      |          ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Repel.cpp: In member function ‘void ConstrainedDynamics::runAllSteps()’:
/<<PKGBUILDDIR>>/src/Repel.cpp:1027:22: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1027 |     for(; _nextFrame <= _parameterReader->numReportingIntervals; _nextFrame++){
      |           ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::addAllMutualChainResidues(double, std::vector<SimTK::String>, std::vector<SimTK::String>, BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]’:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:210:4:   required from ‘void ResidueStretchContainer<ResidueStretchType>::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]’
  210 |                         addAllMutualChainResidues(tempInterface.Depth, tempInterface.Chains, tempInterface.PartnerChains, myBiopolymerClassContainer);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Repel.cpp:470:84:   required from here
  470 |     _parameterReader->mobilizerContainer.addStretchesToVectorFromInterfaceContainer(_parameterReader->myBiopolymerClassContainer);
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:232:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  232 |             for (int i = 0; i < concatenatedAtomInfoVector.size() ; i++) {
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:244:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<unsigned int, unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  244 |             for ( int j = 0 ; j < neighborList.size(); j++) {
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::addAllMutualChainResidues(double, std::vector<SimTK::String>, std::vector<SimTK::String>, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:210:4:   required from ‘void ResidueStretchContainer<ResidueStretchType>::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’
  210 |                         addAllMutualChainResidues(tempInterface.Depth, tempInterface.Chains, tempInterface.PartnerChains, myBiopolymerClassContainer);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Repel.cpp:573:84:   required from here
  573 |     _parameterReader->  physicsContainer.addStretchesToVectorFromInterfaceContainer(_parameterReader->myBiopolymerClassContainer);
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:232:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  232 |             for (int i = 0; i < concatenatedAtomInfoVector.size() ; i++) {
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:244:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<unsigned int, unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  244 |             for ( int j = 0 ; j < neighborList.size(); j++) {
      |                               ~~^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘bool ResidueStretchContainer<ResidueStretchType>::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = MobilizerStretch]’:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:264:27:   required from ‘void ResidueStretchContainer<ResidueStretchType>::addAllMutualChainResidues(double, std::vector<SimTK::String>, std::vector<SimTK::String>, BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]’
  264 |                     if (!(vectorHasResidueStretch(myResidueStretch1))) {addStretch(myResidueStretch1);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:210:4:   required from ‘void ResidueStretchContainer<ResidueStretchType>::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = MobilizerStretch]’
  210 |                         addAllMutualChainResidues(tempInterface.Depth, tempInterface.Chains, tempInterface.PartnerChains, myBiopolymerClassContainer);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Repel.cpp:470:84:   required from here
  470 |     _parameterReader->mobilizerContainer.addStretchesToVectorFromInterfaceContainer(_parameterReader->myBiopolymerClassContainer);
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:104:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MobilizerStretch>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  104 |                 for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘bool ResidueStretchContainer<ResidueStretchType>::vectorHasResidueStretch(ResidueStretchType&) [with ResidueStretchType = SingleResidue]’:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:264:27:   required from ‘void ResidueStretchContainer<ResidueStretchType>::addAllMutualChainResidues(double, std::vector<SimTK::String>, std::vector<SimTK::String>, BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’
  264 |                     if (!(vectorHasResidueStretch(myResidueStretch1))) {addStretch(myResidueStretch1);
      |                           ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:210:4:   required from ‘void ResidueStretchContainer<ResidueStretchType>::addStretchesToVectorFromInterfaceContainer(BiopolymerClassContainer&) [with ResidueStretchType = SingleResidue]’
  210 |                         addAllMutualChainResidues(tempInterface.Depth, tempInterface.Chains, tempInterface.PartnerChains, myBiopolymerClassContainer);
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Repel.cpp:573:84:   required from here
  573 |     _parameterReader->  physicsContainer.addStretchesToVectorFromInterfaceContainer(_parameterReader->myBiopolymerClassContainer);
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:104:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SingleResidue>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  104 |                 for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Repel.cpp: At global scope:
/<<PKGBUILDDIR>>/src/Repel.cpp:97:17: warning: ‘bool compareUpper(const std::string&, const char*)’ defined but not used [-Wunused-function]
   97 |     static bool compareUpper( const string& param, const char* symbol ) {
      |                 ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 40%] Building CXX object CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o -MF CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o.d -o CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o -c /<<PKGBUILDDIR>>/src/MonoAtoms.cpp
In file included from /<<PKGBUILDDIR>>/src/MonoAtoms.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 43%] Building CXX object CMakeFiles/MMB.dir/src/Spiral.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/Spiral.cpp.o -MF CMakeFiles/MMB.dir/src/Spiral.cpp.o.d -o CMakeFiles/MMB.dir/src/Spiral.cpp.o -c /<<PKGBUILDDIR>>/src/Spiral.cpp
In file included from /<<PKGBUILDDIR>>/include/Spiral.h:16,
                 from /<<PKGBUILDDIR>>/src/Spiral.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Spiral.cpp: In member function ‘void Spiral::clear()’:
/<<PKGBUILDDIR>>/src/Spiral.cpp:92:12: warning: unused variable ‘helixAdvancePerBasePair’ [-Wunused-variable]
   92 |     double helixAdvancePerBasePair = -11111. ;  // in nm // should be user specified.
      |            ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Spiral.cpp: In member function ‘double Spiral::harmonicThetaAdjustment(double)’:
/<<PKGBUILDDIR>>/src/Spiral.cpp:124:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<frequencyPhaseAmplitude>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  124 |     for (int i =0; i < frequencyPhaseAmplitudeVector.size(); i++){
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/Spiral.cpp: In member function ‘void Spiral::writeCylindricalSpiralCommandFile(MonoAtomsContainer&)’:
/<<PKGBUILDDIR>>/src/Spiral.cpp:140:10: warning: variable ‘deltaZ’ set but not used [-Wunused-but-set-variable]
  140 |     Vec3 deltaZ = Vec3(0,0,1) * sin(cylindricalSpiralSlopeAngle(pitch,radius))*helixAdvancePerBasePair ;
      |          ^~~~~~
/<<PKGBUILDDIR>>/src/Spiral.cpp: In member function ‘void Spiral::writeSphericalSpiralCommandFile(MonoAtomsContainer&)’:
/<<PKGBUILDDIR>>/src/Spiral.cpp:238:16: warning: unused variable ‘currentPhi’ [-Wunused-variable]
  238 |         double currentPhi = priorPhi + deltaPhi ; // phiFromTheta(currentTheta, pitch, radius, phiOffset);
      |                ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/Spiral.cpp:221:12: warning: unused variable ‘phiOffsetFromStartingTheta’ [-Wunused-variable]
  221 |     double phiOffsetFromStartingTheta = phiFromTheta(startTheta, pitch, radius, 0.0, spiralIsRightHanded); // use offset = 0 to retreive the original, non-offset phi
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 46%] Building CXX object CMakeFiles/MMB.dir/src/ParameterReader.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ParameterReader.cpp.o -MF CMakeFiles/MMB.dir/src/ParameterReader.cpp.o.d -o CMakeFiles/MMB.dir/src/ParameterReader.cpp.o -c /<<PKGBUILDDIR>>/src/ParameterReader.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/src/ParameterReader.cpp:17:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::removeNonPriorityBasePairs(int)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:727:9: warning: unused variable ‘oldDutyCyclePriority’ [-Wunused-variable]
  727 |     int oldDutyCyclePriority=0;
      |         ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::updateAllResiduesWithin(int, SimTK::String, int, double)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:776:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<AllResiduesWithin>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  776 |     if(index < 0 || index >= includeAllResiduesWithinVector.size()){
      |                     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::deleteAllResiduesWithin(int)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:785:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<AllResiduesWithin>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  785 |     if(index < 0 || index >= includeAllResiduesWithinVector.size()){
      |                     ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:1582:17: warning: unused variable ‘myForceConstant’ [-Wunused-variable]
 1582 |          double myForceConstant = 1000000000.0; // set to super high value just to make sure it's being reset later.
      |                 ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2069:16: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
 2069 |             if ((parameterStringClass.getString(0).compare("constraint") == 0) || (parameterStringClass.getString(0).compare("restraint") == 0))
      |                ^
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2658:27: warning: variable ‘residueID1’ set but not used [-Wunused-but-set-variable]
 2658 |                 ResidueID residueID1 = ResidueID(-11111,'X');
      |                           ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2659:27: warning: variable ‘residueID2’ set but not used [-Wunused-but-set-variable]
 2659 |                 ResidueID residueID2 = ResidueID(-11111,'X');
      |                           ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2735:16: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
 2735 |             if ((parameterStringClass.getString(0).compare("constraint") == 0) || (parameterStringClass.getString(0).compare("restraint") == 0))
      |                ^
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = SingleResidue]’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:814:42:   required from here
  814 |     physicsContainer.deleteResidueStretch(index);
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SingleResidue>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93,
                 from /usr/include/simbody/SimTKcommon/Simmatrix.h:37,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/SimTKsimbody.h:43,
                 from /<<PKGBUILDDIR>>/include/Utils.h:22:
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘Displacement::Displacement()’ at /<<PKGBUILDDIR>>/include/Utils.h:544:8,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2223:19:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘Displacement [1]’ [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2223:26: note: at offset 56 into object ‘myDisplacement’ of size 128
 2223 |             Displacement myDisplacement;
      |                          ^~~~~~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘Displacement::Displacement()’ at /<<PKGBUILDDIR>>/include/Utils.h:544:8,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2223:19:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘Displacement [1]’ [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2223:26: note: at offset 56 into object ‘myDisplacement’ of size 128
 2223 |             Displacement myDisplacement;
      |                          ^~~~~~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘Displacement::Displacement()’ at /<<PKGBUILDDIR>>/include/Utils.h:544:8,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2223:19:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘Displacement [1]’ [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2223:26: note: at offset 56 into object ‘myDisplacement’ of size 128
 2223 |             Displacement myDisplacement;
      |                          ^~~~~~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2224:22:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72
 2224 |             Rotation myRotation;
      |                      ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2224:22:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72
 2224 |             Rotation myRotation;
      |                      ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2224:22:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72
 2224 |             Rotation myRotation;
      |                      ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70,
    inlined from ‘SimTK::Rotation_<P>& SimTK::Rotation_<P>::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2225:52:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72
 2224 |             Rotation myRotation;
      |                      ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70,
    inlined from ‘SimTK::Rotation_<P>& SimTK::Rotation_<P>::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2225:52:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72
 2224 |             Rotation myRotation;
      |                      ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70,
    inlined from ‘SimTK::Rotation_<P>& SimTK::Rotation_<P>::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2225:52:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2224:22: note: object ‘myRotation’ of size 72
 2224 |             Rotation myRotation;
      |                      ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘Displacement::Displacement()’ at /<<PKGBUILDDIR>>/include/Utils.h:544:8,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2207:30:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘Displacement [1]’ [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2207:30: note: at offset 56 into object ‘myDisplacement’ of size 128
 2207 |                 Displacement myDisplacement;
      |                              ^~~~~~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘Displacement::Displacement()’ at /<<PKGBUILDDIR>>/include/Utils.h:544:8,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2207:30:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘Displacement [1]’ [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2207:30: note: at offset 56 into object ‘myDisplacement’ of size 128
 2207 |                 Displacement myDisplacement;
      |                              ^~~~~~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘Displacement::Displacement()’ at /<<PKGBUILDDIR>>/include/Utils.h:544:8,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2207:30:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘Displacement [1]’ [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2207:30: note: at offset 56 into object ‘myDisplacement’ of size 128
 2207 |                 Displacement myDisplacement;
      |                              ^~~~~~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2209:26:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72
 2209 |                 Rotation myRotation;
      |                          ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2209:26:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72
 2209 |                 Rotation myRotation;
      |                          ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2209:26:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72
 2209 |                 Rotation myRotation;
      |                          ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70,
    inlined from ‘SimTK::Rotation_<P>& SimTK::Rotation_<P>::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2210:56:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72
 2209 |                 Rotation myRotation;
      |                          ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70,
    inlined from ‘SimTK::Rotation_<P>& SimTK::Rotation_<P>::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2210:56:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72
 2209 |                 Rotation myRotation;
      |                          ^~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70,
    inlined from ‘SimTK::Rotation_<P>& SimTK::Rotation_<P>::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20,
    inlined from ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’ at /<<PKGBUILDDIR>>/src/ParameterReader.cpp:2210:56:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/ParameterReader.cpp: In member function ‘void ParameterReader::parameterStringInterpreter(const ParameterStringClass&, int, bool, bool, bool)’:
/<<PKGBUILDDIR>>/src/ParameterReader.cpp:2209:26: note: object ‘myRotation’ of size 72
 2209 |                 Rotation myRotation;
      |                          ^~~~~~~~~~
[ 50%] Building CXX object CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o -MF CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o.d -o CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o -c /<<PKGBUILDDIR>>/src/BaseInteractionParameterReader.cpp
In file included from /<<PKGBUILDDIR>>/include/BaseInteractionParameterReader.h:22,
                 from /<<PKGBUILDDIR>>/src/BaseInteractionParameterReader.cpp:18:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 53%] Building CXX object CMakeFiles/MMB.dir/src/TetherForce.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/TetherForce.cpp.o -MF CMakeFiles/MMB.dir/src/TetherForce.cpp.o.d -o CMakeFiles/MMB.dir/src/TetherForce.cpp.o -c /<<PKGBUILDDIR>>/src/TetherForce.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/TetherForce.h:19,
                 from /<<PKGBUILDDIR>>/src/TetherForce.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 56%] Building CXX object CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o -MF CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o.d -o CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o -c /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClassTwoTransformForces.h:17,
                 from /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:10:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:279:16: warning: variable ‘dutyCycle’ set but not used [-Wunused-but-set-variable]
  279 |         double dutyCycle; //must be between 0 and 1.  at 1, force is applied all the time.  at 0, basically never applied.
      |                ^~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:280:16: warning: variable ‘scrubberPeriod’ set but not used [-Wunused-but-set-variable]
  280 |         double scrubberPeriod;
      |                ^~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
In file included from /usr/include/simbody/SimTKcommon/SmallMatrix.h:93,
                 from /usr/include/simbody/SimTKcommon/Simmatrix.h:37,
                 from /usr/include/simbody/SimTKcommon.h:35,
                 from /usr/include/simbody/Simbody.h:38,
                 from /usr/include/molmodel/SimTKmolmodel.h:47,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClassTwoTransformForces.h:16:
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’ at /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:116:22:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72
  116 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’ at /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:116:22:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72
  116 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’ at /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:116:22:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72
  116 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70,
    inlined from ‘SimTK::Rotation_<P>& SimTK::Rotation_<P>::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20,
    inlined from ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’ at /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:117:50:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72
  116 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70,
    inlined from ‘SimTK::Rotation_<P>& SimTK::Rotation_<P>::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20,
    inlined from ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’ at /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:117:50:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72
  116 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70,
    inlined from ‘SimTK::Rotation_<P>& SimTK::Rotation_<P>::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20,
    inlined from ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’ at /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:117:50:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual void AllTwoTransformLinearSprings::calcForce(const SimTK::State&, SimTK::Vector_<SimTK::Vec<2, SimTK::Vec<3> > >&, SimTK::Vector_<SimTK::Vec<3> >&, SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:116:22: note: object ‘rotation2’ of size 72
  116 |             Rotation rotation2;
      |                      ^~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:254:29: warning: ‘myFrcScalar’ may be used uninitialized [-Wmaybe-uninitialized]
  254 |                 myFrcScalar *= myParameterReader.twoTransformForceMultiplier;
      |                 ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:167:20: note: ‘myFrcScalar’ was declared here
  167 |             double myFrcScalar;
      |                    ^~~~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’ at /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:319:22:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72
  319 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’ at /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:319:22:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72
  319 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::operator=(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’ at /usr/include/simbody/SimTKcommon/internal/Vec.h:775:70,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(const E&) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:361:56,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>::Mat(int) [with int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:377:9,
    inlined from ‘SimTK::Rotation_<P>::Rotation_() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:137:23,
    inlined from ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’ at /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:319:22:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72
  319 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70,
    inlined from ‘SimTK::Rotation_<P>& SimTK::Rotation_<P>::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20,
    inlined from ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’ at /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:320:50:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72
  319 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70,
    inlined from ‘SimTK::Rotation_<P>& SimTK::Rotation_<P>::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20,
    inlined from ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’ at /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:320:50:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72
  319 |             Rotation rotation2;
      |                      ^~~~~~~~~
In member function ‘SimTK::Vec<M, ELT, STRIDE>& SimTK::Vec<M, ELT, STRIDE>::scalarEq(const EE&) [with EE = double; int M = 3; ELT = double; int STRIDE = 4]’,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::scalarEq(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:882:24,
    inlined from ‘SimTK::Mat<M, N, ELT, CS, RS>& SimTK::Mat<M, N, ELT, CS, RS>::operator=(const EE&) [with EE = double; int M = 3; int N = 3; ELT = double; int CS = 3; int RS = 1]’ at /usr/include/simbody/SimTKcommon/internal/Mat.h:872:70,
    inlined from ‘SimTK::Rotation_<P>& SimTK::Rotation_<P>::setRotationToIdentityMatrix() [with P = double]’ at /usr/include/simbody/SimTKcommon/internal/Rotation.h:157:20,
    inlined from ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’ at /<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:320:50:
/usr/include/simbody/SimTKcommon/internal/Vec.h:784:42: warning: array subscript ‘SimTK::Vec<3, double, 4>[0]’ is partly outside array bounds of ‘SimTK::Rotation [1]’ {aka ‘SimTK::Rotation_<double> [1]’} [-Warray-bounds=]
  784 |       { for(int i=0;i<M;++i) d[i*STRIDE] = ee; return *this; }
      |                              ~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp: In member function ‘virtual SimTK::Real AllTwoTransformLinearSprings::calcPotentialEnergy(const SimTK::State&) const’:
/<<PKGBUILDDIR>>/src/BiopolymerClassTwoTransformForces.cpp:319:22: note: object ‘rotation2’ of size 72
  319 |             Rotation rotation2;
      |                      ^~~~~~~~~
[ 59%] Building CXX object CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o -MF CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o.d -o CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o -c /<<PKGBUILDDIR>>/src/WaterDroplet.cpp
In file included from /<<PKGBUILDDIR>>/include/WaterDroplet.h:16,
                 from /<<PKGBUILDDIR>>/src/WaterDroplet.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/WaterDroplet.h:17:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 62%] Building CXX object CMakeFiles/MMB.dir/src/DensityMap.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DensityMap.cpp.o -MF CMakeFiles/MMB.dir/src/DensityMap.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityMap.cpp.o -c /<<PKGBUILDDIR>>/src/DensityMap.cpp
In file included from /<<PKGBUILDDIR>>/src/DensityMap.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp: In member function ‘void DensityMap::resizeVectorOfAmplitudeAndRandomPhases()’:
/<<PKGBUILDDIR>>/src/DensityMap.cpp:177:62: warning: comparison of integer expressions of different signedness: ‘std::vector<std::vector<std::vector<AmplitudeFrequencyAndRandomPhases> > >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  177 |         if (vectorOfAmplitudeFrequencyAndRandomPhases.size() != (unitCellParameters.calcMaxFrequencyDoublingsZ()+1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:181:78: warning: comparison of integer expressions of different signedness: ‘std::vector<std::vector<AmplitudeFrequencyAndRandomPhases> >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  181 |                 if (vectorOfAmplitudeFrequencyAndRandomPhases[zIndex].size() != (unitCellParameters.calcMaxFrequencyDoublingsY()+1) ) {
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:185:90: warning: comparison of integer expressions of different signedness: ‘std::vector<AmplitudeFrequencyAndRandomPhases>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  185 |                     if (vectorOfAmplitudeFrequencyAndRandomPhases[zIndex][yIndex].size() != (unitCellParameters.calcMaxFrequencyDoublingsX()+1 )) {
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp: In member function ‘void DensityMap::densityAutocorrelation(bool, bool) const’:
/<<PKGBUILDDIR>>/src/DensityMap.cpp:209:12: warning: unused variable ‘ySquared’ [-Wunused-variable]
  209 |     double ySquared = 0.;
      |            ^~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:210:12: warning: unused variable ‘zSquared’ [-Wunused-variable]
  210 |     double zSquared = 0.;
      |            ^~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp: In member function ‘void DensityMap::populateNoiseMap()’:
/<<PKGBUILDDIR>>/src/DensityMap.cpp:307:12: warning: unused variable ‘groundFrequencyX’ [-Wunused-variable]
  307 |     double groundFrequencyX = 1/unitCellParameters.getNa()/unitCellParameters.geta()/2;
      |            ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:308:12: warning: unused variable ‘groundFrequencyY’ [-Wunused-variable]
  308 |     double groundFrequencyY = 1/unitCellParameters.getNb()/unitCellParameters.getb()/2;
      |            ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:309:12: warning: unused variable ‘groundFrequencyZ’ [-Wunused-variable]
  309 |     double groundFrequencyZ = 1/unitCellParameters.getNc()/unitCellParameters.getc()/2;
      |            ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:311:12: warning: unused variable ‘maxFrequencyX’ [-Wunused-variable]
  311 |     double maxFrequencyX = 1/unitCellParameters.geta()/2;
      |            ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:312:12: warning: unused variable ‘maxFrequencyY’ [-Wunused-variable]
  312 |     double maxFrequencyY = 1/unitCellParameters.getb()/2;
      |            ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:313:12: warning: unused variable ‘maxFrequencyZ’ [-Wunused-variable]
  313 |     double maxFrequencyZ = 1/unitCellParameters.getc()/2;
      |            ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:318:12: warning: variable ‘signalToNoiseRatio’ set but not used [-Wunused-but-set-variable]
  318 |     double signalToNoiseRatio = 0.;
      |            ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:319:12: warning: unused variable ‘inverseNoiseTemperatureToPower4’ [-Wunused-variable]
  319 |     double inverseNoiseTemperatureToPower4 = 1/pow(noiseTemperature,4); //Stefan–Boltzmann law says total radiance goes like T^4. So we normalize by this number to keep noise sort of constant with temperatuere. Of course our oven has a maximum wavenumber, so this won't be perfect.
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp: In member function ‘void DensityMap::loadParametersAndDensity_CCP4MAP()’:
/<<PKGBUILDDIR>>/src/DensityMap.cpp:543:13: warning: unused variable ‘newU’ [-Wunused-variable]
  543 |         int newU, newV, newW;
      |             ^~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:543:19: warning: unused variable ‘newV’ [-Wunused-variable]
  543 |         int newU, newV, newW;
      |                   ^~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:543:25: warning: unused variable ‘newW’ [-Wunused-variable]
  543 |         int newU, newV, newW;
      |                         ^~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:507:9: warning: unused variable ‘xGridInds’ [-Wunused-variable]
  507 |     int xGridInds                                     = xDimInds;
      |         ^~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:508:9: warning: unused variable ‘yGridInds’ [-Wunused-variable]
  508 |     int yGridInds                                     = yDimInds;
      |         ^~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp:509:9: warning: unused variable ‘zGridInds’ [-Wunused-variable]
  509 |     int zGridInds                                     = zDimInds;
      |         ^~~~~~~~~
/<<PKGBUILDDIR>>/src/DensityMap.cpp: In member function ‘void DensityMap::writeDensityMapXplor(SimTK::String, bool, bool)’:
/<<PKGBUILDDIR>>/src/DensityMap.cpp:689:13: warning: unused variable ‘densitiesPerLine’ [-Wunused-variable]
  689 |         int densitiesPerLine = 6;
      |             ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 65%] Building CXX object CMakeFiles/MMB.dir/src/DensityForce.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/DensityForce.cpp.o -MF CMakeFiles/MMB.dir/src/DensityForce.cpp.o.d -o CMakeFiles/MMB.dir/src/DensityForce.cpp.o -c /<<PKGBUILDDIR>>/src/DensityForce.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/DensityForce.h:20,
                 from /<<PKGBUILDDIR>>/src/DensityForce.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 68%] Building CXX object CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o -MF CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o.d -o CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o -c /<<PKGBUILDDIR>>/src/ElectrostaticPotentialGridForce.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/ElectrostaticPotentialGridForce.h:19,
                 from /<<PKGBUILDDIR>>/src/ElectrostaticPotentialGridForce.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 71%] Building CXX object CMakeFiles/MMB.dir/src/MMBLogger.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/MMBLogger.cpp.o -MF CMakeFiles/MMB.dir/src/MMBLogger.cpp.o.d -o CMakeFiles/MMB.dir/src/MMBLogger.cpp.o -c /<<PKGBUILDDIR>>/src/MMBLogger.cpp
[ 75%] Building CXX object CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -MF CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o.d -o CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o -c /<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/PeriodicPdbAndEnergyWriter.h:13,
                 from /<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:18:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp: In member function ‘virtual void SimTK::PeriodicPdbAndEnergyWriter::handleEvent(SimTK::State&, SimTK::Real, bool&) const’:
/<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:201:30: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  201 |         if(myEnergies.size() > myParameterReader.convergenceTimeout) {
      |            ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:202:20: warning: unused variable ‘lastEnergy’ [-Wunused-variable]
  202 |             double lastEnergy = myEnergies.back();
      |                    ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:49:9: warning: unused variable ‘compoundNumber’ [-Wunused-variable]
   49 |     int compoundNumber                                = 1;
      |         ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/PeriodicPdbAndEnergyWriter.cpp:50:9: warning: unused variable ‘requiredPrecision’ [-Wunused-variable]
   50 |     int requiredPrecision                             = 12;
      |         ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 78%] Building CXX object CMakeFiles/MMB.dir/src/CifOutput.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/CifOutput.cpp.o -MF CMakeFiles/MMB.dir/src/CifOutput.cpp.o.d -o CMakeFiles/MMB.dir/src/CifOutput.cpp.o -c /<<PKGBUILDDIR>>/src/CifOutput.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20,
                 from /<<PKGBUILDDIR>>/include/CifOutput.h:5,
                 from /<<PKGBUILDDIR>>/src/CifOutput.cpp:1:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/PeriodicPdbAndEnergyWriter.h:13,
                 from /<<PKGBUILDDIR>>/include/CifOutput.h:12:
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 81%] Building CXX object CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o -MF CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o.d -o CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o -c /<<PKGBUILDDIR>>/src/ProgressWriter.cpp
[ 84%] Building CXX object CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o -MF CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o.d -o CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o -c /<<PKGBUILDDIR>>/src/NTC_PARAMETER_READER.cpp
In file included from /<<PKGBUILDDIR>>/include/NtC_Class_Container.h:14,
                 from /<<PKGBUILDDIR>>/src/NTC_PARAMETER_READER.cpp:16:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/NTC_FORCE_CLASS.h:4,
                 from /<<PKGBUILDDIR>>/src/NTC_PARAMETER_READER.cpp:17:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 87%] Building CXX object CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o -MF CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o.d -o CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o -c /<<PKGBUILDDIR>>/src/NtCClassContainer.cpp
In file included from /<<PKGBUILDDIR>>/include/Mutation.h:4,
                 from /<<PKGBUILDDIR>>/include/BiopolymerClass.h:20,
                 from /<<PKGBUILDDIR>>/src/NtCClassContainer.cpp:13:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 90%] Building CXX object CMakeFiles/MMB.dir/src/NtCForces.cpp.o
/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DMMB_BUILDING_SHARED_LIBRARY -DMMB_EXPORTS -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -fPIC -MD -MT CMakeFiles/MMB.dir/src/NtCForces.cpp.o -MF CMakeFiles/MMB.dir/src/NtCForces.cpp.o.d -o CMakeFiles/MMB.dir/src/NtCForces.cpp.o -c /<<PKGBUILDDIR>>/src/NtCForces.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/include/NtCForces.h:13,
                 from /<<PKGBUILDDIR>>/src/NtCForces.cpp:11:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
[ 93%] Linking CXX shared library libMMB.so
/usr/bin/cmake -E cmake_link_script CMakeFiles/MMB.dir/link.txt --verbose=1
/usr/bin/riscv64-linux-gnu-g++ -fPIC -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -Wl,--dependency-file=CMakeFiles/MMB.dir/link.d -Wl,-z,relro -shared -Wl,-soname,libMMB.so.4.0 -o libMMB.so.4.0 CMakeFiles/MMB.dir/src/Utils.cpp.o CMakeFiles/MMB.dir/src/BiopolymerClass.cpp.o CMakeFiles/MMB.dir/src/UnitCellParameters.cpp.o CMakeFiles/MMB.dir/src/AtomSpringContainer.cpp.o CMakeFiles/MMB.dir/src/DisplacementContainer.cpp.o CMakeFiles/MMB.dir/src/MobilizerContainer.cpp.o CMakeFiles/MMB.dir/src/MoleculeContainer.cpp.o CMakeFiles/MMB.dir/src/DensityContainer.cpp.o CMakeFiles/MMB.dir/src/BasePairContainer.cpp.o CMakeFiles/MMB.dir/src/ContactContainer.cpp.o CMakeFiles/MMB.dir/src/ConstraintContainer.cpp.o CMakeFiles/MMB.dir/src/Repel.cpp.o CMakeFiles/MMB.dir/src/MonoAtoms.cpp.o CMakeFiles/MMB.dir/src/Spiral.cpp.o CMakeFiles/MMB.dir/src/ParameterReader.cpp.o CMakeFiles/MMB.dir/src/BaseInteractionParameterReader.cpp.o CMakeFiles/MMB.dir/src/TetherForce.cpp.o CMakeFiles/MMB.dir/src/BiopolymerClassTwoTransformForces.cpp.o CMakeFiles/MMB.dir/src/WaterDroplet.cpp.o CMakeFiles/MMB.dir/src/DensityMap.cpp.o CMakeFiles/MMB.dir/src/DensityForce.cpp.o CMakeFiles/MMB.dir/src/ElectrostaticPotentialGridForce.cpp.o CMakeFiles/MMB.dir/src/MMBLogger.cpp.o CMakeFiles/MMB.dir/src/PeriodicPdbAndEnergyWriter.cpp.o CMakeFiles/MMB.dir/src/CifOutput.cpp.o CMakeFiles/MMB.dir/src/ProgressWriter.cpp.o CMakeFiles/MMB.dir/src/NTC_PARAMETER_READER.cpp.o CMakeFiles/MMB.dir/src/NtCClassContainer.cpp.o CMakeFiles/MMB.dir/src/NtCForces.cpp.o   -L/<<PKGBUILDDIR>>/SYSTEM  -Wl,-rpath,/<<PKGBUILDDIR>>/SYSTEM: /usr/lib/riscv64-linux-gnu/libSimTKmolmodel.so.3.1 /usr/lib/riscv64-linux-gnu/libOpenMM.so /usr/lib/riscv64-linux-gnu/libz.so -lgemmi_cpp /usr/lib/riscv64-linux-gnu/libSimTKsimbody.so.3.7 /usr/lib/riscv64-linux-gnu/libSimTKmath.so.3.7 /usr/lib/riscv64-linux-gnu/libSimTKcommon.so.3.7 /usr/lib/riscv64-linux-gnu/libblas.so /usr/lib/riscv64-linux-gnu/liblapack.so /usr/lib/riscv64-linux-gnu/libblas.so /usr/lib/riscv64-linux-gnu/liblapack.so -lpthread -lrt -ldl -lm
/usr/bin/cmake -E cmake_symlink_library libMMB.so.4.0 libMMB.so.4.0 libMMB.so
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/usr/bin/riscv64-linux-gnu-g++ -DHAVE_COPY_FILE_RANGE -DHAVE_SENDFILE -DUSE_MMB_CONSTEXPR -I/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>>/include -isystem /usr/include/simbody -isystem /usr/include/molmodel -D BuildNtC -D USE_OPENMM -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fvisibility=hidden -Wall -pedantic -O3 -DNDEBUG -MD -MT CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o -MF CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o.d -o CMakeFiles/MMB_EXEC.dir/src/RNABuilder.cpp.o -c /<<PKGBUILDDIR>>/src/RNABuilder.cpp
In file included from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:14,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:20,
                 from /<<PKGBUILDDIR>>/src/RNABuilder.cpp:22:
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘virtual SimTK::Real ConstraintFunction::calcDerivative(const SimTK::Array_<int>&, const SimTK::Vector&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:290:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  290 |          if (derivComponents.size() == 1)
      |          ^~
/<<PKGBUILDDIR>>/include/Utils.h:292:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  292 |              return 0;
      |              ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘ResidueID::ResidueID(SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:321:14: warning: unused variable ‘endChar’ [-Wunused-variable]
  321 |         char endChar = *(inputString.substr(stringLength-1, 1)).c_str();
      |              ^~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘const SimTK::String ResidueID::chainIDResidueID(const SimTK::String&) const’:
/<<PKGBUILDDIR>>/include/Utils.h:386:45: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  386 |         if ((myStringStream.str()).length() != (totalWidth - 1)) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void Interface::print()’:
/<<PKGBUILDDIR>>/include/Utils.h:666:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  666 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:670:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  670 |                    for (int i = 0; i < Chains.size(); i ++) {
      |                                    ~~^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1308:9: warning:   when initialized here [-Wreorder]
 1308 |         MMBAtomInfo(String myChain, ResidueID myResidueID, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In constructor ‘MMBAtomInfo::MMBAtomInfo(SimTK::String, ResidueID, SimTK::ResidueInfo::Index, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1294:16: warning: ‘MMBAtomInfo::chain’ will be initialized after [-Wreorder]
 1294 |         String chain;
      |                ^~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1292:19: warning:   ‘ResidueID MMBAtomInfo::residueID’ [-Wreorder]
 1292 |         ResidueID residueID;
      |                   ^~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:1314:9: warning:   when initialized here [-Wreorder]
 1314 |         MMBAtomInfo(String myChain, ResidueID myResidueID, ResidueInfo::Index myResidueIndex, String myAtomName) :
      |         ^~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: In member function ‘void InterfaceContainer::addInterface(std::vector<SimTK::String>, double, SimTK::String)’:
/<<PKGBUILDDIR>>/include/Utils.h:1379:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SimTK::String>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1379 |             for (int i = 0; i < myChains.size(); i++) {myInterface.Chains.push_back( myChains[i]);}  myInterface.Depth = myDepth; myInterface.MobilizerString = myMobilizerString; interfaceVector.push_back(myInterface); };
      |                             ~~^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/Threading.h:2,
                 from /<<PKGBUILDDIR>>/include/AtomSpringContainer.h:15:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h: In member function ‘void BiopolymerClass::printAtomInfoVector()’:
/<<PKGBUILDDIR>>/include/BiopolymerClass.h:255:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<MMBAtomInfo>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  255 |     void printAtomInfoVector(){for (int i = 0 ; i < atomInfoVector.size(); i++) atomInfoVector[i].print(); };
      |                                                 ~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘bool ThreadingStruct::hasResidue(ResidueID, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:71:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   71 |             for (int i = 0; i < threadingPartners[biopolymerIndex].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Threading.h: In member function ‘void ThreadingStruct::supplementIncludedResidues(int, int)’:
/<<PKGBUILDDIR>>/include/Threading.h:78:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ResidueID>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   78 |             for (int i = 0; i < threadingPartners[fromBiopolymer].includedResidues.size() ;  i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h: In member function ‘void AtomSpringContainer::printAllAlignmentStats()’:
/<<PKGBUILDDIR>>/include/AtomSpringContainer.h:73:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ThreadingStruct>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |         void printAllAlignmentStats(){for (int i = 0; i < threadingStructVector.size(); i++){threadingStructVector[i].printAlignmentStats();}}
      |                                                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/include/ContactContainer.h:15,
                 from /<<PKGBUILDDIR>>/include/ParameterReader.h:21:
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::printResidueStretchVector() [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:22:59:   required from here
   22 |     void printDensityStretches(){printResidueStretchVector();}; // just use printResidueStretchVector()
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:61:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   61 |         for (int i = 0 ; i <residueStretchVector.size(); i++) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h: In instantiation of ‘void ResidueStretchContainer<ResidueStretchType>::deleteResidueStretch(int) [with ResidueStretchType = DensityStretch]’:
/<<PKGBUILDDIR>>/include/DensityContainer.h:25:59:   required from here
   25 |     void deleteDensityStretch(int id){deleteResidueStretch(id);}; // just use parent's deleteResidueStretch(int id)
      |                                       ~~~~~~~~~~~~~~~~~~~~^~~~
/<<PKGBUILDDIR>>/include/ResidueStretchContainer.h:144:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<DensityStretch, std::allocator<DensityStretch> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  144 |         if(id >= 0 && id < residueStretchVector.size())
      |                       ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/include/Utils.h: At global scope:
/<<PKGBUILDDIR>>/include/Utils.h:257:17: warning: ‘{anonymous}::digits’ defined but not used [-Wunused-variable]
  257 |     const char* digits = "0123456789";
      |                 ^~~~~~
/<<PKGBUILDDIR>>/include/Utils.h:256:17: warning: ‘{anonymous}::spaces’ defined but not used [-Wunused-variable]
  256 |     const char* spaces = " \t";
      |                 ^~~~~~
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/usr/bin/cmake -E cmake_link_script CMakeFiles/MMB_EXEC.dir/link.txt --verbose=1
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-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/PeriodicScrubber.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/ProgressWriter.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/RandomizeRNACoordinates.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/Repel.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/ResidueStretchContainer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/RigidifyFormedHelices.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/SetChiMobility.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/SetSingleBondMobility.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/Spiral.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/StackingForceSubsystem.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/Sterics.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/TetherForce.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/Threading.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/UnitCellParameters.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/Utils.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/WadleyKeatingDuartePyleTorsionForce.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/Water.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/WaterDroplet.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/superimposer.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/MMB/MMB_config.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/riscv64-linux-gnu/libMMB.so.4.0
-- Set non-toolchain portion of runtime path of "/<<PKGBUILDDIR>>/debian/tmp/usr/lib/riscv64-linux-gnu/libMMB.so.4.0" to ""
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/riscv64-linux-gnu/libMMB.so
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/share/MMB/parameters.csv
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/MMB
-- Set non-toolchain portion of runtime path of "/<<PKGBUILDDIR>>/debian/tmp/usr/bin/MMB" to ""
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/riscv64-linux-gnu/cmake/mmb/MmbConfigVersion.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/riscv64-linux-gnu/cmake/mmb/MmbTargets.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/riscv64-linux-gnu/cmake/mmb/MmbTargets-release.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/riscv64-linux-gnu/pkgconfig/mmb.pc
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-riscv64-linux-gnu'
   dh_install -a
   dh_installdocs -a
   dh_installchangelogs -a
   debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
a2x -d manpage -f manpage -D debian/tmp debian/MMB.1.asciidoc
dh_installman
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_lintian -a
   dh_perl -a
   dh_link -a
   dh_strip_nondeterminism -a
   dh_compress -a
   dh_fixperms -a
   dh_missing -a
   dh_dwz -a
   dh_strip -a
   dh_makeshlibs -a
   dh_shlibdeps -a
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 from: /lib/ld-linux-riscv64-lp64d.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 to: /lib/ld-linux-riscv64-lp64d.so.1.usr-is-merged
dpkg-shlibdeps: warning: symbol gzgets used by debian/libmmb4.0t64/usr/lib/riscv64-linux-gnu/libMMB.so.4.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzclose_r used by debian/libmmb4.0t64/usr/lib/riscv64-linux-gnu/libMMB.so.4.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzopen used by debian/libmmb4.0t64/usr/lib/riscv64-linux-gnu/libMMB.so.4.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzerror used by debian/libmmb4.0t64/usr/lib/riscv64-linux-gnu/libMMB.so.4.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzeof used by debian/libmmb4.0t64/usr/lib/riscv64-linux-gnu/libMMB.so.4.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzbuffer used by debian/libmmb4.0t64/usr/lib/riscv64-linux-gnu/libMMB.so.4.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzungetc used by debian/libmmb4.0t64/usr/lib/riscv64-linux-gnu/libMMB.so.4.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzgetc used by debian/libmmb4.0t64/usr/lib/riscv64-linux-gnu/libMMB.so.4.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol gzread used by debian/libmmb4.0t64/usr/lib/riscv64-linux-gnu/libMMB.so.4.0 found in none of the libraries
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 from: /lib/ld-linux-riscv64-lp64d.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 to: /lib/ld-linux-riscv64-lp64d.so.1.usr-is-merged
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mmb/usr/bin/MMB was not linked against libz.so.1 (it uses none of the library's symbols)
   dh_installdeb -a
   dh_gencontrol -a
   dh_md5sums -a
   dh_builddeb -a
dpkg-deb: building package 'libmmb-dev' in '../libmmb-dev_4.0.0+dfsg-5_riscv64.deb'.
dpkg-deb: building package 'libmmb4.0t64' in '../libmmb4.0t64_4.0.0+dfsg-5_riscv64.deb'.
dpkg-deb: building package 'libmmb4.0t64-dbgsym' in '../libmmb4.0t64-dbgsym_4.0.0+dfsg-5_riscv64.deb'.
dpkg-deb: building package 'mmb' in '../mmb_4.0.0+dfsg-5_riscv64.deb'.
dpkg-deb: building package 'mmb-dbgsym' in '../mmb-dbgsym_4.0.0+dfsg-5_riscv64.deb'.
 dpkg-genbuildinfo --build=any -O../macromoleculebuilder_4.0.0+dfsg-5_riscv64.buildinfo
 dpkg-genchanges --build=any -O../macromoleculebuilder_4.0.0+dfsg-5_riscv64.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 2025-01-06T22:51:52Z

+------------------------------------------------------------------------------+
| Finished Timed Build Commands                                                |
+------------------------------------------------------------------------------+


rm -Rf /<<PKGBUILDDIR>>/
--------------------------------------------------------------------------


I: Finished running 'rm -Rf /<<PKGBUILDDIR>>/'.

Finished processing commands.
--------------------------------------------------------------------------------

Finished
--------

I: Built successfully

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


macromoleculebuilder_4.0.0+dfsg-5_riscv64.changes:
--------------------------------------------------

Format: 1.8
Date: Wed, 27 Nov 2024 02:07:37 -0500
Source: macromoleculebuilder
Binary: libmmb-dev libmmb4.0t64 libmmb4.0t64-dbgsym mmb mmb-dbgsym
Built-For-Profiles: cross nocheck
Architecture: riscv64
Version: 4.0.0+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Changed-By: Andrius Merkys <merkys@debian.org>
Description:
 libmmb-dev - development files of MacroMoleculeBuilder
 libmmb4.0t64 - shared library of MacroMoleculeBuilder
 mmb        - model the structure and dynamics of macromolecules
Closes: 1086362
Changes:
 macromoleculebuilder (4.0.0+dfsg-5) unstable; urgency=medium
 .
   * Link MMB_SHARED_TARGET with ZLIB_LIBRARIES via patch (Closes: #1086362)
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 16f7f90960fdd32c8df1e3f7bbcb54290e763841 1118564 libmmb4.0t64_4.0.0+dfsg-5_riscv64.deb
 6c8ae2c7a7bb6163c5f0b88de1dbe46de1c7333b 10281 macromoleculebuilder_4.0.0+dfsg-5_riscv64.buildinfo
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Files:
 ea92138a8e1d01bef57717ed3edf53f4 76628 libdevel optional libmmb-dev_4.0.0+dfsg-5_riscv64.deb
 c0d772bdd8d625b1c6b9c824559886b2 20665148 debug optional libmmb4.0t64-dbgsym_4.0.0+dfsg-5_riscv64.deb
 e09305570bdc3c4afca23263dd633fe6 1118564 libs optional libmmb4.0t64_4.0.0+dfsg-5_riscv64.deb
 89a3eb4e998024926dfc5f16bdcb5759 10281 science optional macromoleculebuilder_4.0.0+dfsg-5_riscv64.buildinfo
 82372673c1014c1c0abd10154ce237c8 1508364 debug optional mmb-dbgsym_4.0.0+dfsg-5_riscv64.deb
 0a9149f595aa980bf2777e265db8137c 28268 science optional mmb_4.0.0+dfsg-5_riscv64.deb

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

Format: 1.0
Source: macromoleculebuilder
Binary: libmmb-dev libmmb4.0t64 libmmb4.0t64-dbgsym mmb mmb-dbgsym
Architecture: riscv64
Version: 4.0.0+dfsg-5
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Build-Origin: Debian
Build-Architecture: amd64
Build-Date: Mon, 06 Jan 2025 22:51:51 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
 architecture-properties (= 0.2.3),
 asciidoc-base (= 10.2.1-1),
 asciidoc-common (= 10.2.1-1),
 autoconf (= 2.72-3),
 automake (= 1:1.16.5-1.3),
 autopoint (= 0.22.5-4),
 autotools-dev (= 20220109.1),
 base-files (= 13.6),
 base-passwd (= 3.6.6),
 bash (= 5.2.37-1),
 binutils (= 2.43.50.20241230-1),
 binutils-common (= 2.43.50.20241230-1),
 binutils-x86-64-linux-gnu (= 2.43.50.20241230-1),
 bsdextrautils (= 2.40.2-13),
 bsdutils (= 1:2.40.2-13),
 build-essential (= 12.12),
 bzip2 (= 1.0.8-6),
 cmake (= 3.31.3-1),
 cmake-data (= 3.31.3-1),
 coreutils (= 9.5-1+b1),
 cpp (= 4:14.2.0-1),
 cpp-14 (= 14.2.0-12),
 cpp-14-x86-64-linux-gnu (= 14.2.0-12),
 cpp-x86-64-linux-gnu (= 4:14.2.0-1),
 dash (= 0.5.12-10),
 debconf (= 1.5.89),
 debhelper (= 13.23),
 debianutils (= 5.21),
 dh-autoreconf (= 20),
 dh-strip-nondeterminism (= 1.14.0-1),
 diffutils (= 1:3.10-1),
 docbook-xml (= 4.5-13),
 docbook-xsl (= 1.79.2+dfsg-7),
 dpkg (= 1.22.13),
 dpkg-dev (= 1.22.13),
 dwz (= 0.15-1+b1),
 file (= 1:5.45-3+b1),
 findutils (= 4.10.0-3),
 freeglut3-dev (= 3.4.0-4),
 g++ (= 4:14.2.0-1),
 g++-14 (= 14.2.0-12),
 g++-14-x86-64-linux-gnu (= 14.2.0-12),
 g++-x86-64-linux-gnu (= 4:14.2.0-1),
 gcc (= 4:14.2.0-1),
 gcc-14 (= 14.2.0-12),
 gcc-14-base (= 14.2.0-12),
 gcc-14-x86-64-linux-gnu (= 14.2.0-12),
 gcc-x86-64-linux-gnu (= 4:14.2.0-1),
 gemmi-dev (= 0.6.5+ds-2),
 gettext (= 0.22.5-4),
 gettext-base (= 0.22.5-4),
 grep (= 3.11-4),
 groff-base (= 1.23.0-7),
 gzip (= 1.12-1.2),
 hostname (= 3.25),
 init-system-helpers (= 1.68),
 intltool-debian (= 0.35.0+20060710.6),
 libacl1 (= 2.3.2-2+b1),
 libarchive-zip-perl (= 1.68-1),
 libarchive13t64 (= 3.7.4-1.1),
 libasan8 (= 14.2.0-12),
 libatomic1 (= 14.2.0-12),
 libattr1 (= 1:2.5.2-2),
 libaudit-common (= 1:4.0.2-2),
 libaudit1 (= 1:4.0.2-2),
 libbinutils (= 2.43.50.20241230-1),
 libblas-dev (= 3.12.0-4),
 libblas3 (= 3.12.0-4),
 libblkid1 (= 2.40.2-13),
 libbrotli1 (= 1.1.0-2+b6),
 libbsd0 (= 0.12.2-2),
 libbz2-1.0 (= 1.0.8-6),
 libc-bin (= 2.40-5),
 libc-dev-bin (= 2.40-5),
 libc6 (= 2.40-5),
 libc6-dev (= 2.40-5),
 libcap-ng0 (= 0.8.5-4),
 libcap2 (= 1:2.66-5+b1),
 libcc1-0 (= 14.2.0-12),
 libcom-err2 (= 1.47.2-1),
 libcrypt-dev (= 1:4.4.36-5),
 libcrypt1 (= 1:4.4.36-5),
 libctf-nobfd0 (= 2.43.50.20241230-1),
 libctf0 (= 2.43.50.20241230-1),
 libcurl4t64 (= 8.11.1-1),
 libdb5.3t64 (= 5.3.28+dfsg2-9),
 libdebconfclient0 (= 0.277),
 libdebhelper-perl (= 13.23),
 libdpkg-perl (= 1.22.13),
 libdrm-amdgpu1 (= 2.4.123-1),
 libdrm-common (= 2.4.123-1),
 libdrm-radeon1 (= 2.4.123-1),
 libdrm2 (= 2.4.123-1),
 libedit2 (= 3.1-20240808-1),
 libelf1t64 (= 0.192-4),
 libexpat1 (= 2.6.4-1),
 libffi8 (= 3.4.6-1),
 libfile-stripnondeterminism-perl (= 1.14.0-1),
 libgbm1 (= 24.2.8-1),
 libgcc-14-dev (= 14.2.0-12),
 libgcc-s1 (= 14.2.0-12),
 libgcrypt20 (= 1.11.0-7),
 libgdbm-compat4t64 (= 1.24-2),
 libgdbm6t64 (= 1.24-2),
 libgfortran5 (= 14.2.0-12),
 libgl-dev (= 1.7.0-1+b2),
 libgl1 (= 1.7.0-1+b2),
 libgl1-mesa-dri (= 24.2.8-1),
 libglapi-mesa (= 24.2.8-1),
 libglu1-mesa (= 9.0.2-1.1+b3),
 libglu1-mesa-dev (= 9.0.2-1.1+b3),
 libglut-dev (= 3.4.0-4),
 libglut3.12 (= 3.4.0-4),
 libglvnd0 (= 1.7.0-1+b2),
 libglx-dev (= 1.7.0-1+b2),
 libglx-mesa0 (= 24.2.8-1),
 libglx0 (= 1.7.0-1+b2),
 libgmp10 (= 2:6.3.0+dfsg-3),
 libgnutls30t64 (= 3.8.8-2),
 libgomp1 (= 14.2.0-12),
 libgpg-error0 (= 1.51-3),
 libgprofng0 (= 2.43.50.20241230-1),
 libgssapi-krb5-2 (= 1.21.3-3),
 libhogweed6t64 (= 3.10-1+b1),
 libhwasan0 (= 14.2.0-12),
 libice-dev (= 2:1.1.1-1),
 libice6 (= 2:1.1.1-1),
 libicu72 (= 72.1-5+b1),
 libidn2-0 (= 2.3.7-2+b1),
 libisl23 (= 0.27-1),
 libitm1 (= 14.2.0-12),
 libjansson4 (= 2.14-2+b3),
 libjsoncpp26 (= 1.9.6-3),
 libk5crypto3 (= 1.21.3-3),
 libkeyutils1 (= 1.6.3-4),
 libkrb5-3 (= 1.21.3-3),
 libkrb5support0 (= 1.21.3-3),
 liblapack-dev (= 3.12.0-4),
 liblapack3 (= 3.12.0-4),
 libldap-2.5-0 (= 2.5.19+dfsg-1),
 libllvm19 (= 1:19.1.6-1),
 liblsan0 (= 14.2.0-12),
 liblz4-1 (= 1.9.4-4),
 liblzma5 (= 5.6.3-1+b1),
 libmagic-mgc (= 1:5.45-3+b1),
 libmagic1t64 (= 1:5.45-3+b1),
 libmd0 (= 1.1.0-2+b1),
 libmount1 (= 2.40.2-13),
 libmpc3 (= 1.3.1-1+b3),
 libmpfr6 (= 4.2.1-1+b2),
 libncursesw6 (= 6.5-2+b1),
 libnettle8t64 (= 3.10-1+b1),
 libnghttp2-14 (= 1.64.0-1),
 libnsl2 (= 1.3.0-3+b3),
 libopengl-dev (= 1.7.0-1+b2),
 libopengl0 (= 1.7.0-1+b2),
 libopenmm-dev (= 8.1.2+dfsg-2),
 libopenmm8.1 (= 8.1.2+dfsg-2),
 libp11-kit0 (= 0.25.5-3),
 libpam-modules (= 1.5.3-7+b1),
 libpam-modules-bin (= 1.5.3-7+b1),
 libpam-runtime (= 1.5.3-7),
 libpam0g (= 1.5.3-7+b1),
 libpcre2-8-0 (= 10.44-5),
 libperl5.40 (= 5.40.0-8),
 libpipeline1 (= 1.5.8-1),
 libproc2-0 (= 2:4.0.4-6),
 libpsl5t64 (= 0.21.2-1.1+b1),
 libpython3-stdlib (= 3.12.8-1),
 libpython3.12-minimal (= 3.12.8-3),
 libpython3.12-stdlib (= 3.12.8-3),
 libquadmath0 (= 14.2.0-12),
 libreadline8t64 (= 8.2-6),
 librhash1 (= 1.4.5-1),
 librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b5),
 libsasl2-2 (= 2.1.28+dfsg1-8),
 libsasl2-modules-db (= 2.1.28+dfsg1-8),
 libseccomp2 (= 2.5.5-2),
 libselinux1 (= 3.7-3+b1),
 libsensors-config (= 1:3.6.0-10),
 libsensors5 (= 1:3.6.0-10+b1),
 libseqan2-dev (= 2.4.0+dfsg-16),
 libsframe1 (= 2.43.50.20241230-1),
 libsimbody-dev (= 3.7+dfsg-3),
 libsimbody3.7 (= 3.7+dfsg-3),
 libsimtkmolmodel-dev (= 3.1.0-4.1),
 libsimtkmolmodel-plugins (= 3.1.0-4.1),
 libsimtkmolmodel3.1t64 (= 3.1.0-4.1),
 libsm-dev (= 2:1.2.4-1),
 libsm6 (= 2:1.2.4-1),
 libsmartcols1 (= 2.40.2-13),
 libsqlite3-0 (= 3.46.1-1),
 libssh2-1t64 (= 1.11.1-1),
 libssl3t64 (= 3.4.0-2),
 libstb-dev (= 0.0~git20240715.f7f20f39fe4f+ds-1),
 libstb0t64 (= 0.0~git20240715.f7f20f39fe4f+ds-1),
 libstdc++-14-dev (= 14.2.0-12),
 libstdc++6 (= 14.2.0-12),
 libsystemd0 (= 257.1-7),
 libtasn1-6 (= 4.19.0-3+b3),
 libtinfo6 (= 6.5-2+b1),
 libtirpc-common (= 1.3.4+ds-1.3),
 libtirpc3t64 (= 1.3.4+ds-1.3+b1),
 libtool (= 2.5.4-2),
 libtsan2 (= 14.2.0-12),
 libubsan1 (= 14.2.0-12),
 libuchardet0 (= 0.0.8-1+b2),
 libudev1 (= 257.1-7),
 libunistring5 (= 1.3-1),
 libuuid1 (= 2.40.2-13),
 libuv1t64 (= 1.48.0-7),
 libvulkan1 (= 1.3.296.0-1),
 libwayland-server0 (= 1.23.0-1+b1),
 libx11-6 (= 2:1.8.10-2),
 libx11-data (= 2:1.8.10-2),
 libx11-dev (= 2:1.8.10-2),
 libx11-xcb1 (= 2:1.8.10-2),
 libxau-dev (= 1:1.0.11-1),
 libxau6 (= 1:1.0.11-1),
 libxcb-dri2-0 (= 1.17.0-2+b1),
 libxcb-dri3-0 (= 1.17.0-2+b1),
 libxcb-glx0 (= 1.17.0-2+b1),
 libxcb-present0 (= 1.17.0-2+b1),
 libxcb-randr0 (= 1.17.0-2+b1),
 libxcb-shm0 (= 1.17.0-2+b1),
 libxcb-sync1 (= 1.17.0-2+b1),
 libxcb-xfixes0 (= 1.17.0-2+b1),
 libxcb1 (= 1.17.0-2+b1),
 libxcb1-dev (= 1.17.0-2+b1),
 libxdmcp-dev (= 1:1.1.5-1),
 libxdmcp6 (= 1:1.1.5-1),
 libxext-dev (= 2:1.3.4-1+b3),
 libxext6 (= 2:1.3.4-1+b3),
 libxfixes-dev (= 1:6.0.0-2+b3),
 libxfixes3 (= 1:6.0.0-2+b3),
 libxi-dev (= 2:1.8.2-1),
 libxi6 (= 2:1.8.2-1),
 libxml2 (= 2.12.7+dfsg+really2.9.14-0.2+b1),
 libxml2-utils (= 2.12.7+dfsg+really2.9.14-0.2+b1),
 libxmu-dev (= 2:1.1.3-3+b4),
 libxmu-headers (= 2:1.1.3-3),
 libxmu6 (= 2:1.1.3-3+b4),
 libxshmfence1 (= 1.3-1+b3),
 libxslt1.1 (= 1.1.35-1.1+b1),
 libxt-dev (= 1:1.2.1-1.2+b2),
 libxt6t64 (= 1:1.2.1-1.2+b2),
 libxxf86vm1 (= 1:1.1.4-1+b4),
 libxxhash0 (= 0.8.3-2),
 libz3-4 (= 4.13.3-1),
 libzstd1 (= 1.5.6+dfsg-2),
 linux-libc-dev (= 6.12.8-1),
 m4 (= 1.4.19-4),
 make (= 4.4.1-1),
 man-db (= 2.13.0-1),
 mawk (= 1.3.4.20240905-1),
 media-types (= 10.1.0),
 mesa-libgallium (= 24.2.8-1),
 ncurses-base (= 6.5-2),
 ncurses-bin (= 6.5-2+b1),
 netbase (= 6.4),
 openssl-provider-legacy (= 3.4.0-2),
 patch (= 2.7.6-7),
 perl (= 5.40.0-8),
 perl-base (= 5.40.0-8),
 perl-modules-5.40 (= 5.40.0-8),
 po-debconf (= 1.0.21+nmu1),
 procps (= 2:4.0.4-6),
 python3 (= 3.12.8-1),
 python3-minimal (= 3.12.8-1),
 python3.12 (= 3.12.8-3),
 python3.12-minimal (= 3.12.8-3),
 readline-common (= 8.2-6),
 rpcsvc-proto (= 1.4.3-1),
 sed (= 4.9-2),
 sensible-utils (= 0.0.24),
 sgml-base (= 1.31),
 sgml-data (= 2.0.11+nmu1),
 sysvinit-utils (= 3.11-1),
 tao-pegtl-dev (= 3.2.7-1),
 tar (= 1.35+dfsg-3.1),
 tzdata (= 2024b-4),
 util-linux (= 2.40.2-13),
 uuid-dev (= 2.40.2-13),
 x11-common (= 1:7.7+23.1),
 x11proto-dev (= 2024.1-1),
 xml-core (= 0.19),
 xorg-sgml-doctools (= 1:1.11-1.1),
 xsltproc (= 1.1.35-1.1+b1),
 xtrans-dev (= 1.4.0-1),
 xz-utils (= 5.6.3-1+b1),
 zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1),
 zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1)
Environment:
 DEB_BUILD_OPTIONS="nocheck parallel=1"
 DEB_BUILD_PROFILES="cross nocheck"
 LANG="C.UTF-8"
 LC_COLLATE="C.UTF-8"
 LC_CTYPE="C.UTF-8"
 SOURCE_DATE_EPOCH="1732691257"


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


libmmb-dev_4.0.0+dfsg-5_riscv64.deb
-----------------------------------

 new Debian package, version 2.0.
 size 76628 bytes: control archive=2900 bytes.
     779 bytes,    20 lines      control
    5113 bytes,    72 lines      md5sums
 Package: libmmb-dev
 Source: macromoleculebuilder
 Version: 4.0.0+dfsg-5
 Architecture: riscv64
 Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
 Installed-Size: 559
 Depends: libmmb4.0t64 (= 4.0.0+dfsg-5)
 Breaks: libmmblib-dev (<< 4.0.0)
 Replaces: libmmblib-dev (<< 4.0.0)
 Section: libdevel
 Priority: optional
 Multi-Arch: same
 Homepage: https://simtk.org/projects/rnatoolbox
 Description: development files of MacroMoleculeBuilder
  MacroMoleculeBuilder, previously known as RNABuilder, can be used for morphing,
  homology modeling, folding (e.g. using base pairing contacts), redesigning
  complexes, fitting to low-resolution density maps, predicting local
  rearrangements upon mutation, and many other applications.
  .
  This package contains the development files.

drwxr-xr-x root/root         0 2024-11-27 07:07 ./
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/include/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/include/MMB/
-rw-r--r-- root/root      8108 2022-11-29 12:01 ./usr/include/MMB/AddBackboneOxygenForces.h
-rw-r--r-- root/root      6293 2022-11-29 12:01 ./usr/include/MMB/AddNASTForces.h
-rw-r--r-- root/root      5724 2022-11-29 12:01 ./usr/include/MMB/AtomSpringContainer.h
-rw-r--r-- root/root      3559 2022-11-29 12:01 ./usr/include/MMB/BaseInteractionParameterReader.h
-rw-r--r-- root/root      3477 2022-11-29 12:01 ./usr/include/MMB/BasePairContainer.h
-rw-r--r-- root/root     42905 2022-11-29 12:01 ./usr/include/MMB/BiopolymerClass.h
-rw-r--r-- root/root      2644 2022-11-29 12:01 ./usr/include/MMB/BiopolymerClassTwoTransformForces.h
-rw-r--r-- root/root     19309 2022-11-29 12:01 ./usr/include/MMB/CalcTransformCorrection.h
-rw-r--r-- root/root      3188 2022-11-29 12:01 ./usr/include/MMB/CenterOfMass.h
-rw-r--r-- root/root      1328 2022-11-29 12:01 ./usr/include/MMB/CifOutput.h
-rw-r--r-- root/root       188 2022-11-29 12:01 ./usr/include/MMB/Constexpr.h
-rw-r--r-- root/root      3848 2022-11-29 12:01 ./usr/include/MMB/ConstraintContainer.h
-rw-r--r-- root/root      3295 2022-11-29 12:01 ./usr/include/MMB/ContactContainer.h
-rw-r--r-- root/root      1793 2022-11-29 12:01 ./usr/include/MMB/DensityContainer.h
-rw-r--r-- root/root      2105 2022-11-29 12:01 ./usr/include/MMB/DensityForce.h
-rw-r--r-- root/root      7794 2022-11-29 12:01 ./usr/include/MMB/DensityMap.h
-rw-r--r-- root/root      1912 2022-11-29 12:01 ./usr/include/MMB/DisplacementContainer.h
-rw-r--r-- root/root      2165 2022-11-29 12:01 ./usr/include/MMB/ElectrostaticPotentialGridForce.h
-rw-r--r-- root/root      3001 2022-11-29 12:01 ./usr/include/MMB/ExportMacros.h
-rw-r--r-- root/root       752 2022-11-29 12:01 ./usr/include/MMB/ExtraMath.h
-rw-r--r-- root/root      1756 2022-11-29 12:01 ./usr/include/MMB/GeometricCenter.h
-rw-r--r-- root/root      4613 2022-11-29 12:01 ./usr/include/MMB/HarmonicVelocityRescalingThermostat.h
-rw-r--r-- root/root       227 2022-11-29 12:01 ./usr/include/MMB/Impossible.h
-rw-r--r-- root/root      4871 2022-11-29 12:01 ./usr/include/MMB/KBBackboneTorsionForce.h
-rw-r--r-- root/root       312 2022-11-29 12:01 ./usr/include/MMB/Lepton.h
-rw-r--r-- root/root      8211 2022-11-29 12:01 ./usr/include/MMB/LigandDroplet.h
-rw-r--r-- root/root     16881 2022-11-29 12:01 ./usr/include/MMB/Ligands.h
-rw-r--r-- root/root     16712 2022-11-29 12:01 ./usr/include/MMB/Ligands.sam.h
-rw-r--r-- root/root      3129 2022-11-29 12:01 ./usr/include/MMB/MMBLogger.h
-rw-r--r-- root/root        91 2024-11-27 07:07 ./usr/include/MMB/MMB_config.h
-rw-r--r-- root/root      5172 2022-11-29 12:01 ./usr/include/MMB/MobilizerContainer.h
-rw-r--r-- root/root      3821 2022-11-29 12:01 ./usr/include/MMB/MoleculeContainer.h
-rw-r--r-- root/root      4156 2022-11-29 12:01 ./usr/include/MMB/MonoAtoms.h
-rw-r--r-- root/root      7486 2022-11-29 12:01 ./usr/include/MMB/Mutation.h
-rw-r--r-- root/root       328 2022-11-29 12:01 ./usr/include/MMB/NTC_FORCE_CLASS.h
-rw-r--r-- root/root      4598 2022-11-29 12:01 ./usr/include/MMB/NTC_PARAMETER_READER.h
-rw-r--r-- root/root      4871 2022-11-29 12:01 ./usr/include/MMB/NtCBackboneTorsionForce.h
-rw-r--r-- root/root      1747 2022-11-29 12:01 ./usr/include/MMB/NtCForces.h
-rw-r--r-- root/root      4568 2022-11-29 12:01 ./usr/include/MMB/NtCInteractionParameterReader.h
-rw-r--r-- root/root      2181 2022-11-29 12:01 ./usr/include/MMB/NtC_Class_Container.h
-rw-r--r-- root/root     15506 2022-11-29 12:01 ./usr/include/MMB/ParameterReader.h
-rw-r--r-- root/root     56249 2022-11-29 12:01 ./usr/include/MMB/ParameterReader_wrapper.h
-rw-r--r-- root/root      5300 2022-11-29 12:01 ./usr/include/MMB/PeriodicParameterReaderUpdater.h
-rw-r--r-- root/root      5408 2022-11-29 12:01 ./usr/include/MMB/PeriodicPdbAndCOMWriter.h
-rw-r--r-- root/root      3151 2022-11-29 12:01 ./usr/include/MMB/PeriodicPdbAndEnergySingleFrameWriter.h
-rw-r--r-- root/root      2002 2022-11-29 12:01 ./usr/include/MMB/PeriodicPdbAndEnergyWriter.h
-rw-r--r-- root/root      4985 2022-11-29 12:01 ./usr/include/MMB/PeriodicPdbSingleFrameWriter.h
-rw-r--r-- root/root      4299 2022-11-29 12:01 ./usr/include/MMB/PeriodicScrubber.h
-rw-r--r-- root/root      1615 2022-11-29 12:01 ./usr/include/MMB/ProgressWriter.h
-rw-r--r-- root/root      8487 2022-11-29 12:01 ./usr/include/MMB/RandomizeRNACoordinates.h
-rw-r--r-- root/root      8587 2022-11-29 12:01 ./usr/include/MMB/Repel.h
-rw-r--r-- root/root     23919 2022-11-29 12:01 ./usr/include/MMB/ResidueStretchContainer.h
-rw-r--r-- root/root     12884 2022-11-29 12:01 ./usr/include/MMB/RigidifyFormedHelices.h
-rw-r--r-- root/root      7179 2022-11-29 12:01 ./usr/include/MMB/SetChiMobility.h
-rw-r--r-- root/root      3252 2022-11-29 12:01 ./usr/include/MMB/SetSingleBondMobility.h
-rw-r--r-- root/root      3132 2022-11-29 12:01 ./usr/include/MMB/Spiral.h
-rw-r--r-- root/root      2359 2022-11-29 12:01 ./usr/include/MMB/StackingForceSubsystem.h
-rw-r--r-- root/root     15674 2022-11-29 12:01 ./usr/include/MMB/Sterics.h
-rw-r--r-- root/root      1958 2022-11-29 12:01 ./usr/include/MMB/TetherForce.h
-rw-r--r-- root/root     12675 2022-11-29 12:01 ./usr/include/MMB/Threading.h
-rw-r--r-- root/root      5366 2022-11-29 12:01 ./usr/include/MMB/UnitCellParameters.h
-rw-r--r-- root/root     63474 2022-11-29 12:01 ./usr/include/MMB/Utils.h
-rw-r--r-- root/root     12299 2022-11-29 12:01 ./usr/include/MMB/WadleyKeatingDuartePyleTorsionForce.h
-rw-r--r-- root/root      2817 2022-11-29 12:01 ./usr/include/MMB/Water.h
-rw-r--r-- root/root      3544 2022-11-29 12:01 ./usr/include/MMB/WaterDroplet.h
-rw-r--r-- root/root       845 2022-11-29 12:01 ./usr/include/MMB/superimposer.h
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/lib/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/lib/riscv64-linux-gnu/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/lib/riscv64-linux-gnu/cmake/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/lib/riscv64-linux-gnu/cmake/mmb/
-rw-r--r-- root/root      2756 2024-11-27 07:07 ./usr/lib/riscv64-linux-gnu/cmake/mmb/MmbConfigVersion.cmake
-rw-r--r-- root/root       820 2024-11-27 07:07 ./usr/lib/riscv64-linux-gnu/cmake/mmb/MmbTargets-release.cmake
-rw-r--r-- root/root      4543 2024-11-27 07:07 ./usr/lib/riscv64-linux-gnu/cmake/mmb/MmbTargets.cmake
lrwxrwxrwx root/root         0 2024-11-27 07:07 ./usr/lib/riscv64-linux-gnu/libMMB.so -> libMMB.so.4.0
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/lib/riscv64-linux-gnu/pkgconfig/
-rw-r--r-- root/root       195 2024-11-27 07:07 ./usr/lib/riscv64-linux-gnu/pkgconfig/mmb.pc
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/share/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/share/doc/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/share/doc/libmmb-dev/
-rw-r--r-- root/root      1404 2024-11-27 07:07 ./usr/share/doc/libmmb-dev/changelog.Debian.gz
-rw-r--r-- root/root      1550 2024-11-27 07:07 ./usr/share/doc/libmmb-dev/copyright


libmmb4.0t64-dbgsym_4.0.0+dfsg-5_riscv64.deb
--------------------------------------------

 new Debian package, version 2.0.
 size 20665148 bytes: control archive=568 bytes.
     411 bytes,    13 lines      control
     106 bytes,     1 lines      md5sums
 Package: libmmb4.0t64-dbgsym
 Source: macromoleculebuilder
 Version: 4.0.0+dfsg-5
 Auto-Built-Package: debug-symbols
 Architecture: riscv64
 Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
 Installed-Size: 21867
 Depends: libmmb4.0t64 (= 4.0.0+dfsg-5)
 Section: debug
 Priority: optional
 Multi-Arch: same
 Description: debug symbols for libmmb4.0t64
 Build-Ids: 1784e6e2e040e124a45d86531495a874f564e2ca

drwxr-xr-x root/root         0 2024-11-27 07:07 ./
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/lib/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/lib/debug/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/lib/debug/.build-id/17/
-rw-r--r-- root/root  22381488 2024-11-27 07:07 ./usr/lib/debug/.build-id/17/84e6e2e040e124a45d86531495a874f564e2ca.debug
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/share/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/share/doc/
lrwxrwxrwx root/root         0 2024-11-27 07:07 ./usr/share/doc/libmmb4.0t64-dbgsym -> libmmb4.0t64


libmmb4.0t64_4.0.0+dfsg-5_riscv64.deb
-------------------------------------

 new Debian package, version 2.0.
 size 1118564 bytes: control archive=1072 bytes.
     917 bytes,    21 lines      control
     301 bytes,     4 lines      md5sums
      40 bytes,     1 lines      shlibs
      66 bytes,     2 lines      triggers
 Package: libmmb4.0t64
 Source: macromoleculebuilder
 Version: 4.0.0+dfsg-5
 Architecture: riscv64
 Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
 Installed-Size: 3555
 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.4), libopenmm8.1 (>= 8.1.2+dfsg), libsimbody3.7 (>= 3.7+dfsg), libsimtkmolmodel3.1t64 (>= 3.1.0), libstdc++6 (>= 14)
 Breaks: libmmb4.0 (<< 4.0.0+dfsg-5)
 Replaces: libmmb4.0
 Provides: libmmb4.0 (= 4.0.0+dfsg-5)
 Section: libs
 Priority: optional
 Multi-Arch: same
 Homepage: https://simtk.org/projects/rnatoolbox
 Description: shared library of MacroMoleculeBuilder
  MacroMoleculeBuilder, previously known as RNABuilder, can be used for morphing,
  homology modeling, folding (e.g. using base pairing contacts), redesigning
  complexes, fitting to low-resolution density maps, predicting local
  rearrangements upon mutation, and many other applications.
  .
  This package contains the shared library.

drwxr-xr-x root/root         0 2024-11-27 07:07 ./
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/lib/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/lib/riscv64-linux-gnu/
-rw-r--r-- root/root   3622384 2024-11-27 07:07 ./usr/lib/riscv64-linux-gnu/libMMB.so.4.0
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/share/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/share/doc/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/share/doc/libmmb4.0t64/
-rw-r--r-- root/root      1404 2024-11-27 07:07 ./usr/share/doc/libmmb4.0t64/changelog.Debian.gz
-rw-r--r-- root/root      1550 2024-11-27 07:07 ./usr/share/doc/libmmb4.0t64/copyright
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/share/lintian/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/share/lintian/overrides/
-rw-r--r-- root/root        58 2024-11-27 07:07 ./usr/share/lintian/overrides/libmmb4.0t64


mmb-dbgsym_4.0.0+dfsg-5_riscv64.deb
-----------------------------------

 new Debian package, version 2.0.
 size 1508364 bytes: control archive=544 bytes.
     366 bytes,    12 lines      control
     106 bytes,     1 lines      md5sums
 Package: mmb-dbgsym
 Source: macromoleculebuilder
 Version: 4.0.0+dfsg-5
 Auto-Built-Package: debug-symbols
 Architecture: riscv64
 Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
 Installed-Size: 1587
 Depends: mmb (= 4.0.0+dfsg-5)
 Section: debug
 Priority: optional
 Description: debug symbols for mmb
 Build-Ids: 6e42bf1a37a11686656ba291e5e579cb81f6ff5f

drwxr-xr-x root/root         0 2024-11-27 07:07 ./
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/lib/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/lib/debug/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/lib/debug/.build-id/6e/
-rw-r--r-- root/root   1614344 2024-11-27 07:07 ./usr/lib/debug/.build-id/6e/42bf1a37a11686656ba291e5e579cb81f6ff5f.debug
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/share/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/share/doc/
lrwxrwxrwx root/root         0 2024-11-27 07:07 ./usr/share/doc/mmb-dbgsym -> mmb


mmb_4.0.0+dfsg-5_riscv64.deb
----------------------------

 new Debian package, version 2.0.
 size 28268 bytes: control archive=900 bytes.
     800 bytes,    15 lines      control
     242 bytes,     4 lines      md5sums
 Package: mmb
 Source: macromoleculebuilder
 Version: 4.0.0+dfsg-5
 Architecture: riscv64
 Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
 Installed-Size: 90
 Depends: mmb-common, libc6 (>= 2.34), libgcc-s1 (>= 3.0), libmmb4.0t64 (>= 4.0.0+dfsg), libsimbody3.7 (>= 3.7+dfsg), libsimtkmolmodel3.1t64 (>= 3.1.0), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4)
 Section: science
 Priority: optional
 Homepage: https://simtk.org/projects/rnatoolbox
 Description: model the structure and dynamics of macromolecules
  MacroMoleculeBuilder, previously known as RNABuilder, can be used for morphing,
  homology modeling, folding (e.g. using base pairing contacts), redesigning
  complexes, fitting to low-resolution density maps, predicting local
  rearrangements upon mutation, and many other applications.

drwxr-xr-x root/root         0 2024-11-27 07:07 ./
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/bin/
-rwxr-xr-x root/root     76992 2024-11-27 07:07 ./usr/bin/MMB
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/share/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/share/doc/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/share/doc/mmb/
-rw-r--r-- root/root      1404 2024-11-27 07:07 ./usr/share/doc/mmb/changelog.Debian.gz
-rw-r--r-- root/root      1550 2024-11-27 07:07 ./usr/share/doc/mmb/copyright
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/share/man/
drwxr-xr-x root/root         0 2024-11-27 07:07 ./usr/share/man/man1/
-rw-r--r-- root/root       792 2024-11-27 07:07 ./usr/share/man/man1/MMB.1.gz


lintian
-------


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

Merged Build-Depends: lintian:amd64
Filtered Build-Depends: lintian:amd64
dpkg-deb: warning: root directory /<<RESOLVERDIR>>/sbuild-build-depends-lintian-dummy has unusual owner or group 1000:119
dpkg-deb: Hint: you might need to pass --root-owner-group, see <https://wiki.debian.org/Teams/Dpkg/RootlessBuilds> for further details
dpkg-deb: warning: ignoring 1 warning about the control file(s)
dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-lintian-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [615 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [1554 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [1638 B]
Fetched 3807 B in 0s (0 B/s)
Reading package lists...
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
Execute external solver...
The following package was automatically installed and is no longer required:
  gpgv
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
  appstream ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl
  libappstream5 libapt-pkg-perl libassuan9 libb-hooks-endofscope-perl
  libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl
  libcgi-pm-perl libclass-data-inheritable-perl libclass-inspector-perl
  libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl
  libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl
  libcurl3t64-gnutls libdata-dpath-perl libdata-messagepack-perl
  libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl
  libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl
  libdevel-stacktrace-perl libdynaloader-functions-perl
  libemail-address-xs-perl libencode-locale-perl libexception-class-perl
  libfile-basedir-perl libfile-find-rule-perl libfile-listing-perl
  libfile-sharedir-perl libfont-ttf-perl libglib2.0-0t64 libhtml-form-perl
  libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl
  libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl
  libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl
  libimport-into-perl libio-html-perl libio-interactive-perl
  libio-socket-ssl-perl libio-string-perl libipc-run3-perl
  libipc-system-simple-perl libiterator-perl libiterator-util-perl
  libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl
  liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl
  liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl
  libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl
  libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl
  libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl
  libnetaddr-ip-perl libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8
  libnumber-compare-perl libpackage-stash-perl libparams-classify-perl
  libparams-util-perl libpath-tiny-perl libperlio-gzip-perl
  libperlio-utf8-strict-perl libproc-processtable-perl
  libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl
  libsereal-encoder-perl libsort-versions-perl libstemmer0d libstrictures-perl
  libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl
  libsub-install-perl libsub-name-perl libsub-quote-perl
  libsyntax-keyword-try-perl libterm-readkey-perl libtext-glob-perl
  libtext-levenshteinxs-perl libtext-markdown-discount-perl
  libtext-xslate-perl libtime-duration-perl libtime-moment-perl
  libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl
  libvariable-magic-perl libwww-mechanize-perl libwww-perl
  libwww-robotrules-perl libxml-libxml-perl libxml-namespacesupport-perl
  libxml-sax-base-perl libxml-sax-perl libxmlb2 libxs-parse-keyword-perl
  libyaml-0-2 libyaml-libyaml-perl lintian lzop openssl patchutils
  perl-openssl-defaults plzip shared-mime-info t1utils ucf unzip
Suggested packages:
  apt-config-icons isoquery libxml-parser-perl low-memory-monitor
  libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl
  libbareword-filehandles-perl libindirect-perl libmultidimensional-perl
  libbusiness-isbn-perl libmime-base32-perl libregexp-ipv6-perl
  libauthen-ntlm-perl binutils-multiarch libtext-template-perl zip
Recommended packages:
  gnupg libcgi-fast-perl libglib2.0-data xdg-user-dirs libhtml-format-perl
  libio-compress-brotli-perl liblist-someutils-xs-perl libfreezethaw-perl
  libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl libxstring-perl
  libdata-dump-perl libhttp-daemon-perl libmailtools-perl
  libxml-sax-expat-perl
The following NEW packages will be installed:
  appstream ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl
  libappstream5 libapt-pkg-perl libassuan9 libb-hooks-endofscope-perl
  libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl
  libcgi-pm-perl libclass-data-inheritable-perl libclass-inspector-perl
  libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl
  libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl
  libcurl3t64-gnutls libdata-dpath-perl libdata-messagepack-perl
  libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl
  libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl
  libdevel-stacktrace-perl libdynaloader-functions-perl
  libemail-address-xs-perl libencode-locale-perl libexception-class-perl
  libfile-basedir-perl libfile-find-rule-perl libfile-listing-perl
  libfile-sharedir-perl libfont-ttf-perl libglib2.0-0t64 libhtml-form-perl
  libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl
  libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl
  libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl
  libimport-into-perl libio-html-perl libio-interactive-perl
  libio-socket-ssl-perl libio-string-perl libipc-run3-perl
  libipc-system-simple-perl libiterator-perl libiterator-util-perl
  libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl
  liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl
  liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl
  libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl
  libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl
  libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl
  libnetaddr-ip-perl libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8
  libnumber-compare-perl libpackage-stash-perl libparams-classify-perl
  libparams-util-perl libpath-tiny-perl libperlio-gzip-perl
  libperlio-utf8-strict-perl libproc-processtable-perl
  libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl
  libsereal-encoder-perl libsort-versions-perl libstemmer0d libstrictures-perl
  libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl
  libsub-install-perl libsub-name-perl libsub-quote-perl
  libsyntax-keyword-try-perl libterm-readkey-perl libtext-glob-perl
  libtext-levenshteinxs-perl libtext-markdown-discount-perl
  libtext-xslate-perl libtime-duration-perl libtime-moment-perl
  libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl
  libvariable-magic-perl libwww-mechanize-perl libwww-perl
  libwww-robotrules-perl libxml-libxml-perl libxml-namespacesupport-perl
  libxml-sax-base-perl libxml-sax-perl libxmlb2 libxs-parse-keyword-perl
  libyaml-0-2 libyaml-libyaml-perl lintian lzop openssl patchutils
  perl-openssl-defaults plzip sbuild-build-depends-lintian-dummy:riscv64
  shared-mime-info t1utils ucf unzip
0 upgraded, 143 newly installed, 0 to remove and 0 not upgraded.
Need to get 16.1 MB of archives.
After this operation, 68.7 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 B]
Get:2 http://localhost:3142/debian unstable/main amd64 openssl amd64 3.4.0-2 [1422 kB]
Get:3 http://localhost:3142/debian unstable/main amd64 ca-certificates all 20241223 [164 kB]
Get:4 http://localhost:3142/debian unstable/main amd64 ucf all 3.0046 [41.1 kB]
Get:5 http://localhost:3142/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.4-1 [1501 kB]
Get:6 http://localhost:3142/debian unstable/main amd64 shared-mime-info amd64 2.4-5+b1 [759 kB]
Get:7 http://localhost:3142/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB]
Get:8 http://localhost:3142/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB]
Get:9 http://localhost:3142/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB]
Get:10 http://localhost:3142/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.11.1-1 [360 kB]
Get:11 http://localhost:3142/debian unstable/main amd64 libstemmer0d amd64 2.2.0-4+b2 [119 kB]
Get:12 http://localhost:3142/debian unstable/main amd64 libxmlb2 amd64 0.3.21-1 [63.0 kB]
Get:13 http://localhost:3142/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB]
Get:14 http://localhost:3142/debian unstable/main amd64 libappstream5 amd64 1.0.4-1 [225 kB]
Get:15 http://localhost:3142/debian unstable/main amd64 appstream amd64 1.0.4-1 [523 kB]
Get:16 http://localhost:3142/debian unstable/main amd64 diffstat amd64 1.67-1 [35.5 kB]
Get:17 http://localhost:3142/debian unstable/main amd64 libassuan9 amd64 3.0.1-2 [60.6 kB]
Get:18 http://localhost:3142/debian unstable/main amd64 gpgconf amd64 2.2.45-2 [120 kB]
Get:19 http://localhost:3142/debian unstable/main amd64 gpg amd64 2.2.45-2 [531 kB]
Get:20 http://localhost:3142/debian unstable/main amd64 iso-codes all 4.17.0-1 [3055 kB]
Get:21 http://localhost:3142/debian unstable/main amd64 libaliased-perl all 0.34-3 [13.5 kB]
Get:22 http://localhost:3142/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.40+b6 [67.8 kB]
Get:23 http://localhost:3142/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b2 [10.6 kB]
Get:24 http://localhost:3142/debian unstable/main amd64 libdynaloader-functions-perl all 0.004-1 [12.1 kB]
Get:25 http://localhost:3142/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.009-1+b1 [16.2 kB]
Get:26 http://localhost:3142/debian unstable/main amd64 libparams-classify-perl amd64 0.015-2+b4 [22.5 kB]
Get:27 http://localhost:3142/debian unstable/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get:28 http://localhost:3142/debian unstable/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB]
Get:29 http://localhost:3142/debian unstable/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB]
Get:30 http://localhost:3142/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B]
Get:31 http://localhost:3142/debian unstable/main amd64 libvariable-magic-perl amd64 0.64-1+b1 [44.9 kB]
Get:32 http://localhost:3142/debian unstable/main amd64 libb-hooks-endofscope-perl all 0.28-1 [17.5 kB]
Get:33 http://localhost:3142/debian unstable/main amd64 libberkeleydb-perl amd64 0.66-1 [121 kB]
Get:34 http://localhost:3142/debian unstable/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB]
Get:35 http://localhost:3142/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB]
Get:36 http://localhost:3142/debian unstable/main amd64 liburi-perl all 5.30-1 [105 kB]
Get:37 http://localhost:3142/debian unstable/main amd64 libhtml-parser-perl amd64 3.83-1+b2 [99.7 kB]
Get:38 http://localhost:3142/debian unstable/main amd64 libcgi-pm-perl all 4.66-1 [217 kB]
Get:39 http://localhost:3142/debian unstable/main amd64 libclass-data-inheritable-perl all 0.10-1 [8632 B]
Get:40 http://localhost:3142/debian unstable/main amd64 libclass-inspector-perl all 1.36-3 [17.5 kB]
Get:41 http://localhost:3142/debian unstable/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB]
Get:42 http://localhost:3142/debian unstable/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b4 [36.1 kB]
Get:43 http://localhost:3142/debian unstable/main amd64 libclone-perl amd64 0.47-1+b1 [13.9 kB]
Get:44 http://localhost:3142/debian unstable/main amd64 libconfig-tiny-perl all 2.30-1 [18.9 kB]
Get:45 http://localhost:3142/debian unstable/main amd64 libparams-util-perl amd64 1.102-3+b1 [24.4 kB]
Get:46 http://localhost:3142/debian unstable/main amd64 libsub-install-perl all 0.929-1 [10.5 kB]
Get:47 http://localhost:3142/debian unstable/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB]
Get:48 http://localhost:3142/debian unstable/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB]
Get:49 http://localhost:3142/debian unstable/main amd64 libconst-fast-perl all 0.014-2 [8792 B]
Get:50 http://localhost:3142/debian unstable/main amd64 libcpanel-json-xs-perl amd64 4.38-1+b1 [129 kB]
Get:51 http://localhost:3142/debian unstable/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB]
Get:52 http://localhost:3142/debian unstable/main amd64 libexception-class-perl all 1.45-1 [34.6 kB]
Get:53 http://localhost:3142/debian unstable/main amd64 libiterator-perl all 0.03+ds1-2 [18.8 kB]
Get:54 http://localhost:3142/debian unstable/main amd64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB]
Get:55 http://localhost:3142/debian unstable/main amd64 libdata-dpath-perl all 0.60-1 [41.8 kB]
Get:56 http://localhost:3142/debian unstable/main amd64 libdata-messagepack-perl amd64 1.02-1+b4 [32.8 kB]
Get:57 http://localhost:3142/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-4 [31.5 kB]
Get:58 http://localhost:3142/debian unstable/main amd64 libdata-validate-domain-perl all 0.15-1 [11.9 kB]
Get:59 http://localhost:3142/debian unstable/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB]
Get:60 http://localhost:3142/debian unstable/main amd64 libnet-netmask-perl all 2.0002-2 [28.6 kB]
Get:61 http://localhost:3142/debian unstable/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-2+b4 [98.1 kB]
Get:62 http://localhost:3142/debian unstable/main amd64 libdata-validate-ip-perl all 0.31-1 [20.6 kB]
Get:63 http://localhost:3142/debian unstable/main amd64 libdata-validate-uri-perl all 0.07-3 [11.0 kB]
Get:64 http://localhost:3142/debian unstable/main amd64 libdevel-size-perl amd64 0.84-1+b1 [24.2 kB]
Get:65 http://localhost:3142/debian unstable/main amd64 libemail-address-xs-perl amd64 1.05-1+b4 [29.4 kB]
Get:66 http://localhost:3142/debian unstable/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB]
Get:67 http://localhost:3142/debian unstable/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB]
Get:68 http://localhost:3142/debian unstable/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB]
Get:69 http://localhost:3142/debian unstable/main amd64 libnumber-compare-perl all 0.03-3 [6332 B]
Get:70 http://localhost:3142/debian unstable/main amd64 libtext-glob-perl all 0.11-3 [7676 B]
Get:71 http://localhost:3142/debian unstable/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB]
Get:72 http://localhost:3142/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB]
Get:73 http://localhost:3142/debian unstable/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB]
Get:74 http://localhost:3142/debian unstable/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB]
Get:75 http://localhost:3142/debian unstable/main amd64 libfile-sharedir-perl all 1.118-3 [16.0 kB]
Get:76 http://localhost:3142/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB]
Get:77 http://localhost:3142/debian unstable/main amd64 libfont-ttf-perl all 1.06-2 [318 kB]
Get:78 http://localhost:3142/debian unstable/main amd64 libio-html-perl all 1.004-3 [16.2 kB]
Get:79 http://localhost:3142/debian unstable/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB]
Get:80 http://localhost:3142/debian unstable/main amd64 libhttp-message-perl all 7.00-2 [79.8 kB]
Get:81 http://localhost:3142/debian unstable/main amd64 libhtml-form-perl all 6.12-1 [32.3 kB]
Get:82 http://localhost:3142/debian unstable/main amd64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB]
Get:83 http://localhost:3142/debian unstable/main amd64 libhtml-tree-perl all 5.07-3 [211 kB]
Get:84 http://localhost:3142/debian unstable/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB]
Get:85 http://localhost:3142/debian unstable/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB]
Get:86 http://localhost:3142/debian unstable/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B]
Get:87 http://localhost:3142/debian unstable/main amd64 libnet-ssleay-perl amd64 1.94-2 [339 kB]
Get:88 http://localhost:3142/debian unstable/main amd64 libio-socket-ssl-perl all 2.089-1 [223 kB]
Get:89 http://localhost:3142/debian unstable/main amd64 libnet-http-perl all 6.23-1 [23.9 kB]
Get:90 http://localhost:3142/debian unstable/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB]
Get:91 http://localhost:3142/debian unstable/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB]
Get:92 http://localhost:3142/debian unstable/main amd64 libwww-perl all 6.77-1 [183 kB]
Get:93 http://localhost:3142/debian unstable/main amd64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB]
Get:94 http://localhost:3142/debian unstable/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB]
Get:95 http://localhost:3142/debian unstable/main amd64 libio-interactive-perl all 1.025-1 [11.4 kB]
Get:96 http://localhost:3142/debian unstable/main amd64 libipc-run3-perl all 0.049-1 [31.5 kB]
Get:97 http://localhost:3142/debian unstable/main amd64 libjson-maybexs-perl all 1.004008-1 [12.9 kB]
Get:98 http://localhost:3142/debian unstable/main amd64 liblist-compare-perl all 0.55-2 [65.7 kB]
Get:99 http://localhost:3142/debian unstable/main amd64 liblist-someutils-perl all 0.59-1 [37.1 kB]
Get:100 http://localhost:3142/debian unstable/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB]
Get:101 http://localhost:3142/debian unstable/main amd64 liblz1 amd64 1.15~rc1-1 [38.8 kB]
Get:102 http://localhost:3142/debian unstable/main amd64 liblzo2-2 amd64 2.10-3+b1 [55.1 kB]
Get:103 http://localhost:3142/debian unstable/main amd64 libmarkdown2 amd64 2.2.7-2.1 [36.0 kB]
Get:104 http://localhost:3142/debian unstable/main amd64 libmldbm-perl all 2.05-4 [16.8 kB]
Get:105 http://localhost:3142/debian unstable/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB]
Get:106 http://localhost:3142/debian unstable/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB]
Get:107 http://localhost:3142/debian unstable/main amd64 libmoo-perl all 2.005005-1 [58.0 kB]
Get:108 http://localhost:3142/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB]
Get:109 http://localhost:3142/debian unstable/main amd64 libmoox-aliases-perl all 0.001006-2 [7156 B]
Get:110 http://localhost:3142/debian unstable/main amd64 libmouse-perl amd64 2.5.11-1+b1 [144 kB]
Get:111 http://localhost:3142/debian unstable/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB]
Get:112 http://localhost:3142/debian unstable/main amd64 libsub-identify-perl amd64 0.14-3+b3 [11.3 kB]
Get:113 http://localhost:3142/debian unstable/main amd64 libsub-name-perl amd64 0.28-1 [12.2 kB]
Get:114 http://localhost:3142/debian unstable/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB]
Get:115 http://localhost:3142/debian unstable/main amd64 libpath-tiny-perl all 0.146-1 [56.2 kB]
Get:116 http://localhost:3142/debian unstable/main amd64 libperlio-gzip-perl amd64 0.20-1+b4 [17.5 kB]
Get:117 http://localhost:3142/debian unstable/main amd64 libperlio-utf8-strict-perl amd64 0.010-1+b3 [11.4 kB]
Get:118 http://localhost:3142/debian unstable/main amd64 libproc-processtable-perl amd64 0.636-1+b3 [42.3 kB]
Get:119 http://localhost:3142/debian unstable/main amd64 libregexp-wildcards-perl all 1.05-3 [14.1 kB]
Get:120 http://localhost:3142/debian unstable/main amd64 libsereal-decoder-perl amd64 5.004+ds-1+b3 [100 kB]
Get:121 http://localhost:3142/debian unstable/main amd64 libsereal-encoder-perl amd64 5.004+ds-1+b3 [104 kB]
Get:122 http://localhost:3142/debian unstable/main amd64 libsort-versions-perl all 1.62-3 [8928 B]
Get:123 http://localhost:3142/debian unstable/main amd64 libxs-parse-keyword-perl amd64 0.47-1 [64.7 kB]
Get:124 http://localhost:3142/debian unstable/main amd64 libsyntax-keyword-try-perl amd64 0.30-1+b1 [27.4 kB]
Get:125 http://localhost:3142/debian unstable/main amd64 libterm-readkey-perl amd64 2.38-2+b4 [24.6 kB]
Get:126 http://localhost:3142/debian unstable/main amd64 libtext-levenshteinxs-perl amd64 0.03-5+b4 [8720 B]
Get:127 http://localhost:3142/debian unstable/main amd64 libtext-markdown-discount-perl amd64 0.16-1+b3 [13.0 kB]
Get:128 http://localhost:3142/debian unstable/main amd64 libtext-xslate-perl amd64 3.5.9-2+b1 [174 kB]
Get:129 http://localhost:3142/debian unstable/main amd64 libtime-duration-perl all 1.21-2 [13.1 kB]
Get:130 http://localhost:3142/debian unstable/main amd64 libtime-moment-perl amd64 0.44-2+b4 [73.2 kB]
Get:131 http://localhost:3142/debian unstable/main amd64 libunicode-utf8-perl amd64 0.62-2+b3 [20.4 kB]
Get:132 http://localhost:3142/debian unstable/main amd64 libwww-mechanize-perl all 2.19-1 [114 kB]
Get:133 http://localhost:3142/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB]
Get:134 http://localhost:3142/debian unstable/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB]
Get:135 http://localhost:3142/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-4 [53.4 kB]
Get:136 http://localhost:3142/debian unstable/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-5+b1 [314 kB]
Get:137 http://localhost:3142/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.902.0+ds-2+b1 [35.5 kB]
Get:138 http://localhost:3142/debian unstable/main amd64 plzip amd64 1.12~rc1-1 [65.1 kB]
Get:139 http://localhost:3142/debian unstable/main amd64 lzop amd64 1.04-2 [84.2 kB]
Get:140 http://localhost:3142/debian unstable/main amd64 patchutils amd64 0.4.2-1 [77.5 kB]
Get:141 http://localhost:3142/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB]
Get:142 http://localhost:3142/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB]
Get:143 http://localhost:3142/debian unstable/main amd64 lintian all 2.121.1 [1058 kB]
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Setting up libapt-pkg-perl (0.1.40+b6) ...
Setting up liblz1:amd64 (1.15~rc1-1) ...
Setting up libberkeleydb-perl:amd64 (0.66-1) ...
Setting up plzip (1.12~rc1-1) ...
update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode
update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode
update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode
Setting up libunicode-utf8-perl (0.62-2+b3) ...
Setting up libmouse-perl:amd64 (2.5.11-1+b1) ...
Setting up libdata-messagepack-perl (1.02-1+b4) ...
Setting up libclass-inspector-perl (1.36-3) ...
Setting up libdynaloader-functions-perl (0.004-1) ...
Setting up libtext-glob-perl (0.11-3) ...
Setting up libclass-method-modifiers-perl (2.15-1) ...
Setting up liblist-compare-perl (0.55-2) ...
Setting up libclone-perl:amd64 (0.47-1+b1) ...
Setting up libyaml-0-2:amd64 (0.2.5-2) ...
Setting up libsub-identify-perl (0.14-3+b3) ...
Setting up libcpanel-json-xs-perl:amd64 (4.38-1+b1) ...
Setting up libhtml-tagset-perl (3.24-1) ...
Setting up libdevel-size-perl (0.84-1+b1) ...
Setting up unzip (6.0-28) ...
Setting up liblwp-mediatypes-perl (6.04-2) ...
Setting up libyaml-libyaml-perl (0.902.0+ds-2+b1) ...
Setting up libio-interactive-perl (1.025-1) ...
Setting up libtry-tiny-perl (0.32-1) ...
Setting up perl-openssl-defaults:amd64 (7+b2) ...
Setting up libmldbm-perl (2.05-4) ...
Setting up libxml-namespacesupport-perl (1.12-2) ...
Setting up liblzo2-2:amd64 (2.10-3+b1) ...
Setting up libtime-moment-perl (0.44-2+b4) ...
Setting up libencode-locale-perl (1.05-3) ...
Setting up libconfig-tiny-perl (2.30-1) ...
Setting up libsereal-encoder-perl (5.004+ds-1+b3) ...
Setting up liblist-utilsby-perl (0.12-2) ...
Setting up libnet-netmask-perl (2.0002-2) ...
Setting up libsub-install-perl (0.929-1) ...
Setting up libnumber-compare-perl (0.03-3) ...
Setting up patchutils (0.4.2-1) ...
Setting up libjson-maybexs-perl (1.004008-1) ...
Setting up libxml-sax-base-perl (1.09-3) ...
Setting up libio-string-perl (1.08-4) ...
Setting up libnetaddr-ip-perl (4.079+dfsg-2+b4) ...
Setting up libglib2.0-0t64:amd64 (2.82.4-1) ...
No schema files found: doing nothing.
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Setting up libfile-find-rule-perl (0.34-3) ...
Setting up libipc-system-simple-perl (1.30-2) ...
Setting up libnet-domain-tld-perl (1.75-4) ...
Setting up libperlio-utf8-strict-perl (0.010-1+b3) ...
Setting up t1utils (1.41-4) ...
Setting up shared-mime-info (2.4-5+b1) ...
Setting up diffstat (1.67-1) ...
Setting up libvariable-magic-perl (0.64-1+b1) ...
Setting up libio-html-perl (1.004-3) ...
Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b2) ...
Setting up ucf (3.0046) ...
Setting up libparams-util-perl (1.102-3+b1) ...
Setting up libtime-duration-perl (1.21-2) ...
Setting up libtext-xslate-perl:amd64 (3.5.9-2+b1) ...
Setting up libnghttp3-9:amd64 (1.6.0-2) ...
Setting up libsub-exporter-progressive-perl (0.001013-3) ...
Setting up libcapture-tiny-perl (0.48-2) ...
Setting up libtimedate-perl (2.3300-2) ...
Setting up libsub-name-perl:amd64 (0.28-1) ...
Setting up libdata-validate-domain-perl (0.15-1) ...
Setting up libproc-processtable-perl:amd64 (0.636-1+b3) ...
Setting up libpath-tiny-perl (0.146-1) ...
Setting up lzop (1.04-2) ...
Setting up libassuan9:amd64 (3.0.1-2) ...
Setting up gpgconf (2.2.45-2) ...
Setting up librole-tiny-perl (2.002004-1) ...
Setting up libipc-run3-perl (0.049-1) ...
Setting up libregexp-wildcards-perl (1.05-3) ...
Setting up libfile-sharedir-perl (1.118-3) ...
Setting up libaliased-perl (0.34-3) ...
Setting up libngtcp2-16:amd64 (1.9.1-1) ...
Setting up libstrictures-perl (2.000006-1) ...
Setting up libsub-quote-perl (2.006008-1) ...
Setting up libdevel-stacktrace-perl (2.0500-1) ...
Setting up libclass-xsaccessor-perl (1.19-4+b4) ...
Setting up libstemmer0d:amd64 (2.2.0-4+b2) ...
Setting up libsort-versions-perl (1.62-3) ...
Setting up libterm-readkey-perl (2.38-2+b4) ...
Setting up libfont-ttf-perl (1.06-2) ...
Setting up openssl (3.4.0-2) ...
Setting up libtext-levenshteinxs-perl (0.03-5+b4) ...
Setting up libperlio-gzip-perl (0.20-1+b4) ...
Setting up libhtml-html5-entities-perl (0.004-3) ...
Setting up libsereal-decoder-perl (5.004+ds-1+b3) ...
Setting up libmarkdown2:amd64 (2.2.7-2.1) ...
Setting up liburi-perl (5.30-1) ...
Setting up iso-codes (4.17.0-1) ...
Setting up libnet-ipv6addr-perl (1.02-1) ...
Setting up gpg (2.2.45-2) ...
Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ...
Setting up libdata-validate-ip-perl (0.31-1) ...
Setting up libemail-address-xs-perl (1.05-1+b4) ...
Setting up libnet-ssleay-perl:amd64 (1.94-2) ...
Setting up libhttp-date-perl (6.06-1) ...
Setting up libfile-basedir-perl (0.09-2) ...
Setting up libfile-listing-perl (6.16-1) ...
Setting up libxmlb2:amd64 (0.3.21-1) ...
Setting up libcurl3t64-gnutls:amd64 (8.11.1-1) ...
Setting up libnet-http-perl (6.23-1) ...
Setting up libtext-markdown-discount-perl (0.16-1+b3) ...
Setting up libappstream5:amd64 (1.0.4-1) ...
Setting up libexception-class-perl (1.45-1) ...
Setting up libdevel-callchecker-perl:amd64 (0.009-1+b1) ...
Setting up libxml-sax-perl (1.02+dfsg-4) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
152 added, 0 removed; done.
Setting up libdata-validate-uri-perl (0.07-3) ...
Setting up libxs-parse-keyword-perl (0.47-1) ...
Setting up appstream (1.0.4-1) ...
✔ Metadata cache was updated successfully.
Setting up libdata-optlist-perl (0.114-1) ...
Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-5+b1) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up libwww-robotrules-perl (6.02-1) ...
Setting up libsyntax-keyword-try-perl (0.30-1+b1) ...
Setting up libhtml-parser-perl:amd64 (3.83-1+b2) ...
Setting up libio-socket-ssl-perl (2.089-1) ...
Setting up libsub-exporter-perl (0.990-1) ...
Setting up libhttp-message-perl (7.00-2) ...
Setting up libhtml-form-perl (6.12-1) ...
Setting up libiterator-perl (0.03+ds1-2) ...
Setting up libhttp-negotiate-perl (6.01-2) ...
Setting up libiterator-util-perl (0.02+ds1-2) ...
Setting up libhttp-cookies-perl (6.11-1) ...
Setting up libhtml-tree-perl (5.07-3) ...
Setting up libparams-classify-perl:amd64 (0.015-2+b4) ...
Setting up libcgi-pm-perl (4.66-1) ...
Setting up libmodule-runtime-perl (0.016-2) ...
Setting up libconst-fast-perl (0.014-2) ...
Setting up libdata-dpath-perl (0.60-1) ...
Setting up libmodule-implementation-perl (0.09-2) ...
Setting up libpackage-stash-perl (0.40-1) ...
Setting up libimport-into-perl (1.002005-2) ...
Setting up libmoo-perl (2.005005-1) ...
Setting up liblist-someutils-perl (0.59-1) ...
Setting up libmoox-aliases-perl (0.001006-2) ...
Setting up libb-hooks-endofscope-perl (0.28-1) ...
Setting up libnamespace-clean-perl (0.27-2) ...
Setting up liblwp-protocol-https-perl (6.14-1) ...
Setting up libwww-perl (6.77-1) ...
Setting up libhtml-tokeparser-simple-perl (3.16-4) ...
Setting up libwww-mechanize-perl (2.19-1) ...
Processing triggers for sgml-base (1.31) ...
Processing triggers for libc-bin (2.40-5) ...
Setting up lintian (2.121.1) ...
Processing triggers for man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up sbuild-build-depends-lintian-dummy:riscv64 (0.invalid.0) ...
Processing triggers for ca-certificates (20241223) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Running lintian...

I: Lintian run was successful.

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


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

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

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

Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any
Build-Space: n/a
Build-Time: 532
Distribution: unstable
Foreign Architectures: riscv64
Host Architecture: riscv64
Install-Time: 25
Job: macromoleculebuilder_4.0.0+dfsg-5
Lintian: pass
Machine Architecture: amd64
Package: macromoleculebuilder
Package-Time: 579
Source-Version: 4.0.0+dfsg-5
Space: n/a
Status: successful
Version: 4.0.0+dfsg-5
--------------------------------------------------------------------------------
Finished at 2025-01-06T22:51:52Z
Build needed 00:09:39, no disk space