https://launchpad.net/ubuntu/+source/cpptraj/5.1.0+dfsg-3build3/+build/28000393 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-022 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 aarch64 Buildd toolchain package versions: launchpad-buildd_236~650~ubuntu20.04.1 python3-lpbuildd_236~650~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 1 Apr 10:46:35 ntpdate[1871]: adjust time server 10.211.37.1 offset -0.007170 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-28000393 --image-type chroot /home/buildd/filecache-default/0aaa0d191106d33e51979a9c6a062e50b7f5b3b2 Creating target for build PACKAGEBUILD-28000393 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-28000393 Starting target for build PACKAGEBUILD-28000393 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-28000393 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-28000393 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-28000393 Updating target for build PACKAGEBUILD-28000393 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [89.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 Packages [1406 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 Packages [15.1 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6118 kB] Get:9 http://ftpmaster.internal/ubuntu noble-updates/main arm64 Packages [694 kB] Get:10 http://ftpmaster.internal/ubuntu noble-updates/main Translation-en [242 kB] Get:11 http://ftpmaster.internal/ubuntu noble-updates/universe arm64 Packages [4630 kB] Get:12 http://ftpmaster.internal/ubuntu noble-updates/universe Translation-en [1693 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [658 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [239 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [2724 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [1363 kB] Fetched 35.9 MB in 9s (4185 kB/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: libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libgnutls30* libhogweed6* libnettle8* libnpth0* libpng16-16* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-13-aarch64-linux-gnu gcc-14-base gcc-aarch64-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libpng16-16t64 libreadline8t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-aarch64-linux-gnu binutils-common bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libitm1 libjansson4 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0 liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login logsave lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base pinentry-curses procps psmisc readline-common sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 159 upgraded, 23 newly installed, 14 to remove and 0 not upgraded. Need to get 114 MB of archives. After this operation, 77.1 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnsl-dev arm64 1.3.0-3build3 [72.5 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc6-dev arm64 2.39-0ubuntu8 [1596 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc-dev-bin arm64 2.39-0ubuntu8 [19.7 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.1build1 [8094 B] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc-dev arm64 1.3.4+ds-1.1build1 [201 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libnss-nisplus arm64 1.3-5build1 [22.5 kB] Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1build1 [83.6 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgssapi-krb5-2 arm64 1.20.1-6ubuntu2 [141 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libkrb5-3 arm64 1.20.1-6ubuntu2 [349 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libk5crypto3 arm64 1.20.1-6ubuntu2 [85.6 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libkrb5support0 arm64 1.20.1-6ubuntu2 [33.9 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libacl1 arm64 2.3.2-1 [17.0 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libapparmor1 arm64 4.0.0-beta3-0ubuntu3 [50.0 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcap-ng0 arm64 0.8.4-2build2 [14.8 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libaudit1 arm64 1:3.1.2-2.1build1 [47.6 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libblkid1 arm64 2.39.3-9ubuntu4 [123 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libcap2 arm64 1:2.66-5ubuntu1 [30.1 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libcrypt1 arm64 1:4.4.36-4 [100 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libgpg-error-l10n all 1.47-3build1 [8024 B] Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libgpg-error0 arm64 1.47-3build1 [69.9 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 libgcrypt20 arm64 1.10.3-2 [472 kB] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 liblzma5 arm64 5.6.1+really5.4.5-1build1 [125 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libzstd1 arm64 1.5.5+dfsg2-2 [270 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libkmod2 arm64 31+20240202-2ubuntu5 [51.6 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-8-0 arm64 10.42-4ubuntu1 [211 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libselinux1 arm64 3.5-2ubuntu2 [79.9 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libmount1 arm64 2.39.3-9ubuntu4 [133 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-modules-5.38 all 5.38.2-3.2build1 [3110 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-6build1 [721 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm6t64 arm64 1.23-5.1build1 [34.4 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgdbm-compat4t64 arm64 1.23-5.1build1 [6578 B] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libperl5.38t64 arm64 5.38.2-3.2build1 [4773 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl arm64 5.38.2-3.2build1 [231 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-base arm64 5.38.2-3.2build1 [1777 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 liblocale-gettext-perl arm64 1.07-6ubuntu5 [15.3 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtext-iconv-perl arm64 1.7-8build3 [13.1 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtext-charwidth-perl arm64 0.04-11build3 [9406 B] Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc6 arm64 2.39-0ubuntu8 [2774 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libc-bin arm64 2.39-0ubuntu8 [591 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu3 [984 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsystemd-shared arm64 255.4-1ubuntu6 [2016 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcryptsetup12 arm64 2:2.7.0-1ubuntu3 [262 kB] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu3 [1793 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd-dev all 255.4-1ubuntu6 [104 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd-sysv arm64 255.4-1ubuntu6 [11.9 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd arm64 255.4-1ubuntu6 [3403 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsystemd0 arm64 255.4-1ubuntu6 [424 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpam-modules-bin arm64 1.5.3-5ubuntu4 [50.5 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpam-modules arm64 1.5.3-5ubuntu4 [278 kB] Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnettle8t64 arm64 3.9.1-2.2build1 [192 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libhogweed6t64 arm64 3.9.1-2.2build1 [199 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main arm64 libp11-kit0 arm64 0.25.3-4ubuntu1 [275 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main arm64 libunistring5 arm64 1.1-2 [528 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgnutls30t64 arm64 3.8.3-1.1ubuntu3 [942 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libapt-pkg6.0t64 arm64 2.7.14build2 [935 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 bzip2 arm64 1.0.8-5.1 [34.0 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libbz2-1.0 arm64 1.0.8-5.1 [35.7 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-14-base arm64 14-20240330-1ubuntu2 [47.5 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgcc-s1 arm64 14-20240330-1ubuntu2 [50.4 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libstdc++6 arm64 14-20240330-1ubuntu2 [748 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libudev1 arm64 255.4-1ubuntu6 [173 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libxxhash0 arm64 0.8.2-2 [21.2 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 zlib1g arm64 1:1.3.dfsg-3.1ubuntu2 [61.7 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 libffi8 arm64 3.4.6-1 [22.6 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main arm64 libidn2-0 arm64 2.3.7-2 [67.1 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdebconfclient0 arm64 0.271ubuntu3 [11.3 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 base-passwd arm64 3.6.3 [51.1 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsqlite3-0 arm64 3.45.1-1ubuntu2 [703 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gpg arm64 2.4.4-2ubuntu16 [548 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline8t64 arm64 8.2-4build1 [153 kB] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 readline-common all 8.2-4build1 [56.5 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 libncursesw6 arm64 6.4+20240113-1ubuntu1 [146 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 libtinfo6 arm64 6.4+20240113-1ubuntu1 [104 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gpg-agent arm64 2.4.4-2ubuntu16 [221 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gpgconf arm64 2.4.4-2ubuntu16 [103 kB] Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 pinentry-curses arm64 1.2.1-3ubuntu5 [34.3 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnpth0t64 arm64 1.6-3.1build1 [8144 B] Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gpgv arm64 2.4.4-2ubuntu16 [150 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libseccomp2 arm64 2.5.5-1ubuntu3 [51.1 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 apt-utils arm64 2.7.14build2 [205 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 apt arm64 2.7.14build2 [1336 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 debconf-i18n all 1.5.86 [205 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 debconf all 1.5.86 [124 kB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpam0g arm64 1.5.3-5ubuntu4 [67.7 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libargon2-1 arm64 0~20190702+dfsg-4 [20.5 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdevmapper1.02.1 arm64 2:1.02.185-3ubuntu3 [128 kB] Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libuuid1 arm64 2.39.3-9ubuntu4 [35.3 kB] Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libfdisk1 arm64 2.39.3-9ubuntu4 [142 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 mount arm64 2.39.3-9ubuntu4 [116 kB] Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcom-err2 arm64 1.47.0-2.4~exp1ubuntu3 [22.3 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libkeyutils1 arm64 1.6.3-3 [9550 B] Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnsl2 arm64 1.3.0-3build3 [41.6 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.8.0-20.20 [1570 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 base-files arm64 13ubuntu9 [73.9 kB] Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 debianutils arm64 5.17build1 [90.2 kB] Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 bash arm64 5.2.21-2ubuntu4 [780 kB] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 bsdutils arm64 1:2.39.3-9ubuntu4 [97.6 kB] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 coreutils arm64 9.4-3ubuntu5 [1362 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 tar arm64 1.35+dfsg-3 [248 kB] Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 dpkg arm64 1.22.6ubuntu6 [1265 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 dash arm64 0.5.12-6ubuntu5 [90.4 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main arm64 diffutils arm64 1:3.10-1 [174 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main arm64 grep arm64 3.11-4 [174 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main arm64 gzip arm64 1.12-1ubuntu2 [97.1 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main arm64 hostname arm64 3.23+nmu2ubuntu1 [10.9 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main arm64 login arm64 1:4.13+dfsg1-4ubuntu1 [200 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main arm64 ncurses-bin arm64 6.4+20240113-1ubuntu1 [186 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main arm64 sed arm64 4.9-2 [201 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 util-linux arm64 2.39.3-9ubuntu4 [1114 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main arm64 ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main arm64 sysvinit-utils arm64 3.08-6ubuntu2 [33.8 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 logsave arm64 1.47.0-2.4~exp1ubuntu3 [22.1 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libext2fs2t64 arm64 1.47.0-2.4~exp1ubuntu3 [225 kB] Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 e2fsprogs arm64 1.47.0-2.4~exp1ubuntu3 [594 kB] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 optipng arm64 0.7.8+ds-1build2 [109 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpng16-16t64 arm64 1.6.43-5build1 [185 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main arm64 init arm64 1.66ubuntu1 [6186 B] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsmartcols1 arm64 2.39.3-9ubuntu4 [64.3 kB] Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 uuid-runtime arm64 2.39.3-9ubuntu4 [32.5 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main arm64 libattr1 arm64 1:2.5.2-1 [11.0 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main arm64 libmd0 arm64 1.1.0-2 [24.7 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpam-runtime all 1.5.3-5ubuntu4 [40.8 kB] Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsemanage-common all 3.5-1build5 [10.1 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main arm64 libsepol2 arm64 3.5-2 [289 kB] Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsemanage2 arm64 3.5-1build5 [90.8 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main arm64 passwd arm64 1:4.13+dfsg1-4ubuntu1 [838 kB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libproc2-0 arm64 2:4.0.4-4ubuntu3 [58.5 kB] Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libss2 arm64 1.47.0-2.4~exp1ubuntu3 [16.5 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main arm64 mawk arm64 1.3.4.20240123-1 [124 kB] Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 procps arm64 2:4.0.4-4ubuntu3 [708 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main arm64 sensible-utils all 0.0.22 [22.5 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main arm64 ca-certificates all 20240203 [159 kB] Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main arm64 tzdata all 2024a-1ubuntu1 [273 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main arm64 bash-completion all 1:2.11-8 [180 kB] Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 bsdextrautils arm64 2.39.3-9ubuntu4 [71.5 kB] Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgpm2 arm64 1.20.7-11 [14.7 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main arm64 libip4tc2 arm64 1.8.10-3ubuntu1 [23.3 kB] Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libjansson4 arm64 2.14-2build2 [34.4 kB] Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 psmisc arm64 23.7-1build1 [178 kB] Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 xz-utils arm64 5.6.1+really5.4.5-1build1 [268 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main arm64 libgprofng0 arm64 2.42-4ubuntu2 [777 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main arm64 libctf0 arm64 2.42-4ubuntu2 [95.7 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main arm64 libctf-nobfd0 arm64 2.42-4ubuntu2 [99.8 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main arm64 binutils-aarch64-linux-gnu arm64 2.42-4ubuntu2 [3291 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main arm64 libbinutils arm64 2.42-4ubuntu2 [767 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main arm64 binutils arm64 2.42-4ubuntu2 [18.1 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main arm64 binutils-common arm64 2.42-4ubuntu2 [239 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main arm64 libsframe1 arm64 2.42-4ubuntu2 [14.4 kB] Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libubsan1 arm64 14-20240330-1ubuntu2 [1151 kB] Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 g++-13 arm64 13.2.0-23ubuntu3 [14.5 kB] Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libstdc++-13-dev arm64 13.2.0-23ubuntu3 [2378 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgomp1 arm64 14-20240330-1ubuntu2 [144 kB] Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libitm1 arm64 14-20240330-1ubuntu2 [27.9 kB] Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libatomic1 arm64 14-20240330-1ubuntu2 [11.4 kB] Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libasan8 arm64 14-20240330-1ubuntu2 [2920 kB] Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 liblsan0 arm64 14-20240330-1ubuntu2 [1282 kB] Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libhwasan0 arm64 14-20240330-1ubuntu2 [1599 kB] Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-13 arm64 13.2.0-23ubuntu3 [469 kB] Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgcc-13-dev arm64 13.2.0-23ubuntu3 [2468 kB] Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtsan2 arm64 14-20240330-1ubuntu2 [2688 kB] Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcc1-0 arm64 14-20240330-1ubuntu2 [44.7 kB] Get:167 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 cpp-13 arm64 13.2.0-23ubuntu3 [1030 B] Get:168 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-13-base arm64 13.2.0-23ubuntu3 [48.7 kB] Get:169 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu3 [20.1 MB] Get:170 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu3 [11.7 MB] Get:171 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu3 [10.3 MB] Get:172 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] Get:173 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] Get:174 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] Get:175 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] Get:176 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] Get:177 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 dpkg-dev all 1.22.6ubuntu6 [1074 kB] Get:179 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdpkg-perl all 1.22.6ubuntu6 [268 kB] Get:180 http://ftpmaster.internal/ubuntu noble/main arm64 lto-disabled-list all 47 [12.4 kB] Get:181 http://ftpmaster.internal/ubuntu noble/main arm64 libfakeroot arm64 1.33-1 [32.5 kB] Get:182 http://ftpmaster.internal/ubuntu noble/main arm64 fakeroot arm64 1.33-1 [66.9 kB] Preconfiguring packages ... 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Unpacking systemd (255.4-1ubuntu6) over (253.5-1ubuntu6) ... dpkg: warning: unable to delete old directory '/lib/systemd/system-preset': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system-generators': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@0.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user-.slice.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/timers.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/systemd-localed.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sysinit.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sockets.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rescue.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rc-local.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/multi-user.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-fs.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-device.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/graphical.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/getty.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/network': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/journald.conf.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/modprobe.d': Directory not empty Preparing to unpack .../libsystemd0_255.4-1ubuntu6_arm64.deb ... 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Setting up libgcc-13-dev:arm64 (13.2.0-23ubuntu3) ... Setting up gpgconf (2.4.4-2ubuntu16) ... Setting up libc6-dev:arm64 (2.39-0ubuntu8) ... Setting up gpg (2.4.4-2ubuntu16) ... Setting up libstdc++-13-dev:arm64 (13.2.0-23ubuntu3) ... Setting up gpg-agent (2.4.4-2ubuntu16) ... Setting up cpp-13 (13.2.0-23ubuntu3) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.1build1) ... Setting up binutils-aarch64-linux-gnu (2.42-4ubuntu2) ... Setting up binutils (2.42-4ubuntu2) ... Setting up gcc-13-aarch64-linux-gnu (13.2.0-23ubuntu3) ... Setting up dpkg-dev (1.22.6ubuntu6) ... Setting up libtirpc-dev:arm64 (1.3.4+ds-1.1build1) ... Setting up gcc-13 (13.2.0-23ubuntu3) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libnsl2:arm64 (1.3.0-3build3) ... Setting up g++-13-aarch64-linux-gnu (13.2.0-23ubuntu3) ... Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13 (13.2.0-23ubuntu3) ... Setting up libnss-nisplus:arm64 (1.3-5build1) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up libnsl-dev:arm64 (1.3.0-3build3) ... Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15848 files and directories currently installed.) Purging configuration files for libssl3:arm64 (3.0.10-1ubuntu2) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-28000393 arm64 noble-proposed -c chroot:build-PACKAGEBUILD-28000393 --arch=arm64 --dist=noble-proposed --nolog cpptraj_5.1.0+dfsg-3build3.dsc Initiating build PACKAGEBUILD-28000393 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 aarch64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-022.buildd +==============================================================================+ | cpptraj 5.1.0+dfsg-3build3 (arm64) Mon, 01 Apr 2024 10:47:55 +0000 | +==============================================================================+ Package: cpptraj Version: 5.1.0+dfsg-3build3 Source Version: 5.1.0+dfsg-3build3 Distribution: noble-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-28000393/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/cpptraj-Wt45qe/resolver-GeW7bE' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- cpptraj_5.1.0+dfsg-3build3.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/cpptraj-Wt45qe/cpptraj-5.1.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/cpptraj-Wt45qe' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), gfortran, libarpack2-dev, libbz2-dev, libfftw3-dev, libnetcdf-dev, libopenmm-dev, libreadline-dev, netcdf-bin, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), gfortran, libarpack2-dev, libbz2-dev, libfftw3-dev, libnetcdf-dev, libopenmm-dev, libreadline-dev, netcdf-bin, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [448 B] Get:5 copy:/<>/apt_archive ./ Packages [502 B] Fetched 1907 B in 0s (66.4 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnsl-dev libnsl2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libtirpc-common libtirpc-dev libtirpc3t64 libunistring2 openssl perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-13 gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu groff-base hdf5-helpers icu-devtools intltool-debian libaec-dev libaec0 libarchive-zip-perl libarpack2-dev libarpack2t64 libblas-dev libblas3 libbrotli1 libbz2-dev libcurl3t64-gnutls libcurl4-gnutls-dev libcurl4t64 libdebhelper-perl libdw1t64 libelf1t64 libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-single3 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhdf5-dev libhdf5-fortran-102t64 libhdf5-hl-100t64 libhdf5-hl-cpp-100t64 libhdf5-hl-fortran-100t64 libicu-dev libicu74 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libldap2 libmagic-mgc libmagic1t64 libncurses-dev libncurses6 libnetcdf-dev libnetcdf19t64 libnghttp2-14 libopenmm-dev libopenmm8.0t64 libpipeline1 libpsl5t64 libreadline-dev librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsub-override-perl libsz2 libtool libuchardet0 libxml2 libxml2-dev m4 man-db netcdf-bin po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc gfortran-13-doc libcoarrays-dev groff liblapack-doc libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config libfftw3-doc libhdf5-doc icu-doc ncurses-doc netcdf-doc readline-doc libssl-doc libtool-doc gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libldap-common pkgconf publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-13 gfortran-13-aarch64-linux-gnu gfortran-aarch64-linux-gnu groff-base hdf5-helpers icu-devtools intltool-debian libaec-dev libaec0 libarchive-zip-perl libarpack2-dev libarpack2t64 libblas-dev libblas3 libbrotli1 libbz2-dev libcurl3t64-gnutls libcurl4-gnutls-dev libcurl4t64 libdebhelper-perl libdw1t64 libelf1t64 libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-single3 libfile-stripnondeterminism-perl libgfortran-13-dev libgfortran5 libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhdf5-dev libhdf5-fortran-102t64 libhdf5-hl-100t64 libhdf5-hl-cpp-100t64 libhdf5-hl-fortran-100t64 libicu-dev libicu74 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libldap2 libmagic-mgc libmagic1t64 libncurses-dev libncurses6 libnetcdf-dev libnetcdf19t64 libnghttp2-14 libopenmm-dev libopenmm8.0t64 libpipeline1 libpsl5t64 libreadline-dev librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsub-override-perl libsz2 libtool libuchardet0 libxml2 libxml2-dev m4 man-db netcdf-bin po-debconf sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 89 newly installed, 0 to remove and 0 not upgraded. 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Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [720 B] Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libelf1t64 arm64 0.190-1.1build3 [58.0 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libicu74 arm64 74.2-1ubuntu1 [10.8 MB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxml2 arm64 2.9.14+dfsg-1.3ubuntu3 [735 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libmagic-mgc arm64 1:5.45-3build1 [307 kB] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libmagic1t64 arm64 1:5.45-3build1 [85.7 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 file arm64 1:5.45-3build1 [22.0 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 gettext-base arm64 0.21-14ubuntu1 [37.5 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libuchardet0 arm64 0.0.8-1 [75.1 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 groff-base arm64 1.23.0-3build2 [993 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libncurses6 arm64 6.4+20240113-1ubuntu1 [110 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libnghttp2-14 arm64 1.59.0-1build2 [74.0 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpipeline1 arm64 1.5.7-2 [23.7 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpsl5t64 arm64 0.21.2-1.1build1 [57.4 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 man-db arm64 2.12.0-4build1 [1232 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 m4 arm64 1.4.19-4 [240 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 autoconf all 2.71-3 [339 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 autotools-dev all 20220109.1 [44.9 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 autopoint all 0.21-14ubuntu1 [422 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 libtool all 2.4.7-7 [166 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main arm64 dh-autoreconf all 20 [16.1 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libsub-override-perl all 0.10-1 [10.0 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdw1t64 arm64 0.190-1.1build3 [258 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 debugedit arm64 1:5.0-5build1 [45.4 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 dwz 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[1022 B] Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 gfortran arm64 4:13.2.0-7ubuntu1 [1164 B] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 hdf5-helpers arm64 1.10.10+repack-3.1ubuntu4 [15.8 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 icu-devtools arm64 74.2-1ubuntu1 [209 kB] Get:43 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libarpack2t64 arm64 3.9.1-1.1build2 [90.6 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main arm64 libblas-dev arm64 3.12.0-3 [111 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack-dev arm64 3.12.0-3 [4293 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libarpack2-dev 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noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8-dev arm64 8c-2ubuntu11 [1484 B] Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-dev arm64 8c-2ubuntu11 [1482 B] Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec-dev arm64 1.1.2-1 [18.8 kB] Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl-dev arm64 3.0.13-0ubuntu3 [2334 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 libhdf5-dev arm64 1.10.10+repack-3.1ubuntu4 [3038 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libicu-dev arm64 74.2-1ubuntu1 [11.9 MB] Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 libncurses-dev arm64 6.4+20240113-1ubuntu1 [385 kB] Get:83 http://ftpmaster.internal/ubuntu noble/universe arm64 libnetcdf19t64 arm64 1:4.9.2-5ubuntu3 [471 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libxml2-dev arm64 2.9.14+dfsg-1.3ubuntu3 [798 kB] Get:85 http://ftpmaster.internal/ubuntu noble/universe arm64 libnetcdf-dev arm64 1:4.9.2-5ubuntu3 [58.0 kB] Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenmm8.0t64 arm64 8.0.0+dfsg-6.1ubuntu1 [944 kB] Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 libopenmm-dev arm64 8.0.0+dfsg-6.1ubuntu1 [327 kB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libreadline-dev arm64 8.2-4build1 [177 kB] Get:89 http://ftpmaster.internal/ubuntu noble/universe arm64 netcdf-bin arm64 1:4.9.2-5ubuntu3 [200 kB] Preconfiguring packages ... Fetched 66.6 MB in 4s (18.7 MB/s) Selecting previously unselected package libelf1t64:arm64. (Reading database ... 15848 files and directories currently installed.) Preparing to unpack .../00-libelf1t64_0.190-1.1build3_arm64.deb ... Unpacking libelf1t64:arm64 (0.190-1.1build3) ... Selecting previously unselected package libicu74:arm64. Preparing to unpack .../01-libicu74_74.2-1ubuntu1_arm64.deb ... Unpacking libicu74:arm64 (74.2-1ubuntu1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../02-libxml2_2.9.14+dfsg-1.3ubuntu3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3ubuntu3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3build1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3build1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3build1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3build1) ... 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Setting up libpsl5t64:arm64 (0.21.2-1.1build1) ... Setting up libnghttp2-14:arm64 (1.59.0-1build2) ... Setting up libfftw3-long3:arm64 (3.3.10-1ubuntu3) ... Setting up gettext-base (0.21-14ubuntu1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3build1) ... Setting up libaec0:arm64 (1.1.2-1) ... Setting up libelf1t64:arm64 (0.190-1.1build3) ... Setting up libdw1t64:arm64 (0.190-1.1build3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-5ubuntu2) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2build7) ... Setting up libncurses6:arm64 (6.4+20240113-1ubuntu1) ... Setting up libssl-dev:arm64 (3.0.13-0ubuntu3) ... Setting up autopoint (0.21-14ubuntu1) ... Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... Setting up libfftw3-double3:arm64 (3.3.10-1ubuntu3) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-5ubuntu2) ... Setting up libssh-4:arm64 (0.10.6-2build2) ... Setting up libgfortran5:arm64 (14-20240330-1ubuntu2) ... Setting up autoconf (2.71-3) ... Setting up libicu74:arm64 (74.2-1ubuntu1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3.1ubuntu2) ... Setting up dwz (0.15-1build6) ... Setting up libuchardet0:arm64 (0.0.8-1) ... Setting up debugedit (1:5.0-5build1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libgfortran-13-dev:arm64 (13.2.0-23ubuntu3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3ubuntu3) ... Setting up libldap2:arm64 (2.6.7+dfsg-1~exp1ubuntu7) ... Setting up libblas-dev:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up libsz2:arm64 (1.1.2-1) ... Setting up libopenmm8.0t64 (8.0.0+dfsg-6.1ubuntu1) ... Setting up libbz2-dev:arm64 (1.0.8-5.1) ... Setting up libjpeg8:arm64 (8c-2ubuntu11) ... Setting up automake (1:1.16.5-1.3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libjpeg-turbo8-dev:arm64 (2.1.5-2ubuntu1) ... Setting up liblapack3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libncurses-dev:arm64 (6.4+20240113-1ubuntu1) ... Setting up gettext (0.21-14ubuntu1) ... Setting up libarpack2t64:arm64 (3.9.1-1.1build2) ... Setting up libcurl4t64:arm64 (8.5.0-2ubuntu9) ... Setting up libtool (2.4.7-7) ... Setting up libfftw3-bin (3.3.10-1ubuntu3) ... Setting up libaec-dev:arm64 (1.1.2-1) ... Setting up libcurl3t64-gnutls:arm64 (8.5.0-2ubuntu9) ... Setting up gfortran-13-aarch64-linux-gnu (13.2.0-23ubuntu3) ... Setting up libreadline-dev:arm64 (8.2-4build1) ... Setting up libcurl4-gnutls-dev:arm64 (8.5.0-2ubuntu9) ... Setting up libopenmm-dev (8.0.0+dfsg-6.1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up gfortran-13 (13.2.0-23ubuntu3) ... Setting up liblapack-dev:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up icu-devtools (74.2-1ubuntu1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3build2) ... Setting up gfortran-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libjpeg8-dev:arm64 (8c-2ubuntu11) ... Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu4) ... Setting up libfftw3-dev:arm64 (3.3.10-1ubuntu3) ... Setting up libicu-dev:arm64 (74.2-1ubuntu1) ... Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-3.1ubuntu4) ... Setting up libnetcdf19t64:arm64 (1:4.9.2-5ubuntu3) ... Setting up libarpack2-dev:arm64 (3.9.1-1.1build2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhdf5-cpp-103-1t64:arm64 (1.10.10+repack-3.1ubuntu4) ... Setting up libjpeg-dev:arm64 (8c-2ubuntu11) ... Setting up libhdf5-fortran-102t64:arm64 (1.10.10+repack-3.1ubuntu4) ... Setting up man-db (2.12.0-4build1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up gfortran (4:13.2.0-7ubuntu1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist Setting up netcdf-bin (1:4.9.2-5ubuntu3) ... Setting up libxml2-dev:arm64 (2.9.14+dfsg-1.3ubuntu3) ... Setting up libhdf5-hl-cpp-100t64:arm64 (1.10.10+repack-3.1ubuntu4) ... Setting up libhdf5-hl-fortran-100t64:arm64 (1.10.10+repack-3.1ubuntu4) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up libhdf5-dev (1.10.10+repack-3.1ubuntu4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libnetcdf-dev (1:4.9.2-5ubuntu3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 arm64 (aarch64) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu6 g++-13_13.2.0-23ubuntu3 gcc-13_13.2.0-23ubuntu3 libc6-dev_2.39-0ubuntu8 libstdc++-13-dev_13.2.0-23ubuntu3 libstdc++6_14-20240330-1ubuntu2 linux-libc-dev_6.8.0-20.20 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.14build2 apt-utils_2.7.14build2 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu1 autotools-dev_20220109.1 base-files_13ubuntu9 base-passwd_3.6.3 bash_5.2.21-2ubuntu4 bash-completion_1:2.11-8 binutils_2.42-4ubuntu2 binutils-aarch64-linux-gnu_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 bsdextrautils_2.39.3-9ubuntu4 bsdutils_1:2.39.3-9ubuntu4 build-essential_12.10ubuntu1 bzip2_1.0.8-5.1 ca-certificates_20240203 coreutils_9.4-3ubuntu5 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-23ubuntu3 cpp-13-aarch64-linux-gnu_13.2.0-23ubuntu3 cpp-aarch64-linux-gnu_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu5 debconf_1.5.86 debconf-i18n_1.5.86 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build1 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.6ubuntu6 dpkg-dev_1.22.6ubuntu6 dwz_0.15-1build6 e2fsprogs_1.47.0-2.4~exp1ubuntu3 fakeroot_1.33-1 file_1:5.45-3build1 findutils_4.9.0-5 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-23ubuntu3 g++-13-aarch64-linux-gnu_13.2.0-23ubuntu3 g++-aarch64-linux-gnu_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-23ubuntu3 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xz-utils_5.6.1+really5.4.5-1build1 zlib1g_1:1.3.dfsg-3.1ubuntu2 zlib1g-dev_1:1.3.dfsg-3.1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: cpptraj Binary: cpptraj Architecture: any Version: 5.1.0+dfsg-3build3 Maintainer: Ubuntu Developers Uploaders: Andrius Merkys , Homepage: https://github.com/Amber-MD/cpptraj Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/debichem-team/cpptraj Vcs-Git: https://salsa.debian.org/debichem-team/cpptraj.git Testsuite: autopkgtest Testsuite-Triggers: netcdf-bin Build-Depends: debhelper-compat (= 13), gfortran, libarpack2-dev, libbz2-dev, libfftw3-dev, libnetcdf-dev, libopenmm-dev [amd64 arm64 ppc64el], libreadline-dev, netcdf-bin Package-List: cpptraj deb science optional arch=any Checksums-Sha1: 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dpkg-source: info: applying use-system-libraries.patch dpkg-source: info: applying skip-failing-test.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-28000393 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-28000393 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-28000393 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package cpptraj dpkg-buildpackage: info: source version 5.1.0+dfsg-3build3 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' touch config.h external.config.h dh_auto_clean make -j4 clean make[2]: Entering directory '/<>' cd src && make clean make[3]: Entering directory '/<>/src' /bin/rm -f SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o cpptraj *.LIBCPPTRAJ.o libcpptraj # cd readline && make clean cd xdrfile && make clean make[4]: Entering directory '/<>/src/xdrfile' /bin/rm -f *.o libxdrfile.a a.out test.trr test.xtc test.xdr make[4]: Leaving directory '/<>/src/xdrfile' # cd arpack && make clean cd cuda_kernels && make clean make[4]: Entering directory '/<>/src/cuda_kernels' /bin/rm -f *.o libcpptraj_cuda.a make[4]: Leaving directory '/<>/src/cuda_kernels' cd tng && make clean make[4]: Entering directory '/<>/src/tng' /bin/rm -f *.o libtng_io.a tng_io_testing.o a.out tng_example_out.tng tng_test.tng make[4]: Leaving directory '/<>/src/tng' make[3]: Leaving directory '/<>/src' cd test && make clean make[3]: Entering directory '/<>/test' Cleaning all test directories: make test.complete test.libcpptraj OPT=clean make[4]: Entering directory '/<>/test' make[5]: Entering directory '/<>/test' make[5]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[5]: Leaving directory '/<>/test' make[4]: Leaving directory '/<>/test' make[3]: Leaving directory '/<>/test' cd unitTests && make clean make[3]: Entering directory '/<>/unitTests' Cleaning unit tests. make test.complete OPT=clean make[4]: Entering directory '/<>/unitTests' CPPTRAJ source directory: /<>/src CPPTRAJ config.h file: /<>/config.h make[5]: Entering directory '/<>/unitTests' make[5]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[5]: Leaving directory '/<>/unitTests' make[4]: Leaving directory '/<>/unitTests' make[3]: Leaving directory '/<>/unitTests' make[2]: Leaving directory '/<>' rm -rf bin make[1]: Leaving directory '/<>' 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 '/<>' ./configure gnu --with-arpack=/usr/lib/aarch64-linux-gnu --with-fftw3=/usr/lib/aarch64-linux-gnu --with-readline=/usr/lib/aarch64-linux-gnu --with-openmm=/usr/lib/aarch64-linux-gnu arpack specified: /usr/lib/aarch64-linux-gnu fftw3 specified: /usr/lib/aarch64-linux-gnu readline specified: /usr/lib/aarch64-linux-gnu openmm specified: /usr/lib/aarch64-linux-gnu Testing C++ compiler: OK Testing C compiler: OK Testing basic C++11 support: OK Testing system headers for C++11 support: OK Warning: Compilation of sanderlib requires AMBERHOME to be set Warning: if --with-sanderlib not specified. Checking BZLIB: OK Checking ZLIB: OK Checking NetCDF: OK Checking LAPACK/BLAS: OK Checking ARPACK: OK Checking FFTW3: OK Checking Readline: OK Checking OpenMM: OK vmdplugin disabled due to nonfree source. Configuration summary: Build type: Serial Options: netcdf bzlib tng zlib arpack lapack blas fftw3 readline xdrfile openmm Target platform: Linux, 64-bit. gnu compilers in use. C++11 support enabled. PME support enabled. Compiler optimizations are on. Cleaning source directory. -------------------------------------------------------------------------------- An environment resource file for CPPTRAJ has been created: /<>/cpptraj.sh You may 'source' this file to set up your environment for CPPTRAJ. -------------------------------------------------------------------------------- CPPTRAJ configuration complete. make[1]: Leaving directory '/<>' dh_auto_build -a make -j4 make[1]: Entering directory '/<>' cd src && make install make[2]: Entering directory '/<>/src' CXX SpaceGroup.cpp CXX ActionFrameCounter.cpp CXX ActionList.cpp CXX ActionTopWriter.cpp CXX Action_Align.cpp CXX Action_Angle.cpp CXX Action_AreaPerMol.cpp CXX Action_AtomMap.cpp CXX Action_AtomicCorr.cpp CXX Action_AtomicFluct.cpp CXX Action_AutoImage.cpp CXX Action_Average.cpp CXX Action_Bounds.cpp CXX Action_Box.cpp CXX Action_Center.cpp CXX Action_Channel.cpp CXX Action_CheckChirality.cpp CXX Action_CheckStructure.cpp CXX Action_Closest.cpp CXX Action_ClusterDihedral.cpp CXX Action_Contacts.cpp CXX Action_CreateCrd.cpp CXX Action_CreateReservoir.cpp CXX Action_DNAionTracker.cpp CXX Action_DSSP.cpp CXX Action_Density.cpp CXX Action_Diffusion.cpp CXX Action_Dihedral.cpp CXX Action_DihedralRMS.cpp CXX Action_Dipole.cpp CXX Action_Distance.cpp CXX Action_DistRmsd.cpp CXX Action_Energy.cpp In file included from Ewald_ParticleMesh.h:5, from Action_Energy.cpp:4: helpme_standalone.h:2323: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2323 | #pragma omp parallel for num_threads(nThreads) | helpme_standalone.h:2343: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2343 | #pragma omp parallel for num_threads(nThreads) | helpme_standalone.h:3014: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3014 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) | helpme_standalone.h:3120: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3120 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) | helpme_standalone.h:3247: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3247 | #pragma omp parallel for num_threads(nThreads) | helpme_standalone.h:3701: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3701 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:3739: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3739 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:3802: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3802 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:3840: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3840 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:4044: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4044 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:4052: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 4052 | #pragma omp for | helpme_standalone.h:4097: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4097 | #pragma omp parallel for num_threads(nThreads_) | helpme_standalone.h:4145: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4145 | #pragma omp parallel for num_threads(nThreads_) | helpme_standalone.h:4172: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4172 | #pragma omp parallel for num_threads(nThreads_) | helpme_standalone.h:4224: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4224 | #pragma omp parallel for num_threads(nThreads_) | helpme_standalone.h:4228: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4228 | #pragma omp parallel for num_threads(nThreads_) | helpme_standalone.h:4275: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4275 | #pragma omp parallel for num_threads(nThreads_) | helpme_standalone.h:4388: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4388 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) | helpme_standalone.h:4419: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) | helpme_standalone.h:4503: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4503 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:4510: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 4510 | #pragma omp for | CXX Action_FilterByData.cpp CXX Action_FixAtomOrder.cpp CXX Action_FixImagedBonds.cpp CXX Action_GIST.cpp CXX Action_Grid.cpp CXX Action_GridFreeEnergy.cpp In file included from Matrix_3x3.h:3, from Box.h:3, from Frame.h:5, from Topology.h:10, from DataSet_Coords.h:4, from DataSet_Coords_REF.h:3, from ReferenceFrame.h:3, from DataSetList.h:4, from DataFile.h:4, from DataFileList.h:3, from ActionState.h:3, from Action.h:5, from Action_GIST.h:3, from Action_GIST.cpp:3: In member function ‘Vec3::operator-(Vec3 const&) const’, inlined from ‘Action_GIST::Order(Frame const&)’ at Action_GIST.cpp:814:31: Vec3.h:76:23: warning: ‘WAT’ may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function ‘Action_GIST::Order(Frame const&)’: Action_GIST.cpp:783:10: note: ‘WAT’ declared here 783 | Vec3 WAT[4]; | ^~~ In member function ‘Vec3::operator-(Vec3 const&) const’, inlined from ‘Action_GIST::Order(Frame const&)’ at Action_GIST.cpp:814:31: Vec3.h:76:40: warning: ‘WAT’ may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function ‘Action_GIST::Order(Frame const&)’: Action_GIST.cpp:783:10: note: ‘WAT’ declared here 783 | Vec3 WAT[4]; | ^~~ In member function ‘Vec3::operator-(Vec3 const&) const’, inlined from ‘Action_GIST::Order(Frame const&)’ at Action_GIST.cpp:814:31: Vec3.h:76:57: warning: ‘WAT’ may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function ‘Action_GIST::Order(Frame const&)’: Action_GIST.cpp:783:10: note: ‘WAT’ declared here 783 | Vec3 WAT[4]; | ^~~ In member function ‘Vec3::operator-(Vec3 const&) const’, inlined from ‘Action_GIST::Order(Frame const&)’ at Action_GIST.cpp:815:31: Vec3.h:76:23: warning: ‘WAT’ may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function ‘Action_GIST::Order(Frame const&)’: Action_GIST.cpp:783:10: note: ‘WAT’ declared here 783 | Vec3 WAT[4]; | ^~~ In member function ‘Vec3::operator-(Vec3 const&) const’, inlined from ‘Action_GIST::Order(Frame const&)’ at Action_GIST.cpp:815:31: Vec3.h:76:40: warning: ‘WAT’ may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function ‘Action_GIST::Order(Frame const&)’: Action_GIST.cpp:783:10: note: ‘WAT’ declared here 783 | Vec3 WAT[4]; | ^~~ In member function ‘Vec3::operator-(Vec3 const&) const’, inlined from ‘Action_GIST::Order(Frame const&)’ at Action_GIST.cpp:815:31: Vec3.h:76:57: warning: ‘WAT’ may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function ‘Action_GIST::Order(Frame const&)’: Action_GIST.cpp:783:10: note: ‘WAT’ declared here 783 | Vec3 WAT[4]; | ^~~ CXX Action_HydrogenBond.cpp CXX Action_Image.cpp CXX Action_InfraredSpectrum.cpp CXX Action_Jcoupling.cpp CXX Action_LESsplit.cpp CXX Action_LIE.cpp CXX Action_LipidOrder.cpp CXX Action_MakeStructure.cpp CXX Action_Mask.cpp CXX Action_Matrix.cpp CXX Action_MinImage.cpp CXX Action_Molsurf.cpp CXX Action_MultiDihedral.cpp CXX Action_MultiVector.cpp CXX Action_NAstruct.cpp CXX Action_NativeContacts.cpp CXX Action_NMRrst.cpp CXX Action_OrderParameter.cpp CXX Action_Outtraj.cpp CXX Action_PairDist.cpp CXX Action_Pairwise.cpp CXX Action_Principal.cpp CXX Action_Projection.cpp CXX Action_Pucker.cpp CXX Action_Radgyr.cpp CXX Action_Radial.cpp CXX Action_RandomizeIons.cpp CXX Action_Remap.cpp CXX Action_ReplicateCell.cpp CXX Action_Rmsd.cpp CXX Action_Rotate.cpp CXX Action_RunningAvg.cpp CXX Action_STFC_Diffusion.cpp CXX Action_Scale.cpp CXX Action_SetVelocity.cpp CXX Action_Spam.cpp CXX Action_Strip.cpp CXX Action_Surf.cpp CXX Action_SymmetricRmsd.cpp CXX Action_Temperature.cpp CXX Action_Time.cpp CXX Action_Translate.cpp CXX Action_Unstrip.cpp CXX Action_Unwrap.cpp CXX Action_Vector.cpp CXX Action_VelocityAutoCorr.cpp CXX Action_Volmap.cpp CXX Action_Volume.cpp CXX Action_Watershell.cpp CXX Action_XtalSymm.cpp CXX AnalysisList.cpp CXX Analysis_AmdBias.cpp CXX Analysis_AutoCorr.cpp CXX Analysis_Average.cpp CXX Analysis_Clustering.cpp CXX Analysis_Corr.cpp In file included from /usr/include/c++/13/vector:66, from ArgList.h:3, from Action.h:4, from Action_XtalSymm.h:3, from Action_XtalSymm.cpp:1: In member function ‘std::vector >::assign(unsigned long, Vec3 const&)’, inlined from ‘Action_XtalSymm::Init(ArgList&, ActionInit&, int)’ at Action_XtalSymm.cpp:57:12: /usr/include/c++/13/bits/stl_vector.h:806:23: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] 806 | { _M_fill_assign(__n, __val); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72: /usr/include/c++/13/bits/vector.tcc: In member function ‘Action_XtalSymm::Init(ArgList&, ActionInit&, int)’: /usr/include/c++/13/bits/vector.tcc:270:5: note: by argument 3 of type ‘const struct value_type &’ to ‘std::vector >::_M_fill_assign(unsigned long, Vec3 const&)’ declared here 270 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ Action_XtalSymm.cpp:57:33: note: ‘’ declared here 57 | T_.assign( nCopyTotal, Vec3()); | ^ In member function ‘std::vector >::assign(unsigned long, Vec3 const&)’, inlined from ‘Action_XtalSymm::Init(ArgList&, ActionInit&, int)’ at Action_XtalSymm.cpp:58:15: /usr/include/c++/13/bits/stl_vector.h:806:23: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] 806 | { _M_fill_assign(__n, __val); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function ‘Action_XtalSymm::Init(ArgList&, ActionInit&, int)’: /usr/include/c++/13/bits/vector.tcc:270:5: note: by argument 3 of type ‘const struct value_type &’ to ‘std::vector >::_M_fill_assign(unsigned long, Vec3 const&)’ declared here 270 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ Action_XtalSymm.cpp:58:33: note: ‘’ declared here 58 | RefT_.assign(nCopyTotal, Vec3()); | ^ CXX Analysis_ConstantPHStats.cpp CXX Analysis_CrankShaft.cpp CXX Analysis_CrdFluct.cpp CXX Analysis_CrossCorr.cpp CXX Analysis_CurveFit.cpp CXX Analysis_Divergence.cpp CXX Analysis_EvalPlateau.cpp CXX Analysis_FFT.cpp CXX Analysis_HausdorffDistance.cpp CXX Analysis_Hist.cpp CXX Analysis_Integrate.cpp CXX Analysis_IRED.cpp CXX Analysis_KDE.cpp CXX Analysis_Lifetime.cpp CXX Analysis_LowestCurve.cpp CXX Analysis_Matrix.cpp CXX Analysis_MeltCurve.cpp CXX Analysis_Modes.cpp CXX Analysis_Multicurve.cpp CXX Analysis_MultiHist.cpp CXX Analysis_Overlap.cpp CXX Analysis_PhiPsi.cpp CXX Analysis_Regression.cpp CXX Analysis_RemLog.cpp CXX Analysis_Rms2d.cpp CXX Analysis_RmsAvgCorr.cpp CXX Analysis_Rotdif.cpp CXX Analysis_RunningAvg.cpp CXX Analysis_Slope.cpp CXX Analysis_Spline.cpp CXX Analysis_State.cpp CXX Analysis_Statistics.cpp CXX Analysis_TI.cpp CXX Analysis_Timecorr.cpp CXX Analysis_VectorMath.cpp CXX Analysis_Wavelet.cpp CXX ArgList.cpp CXX Array1D.cpp CXX AssociatedData.cpp CXX Atom.cpp CXX AtomMap.cpp CXX AtomMask.cpp CXX AxisType.cpp CXX BondSearch.cpp CXX Box.cpp CXX BoxArgs.cpp CXX BufferedFrame.cpp CXX BufferedLine.cpp CXX ByteRoutines.cpp CXX CharMask.cpp CXX CharmmParamFile.cpp CXX CIFfile.cpp CXX ClusterDist.cpp CXX ClusterList.cpp CXX ClusterMap.cpp CXX ClusterMatrix.cpp CXX ClusterNode.cpp CXX ClusterSieve.cpp CXX Cluster_DBSCAN.cpp CXX Cluster_DPeaks.cpp CXX Cluster_HierAgglo.cpp CXX Cluster_Kmeans.cpp CXX Cluster_ReadInfo.cpp CXX Cmd.cpp CXX CmdInput.cpp CXX CmdList.cpp CXX CompactFrameArray.cpp CXX ComplexArray.cpp CXX Constraints.cpp CXX ControlBlock_For.cpp CXX CoordinateInfo.cpp CXX Corr.cpp CXX Cph.cpp CXX CpptrajFile.cpp CXX CpptrajState.cpp CXX CpptrajStdio.cpp CXX CurveFit.cpp CXX DataFile.cpp CXX DataFileList.cpp CXX DataFilter.cpp CXX DataIO.cpp CXX DataIO_CCP4.cpp CXX DataIO_CharmmFastRep.cpp CXX DataIO_CharmmOutput.cpp CXX DataIO_CharmmRepLog.cpp CXX DataIO_CharmmRtfPrm.cpp CXX DataIO_Cmatrix.cpp CXX DataIO_Cpout.cpp CXX DataIO_Evecs.cpp CXX DataIO_Gnuplot.cpp CXX DataIO_Grace.cpp CXX DataIO_OpenDx.cpp CXX DataIO_Peaks.cpp CXX DataIO_Mdout.cpp CXX DataIO_NC_Cmatrix.cpp CXX DataIO_RemLog.cpp CXX DataIO_Std.cpp CXX DataIO_VecTraj.cpp CXX DataIO_Xplor.cpp CXX DataIO_XVG.cpp CXX DataSet.cpp CXX DataSetList.cpp CXX DataSet_1D.cpp CXX DataSet_3D.cpp CXX DataSet_Cmatrix.cpp CXX DataSet_Cmatrix_DISK.cpp CXX DataSet_Cmatrix_MEM.cpp CXX DataSet_Cmatrix_NOMEM.cpp CXX DataSet_Coords.cpp CXX DataSet_Coords_CRD.cpp CXX DataSet_Coords_REF.cpp CXX DataSet_Coords_TRJ.cpp CXX DataSet_GridDbl.cpp CXX DataSet_GridFlt.cpp CXX DataSet_Mat3x3.cpp CXX DataSet_MatrixDbl.cpp CXX DataSet_MatrixFlt.cpp CXX DataSet_Mesh.cpp CXX DataSet_Modes.cpp CXX DataSet_Parameters.cpp CXX DataSet_pH.cpp CXX DataSet_PHREMD_Explicit.cpp CXX DataSet_PHREMD_Implicit.cpp CXX DataSet_RemLog.cpp CXX DataSet_Topology.cpp CXX DataSet_Vector.cpp CXX DataSet_Vector_Scalar.cpp CXX DataSet_double.cpp CXX DataSet_float.cpp CXX DataSet_integer_disk.cpp CXX DataSet_integer_mem.cpp CXX DataSet_string.cpp CXX DataSet_StringVar.cpp CXX DataSet_Tensor.cpp CXX DataSet_unsignedInt.cpp CXX Deprecated.cpp CXX DihedralSearch.cpp CXX DistRoutines.cpp CXX Energy.cpp CXX EnergyArray.cpp CXX EnsembleIn.cpp CXX EnsembleIn_Multi.cpp CXX EnsembleIn_Single.cpp CXX EnsembleNavigator.cpp CXX EnsembleOut.cpp CXX EnsembleOut_Multi.cpp CXX EnsembleOut_Single.cpp CXX EnsembleOutList.cpp CXX Ewald.cpp CXX Ewald_ParticleMesh.cpp CXX Ewald_Regular.cpp In file included from Ewald_ParticleMesh.h:5, from Ewald_ParticleMesh.cpp:4: helpme_standalone.h:2323: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2323 | #pragma omp parallel for num_threads(nThreads) | helpme_standalone.h:2343: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2343 | #pragma omp parallel for num_threads(nThreads) | helpme_standalone.h:3014: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3014 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) | helpme_standalone.h:3120: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3120 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) | helpme_standalone.h:3247: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3247 | #pragma omp parallel for num_threads(nThreads) | helpme_standalone.h:3701: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3701 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:3739: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3739 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:3802: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3802 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:3840: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3840 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:4044: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4044 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:4052: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 4052 | #pragma omp for | helpme_standalone.h:4097: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4097 | #pragma omp parallel for num_threads(nThreads_) | helpme_standalone.h:4145: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4145 | #pragma omp parallel for num_threads(nThreads_) | helpme_standalone.h:4172: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4172 | #pragma omp parallel for num_threads(nThreads_) | helpme_standalone.h:4224: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4224 | #pragma omp parallel for num_threads(nThreads_) | helpme_standalone.h:4228: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4228 | #pragma omp parallel for num_threads(nThreads_) | helpme_standalone.h:4275: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4275 | #pragma omp parallel for num_threads(nThreads_) | helpme_standalone.h:4388: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4388 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) | helpme_standalone.h:4419: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) | helpme_standalone.h:4503: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4503 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:4510: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 4510 | #pragma omp for | CXX ExclusionArray.cpp CXX Exec_AddMissingRes.cpp helpme_standalone.h: In instantiation of ‘std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]’: helpme_standalone.h:3898:50: required from ‘void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]’ Ewald_ParticleMesh.cpp:187:32: required from here helpme_standalone.h:1010:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 1010 | for (int val = 0; val < nRows_; ++val) eigenPairs.push_back({eigenValues[val][0], unsortedEigenVectors[val]}); | ~~~~^~~~~~~~ helpme_standalone.h:1013:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 1013 | for (int val = 0; val < nRows_; ++val) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of ‘void helpme::PMEInstance >::sanityChecks(int, const RealMat&, const RealMat&, int) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]’: helpme_standalone.h:5018:9: required from ‘Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]’ Ewald_ParticleMesh.cpp:190:42: required from here helpme_standalone.h:3198:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 3198 | if (parameters.nCols() != (nCartesian(parameterAngMom) - cartesianOffset)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of ‘void helpme::PMEInstance >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]’: helpme_standalone.h:5019:9: required from ‘Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]’ Ewald_ParticleMesh.cpp:190:42: required from here helpme_standalone.h:3746:45: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 3746 | for (size_t row = threadID; row < gridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~ helpme_standalone.h:3753:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 3753 | for (int atom = 0; atom < nAtoms; ++atom) { | ~~~~~^~~~~~~~ helpme_standalone.h:3761:61: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 3761 | if (cGridIterator.size() && thisAtomsThread == threadID) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~ helpme_standalone.h:3750:25: warning: unused variable ‘gridIteratorC’ [-Wunused-variable] 3750 | const auto &gridIteratorC = threadedGridIteratorC_[threadID]; | ^~~~~~~~~~~~~ helpme_standalone.h:3794:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 3794 | for (int atom = splineCache_.size(); atom < newSize; ++atom) | ~~~~~^~~~~~~~~ helpme_standalone.h:3810:47: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 3810 | for (size_t cRow = threadID; cRow < gridDimensionC_; cRow += nThreads_) { | ~~~~~^~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of ‘Real* helpme::PMEInstance >::spreadParameters(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]’: helpme_standalone.h:5020:25: required from ‘Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]’ Ewald_ParticleMesh.cpp:190:42: required from here helpme_standalone.h:3708:45: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 3708 | for (size_t row = threadID; row < myGridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of ‘helpme::PMEInstance >::Complex* helpme::PMEInstance >::forwardTransform(Real*) [with Real = double; typename std::enable_if::value, int>::type = 0; Complex = std::complex]’: helpme_standalone.h:5023:32: required from ‘Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]’ Ewald_ParticleMesh.cpp:190:42: required from here helpme_standalone.h:4004:28: warning: variable ‘realCBA’ set but not used [-Wunused-but-set-variable] 4004 | Real *__restrict__ realCBA; | ^~~~~~~ CXX Exec_Analyze.cpp helpme_standalone.h: In instantiation of ‘void helpme::Matrix::assertSymmetric(const Real&) const [with Real = double]’: helpme_standalone.h:1000:9: required from ‘std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]’ helpme_standalone.h:3898:50: required from ‘void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]’ Ewald_ParticleMesh.cpp:187:32: required from here helpme_standalone.h:796:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 796 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of ‘void helpme::JacobiCyclicDiagonalization(Real*, Real*, const Real*, int) [with Real = double]’: helpme_standalone.h:1006:42: required from ‘std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]’ helpme_standalone.h:3898:50: required from ‘void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]’ Ewald_ParticleMesh.cpp:187:32: required from here helpme_standalone.h:213:20: warning: variable ‘cos_2phi’ set but not used [-Wunused-but-set-variable] 213 | Real sin_2phi, cos_2phi, cot_2phi; | ^~~~~~~~ helpme_standalone.h: In instantiation of ‘helpme::Matrix helpme::Matrix::applyOperation(const std::function&) const [with Real = double]’: helpme_standalone.h:785:26: required from ‘helpme::Matrix helpme::Matrix::inverse() const [with Real = double]’ helpme_standalone.h:3910:44: required from ‘void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]’ Ewald_ParticleMesh.cpp:187:32: required from here helpme_standalone.h:824:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 824 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of ‘void helpme::BSpline::update(short int, Real, short int, short int) [with Real = double]’: helpme_standalone.h:3829:47: required from ‘void helpme::PMEInstance >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]’ helpme_standalone.h:5019:9: required from ‘Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]’ Ewald_ParticleMesh.cpp:190:42: required from here helpme_standalone.h:2208:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2208 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:2208:72: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘short int’ [-Wsign-compare] 2208 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~ CXX Exec_Calc.cpp helpme_standalone.h: In instantiation of ‘helpme::Matrix helpme::Matrix::multiply(const helpme::Matrix&) const [with Real = double]’: helpme_standalone.h:877:64: required from ‘helpme::Matrix helpme::Matrix::operator*(const helpme::Matrix&) const [with Real = double]’ helpme_standalone.h:829:22: required from ‘helpme::Matrix helpme::Matrix::applyOperation(const std::function&) const [with Real = double]’ helpme_standalone.h:785:26: required from ‘helpme::Matrix helpme::Matrix::inverse() const [with Real = double]’ helpme_standalone.h:3910:44: required from ‘void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]’ Ewald_ParticleMesh.cpp:187:32: required from here helpme_standalone.h:860:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 860 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h:862:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 862 | for (int col = 0; col < other.nCols_; ++col) { | ~~~~^~~~~~~~~~~~~~ helpme_standalone.h:863:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 863 | for (int link = 0; link < nCols_; ++link) { | ~~~~~^~~~~~~~ CXX Exec_CatCrd.cpp CXX Exec_Change.cpp CXX Exec_ClusterMap.cpp helpme_standalone.h: In member function ‘helpme::PMEInstance::setupCalculationMetadata(int, double, int, int, int, int, int, int, int, double, int, void*, helpme::PMEInstance::NodeOrder, int, int, int) [clone .isra.0]’: helpme_standalone.h:3470:17: warning: ‘MEM [(struct FFTWWrapper *)&D.208707]’ may be used uninitialized [-Wmaybe-uninitialized] 3470 | fftHelperA_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3470:31: note: ‘’ declared here 3470 | fftHelperA_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3471:17: warning: ‘MEM [(struct FFTWWrapper *)&D.208706]’ may be used uninitialized [-Wmaybe-uninitialized] 3471 | fftHelperB_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3471:31: note: ‘’ declared here 3471 | fftHelperB_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3472:17: warning: ‘MEM [(struct FFTWWrapper *)&D.208705]’ may be used uninitialized [-Wmaybe-uninitialized] 3472 | fftHelperC_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3472:31: note: ‘’ declared here 3472 | fftHelperC_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ In member function ‘helpme::Matrix::operator=(helpme::Matrix&&)’, inlined from ‘helpme::PMEInstance::setupCalculationMetadata(int, double, int, int, int, int, int, int, int, double, int, void*, helpme::PMEInstance::NodeOrder, int, int, int) [clone .isra.0]’ at helpme_standalone.h:3503:43: helpme_standalone.h:519:7: warning: ‘D.208692.data_’ may be used uninitialized [-Wmaybe-uninitialized] 519 | class Matrix { | ^~~~~~ helpme_standalone.h: In member function ‘helpme::PMEInstance::setupCalculationMetadata(int, double, int, int, int, int, int, int, int, double, int, void*, helpme::PMEInstance::NodeOrder, int, int, int) [clone .isra.0]’: helpme_standalone.h:3503:45: note: ‘’ declared here 3503 | compressionCoefficientsA_ = RealMat(); | ^~~~~~~~~ In member function ‘helpme::Matrix::operator=(helpme::Matrix&&)’, inlined from ‘helpme::PMEInstance::setupCalculationMetadata(int, double, int, int, int, int, int, int, int, double, int, void*, helpme::PMEInstance::NodeOrder, int, int, int) [clone .isra.0]’ at helpme_standalone.h:3504:43: helpme_standalone.h:519:7: warning: ‘D.208691.data_’ may be used uninitialized [-Wmaybe-uninitialized] 519 | class Matrix { | ^~~~~~ helpme_standalone.h: In member function ‘helpme::PMEInstance::setupCalculationMetadata(int, double, int, int, int, int, int, int, int, double, int, void*, helpme::PMEInstance::NodeOrder, int, int, int) [clone .isra.0]’: helpme_standalone.h:3504:45: note: ‘’ declared here 3504 | compressionCoefficientsB_ = RealMat(); | ^~~~~~~~~ In member function ‘helpme::Matrix::operator=(helpme::Matrix&&)’, inlined from ‘helpme::PMEInstance::setupCalculationMetadata(int, double, int, int, int, int, int, int, int, double, int, void*, helpme::PMEInstance::NodeOrder, int, int, int) [clone .isra.0]’ at helpme_standalone.h:3505:43: helpme_standalone.h:519:7: warning: ‘D.208690.data_’ may be used uninitialized [-Wmaybe-uninitialized] 519 | class Matrix { | ^~~~~~ helpme_standalone.h: In member function ‘helpme::PMEInstance::setupCalculationMetadata(int, double, int, int, int, int, int, int, int, double, int, void*, helpme::PMEInstance::NodeOrder, int, int, int) [clone .isra.0]’: helpme_standalone.h:3505:45: note: ‘’ declared here 3505 | compressionCoefficientsC_ = RealMat(); | ^~~~~~~~~ CXX Exec_CombineCoords.cpp helpme_standalone.h: In member function ‘helpme::PMEInstance::computeERec(int, helpme::Matrix const&, helpme::Matrix const&)’: helpme_standalone.h:5031:16: warning: ‘energy’ may be used uninitialized [-Wmaybe-uninitialized] 5031 | return energy; | ^~~~~~ helpme_standalone.h:5021:14: note: ‘energy’ was declared here 5021 | Real energy; | ^~~~~~ CXX Exec_Commands.cpp CXX Exec_CompareTop.cpp CXX Exec_CrdAction.cpp CXX Exec_CrdOut.cpp CXX Exec_CreateSet.cpp CXX Exec_DataFile.cpp CXX Exec_DataFilter.cpp CXX Exec_DataSetCmd.cpp CXX Exec_Emin.cpp CXX Exec_Flatten.cpp CXX Exec_GenerateAmberRst.cpp CXX Exec_Graft.cpp CXX Exec_Help.cpp CXX Exec_LoadCrd.cpp CXX Exec_LoadTraj.cpp CXX Exec_ParallelAnalysis.cpp CXX Exec_ParmBox.cpp CXX Exec_ParmSolvent.cpp CXX Exec_ParmStrip.cpp CXX Exec_ParmWrite.cpp CXX Exec_PermuteDihedrals.cpp CXX Exec_Precision.cpp CXX Exec_PrepareForLeap.cpp CXX Exec_PrintData.cpp CXX Exec_Random.cpp CXX Exec_ReadData.cpp CXX Exec_ReadEnsembleData.cpp CXX Exec_ReadInput.cpp CXX Exec_RotateDihedral.cpp CXX Exec_RunAnalysis.cpp CXX Exec_ScaleDihedralK.cpp CXX Exec_Set.cpp CXX Exec_SequenceAlign.cpp CXX Exec_Show.cpp CXX Exec_SortEnsembleData.cpp CXX Exec_SplitCoords.cpp CXX Exec_System.cpp CXX Exec_Top.cpp CXX Exec_Traj.cpp CXX Exec_UpdateParameters.cpp CXX Exec_ViewRst.cpp CXX File_TempName.cpp CXX FileIO_Bzip2.cpp CXX FileIO_Gzip.cpp CXX FileIO_Mpi.cpp CXX FileIO_MpiShared.cpp CXX FileIO_Std.cpp CXX FileName.cpp CXX FileType.cpp CXX FileTypes.cpp CXX ForLoop.cpp CXX ForLoop_dataSetBlocks.cpp CXX ForLoop_integer.cpp CXX ForLoop_list.cpp CXX ForLoop_mask.cpp CXX ForLoop_overSets.cpp CXX Frame.cpp CXX GridAction.cpp CXX HistBin.cpp CXX Hungarian.cpp CXX ImageRoutines.cpp CXX Image_List_Mask.cpp CXX Image_List_Pair.cpp CXX Image_List_Unit.cpp CXX InputTrajCommon.cpp CXX KDE.cpp CXX MapAtom.cpp CXX MaskArray.cpp CXX MaskToken.cpp CXX Matrix_3x3.cpp CXX MdOpts.cpp CXX MetaData.cpp CXX Minimize_SteepestDescent.cpp CXX Mol.cpp CXX Mol2File.cpp CXX NameType.cpp CXX NC_Cmatrix.cpp CXX NC_Routines.cpp CXX NetcdfFile.cpp CXX OMM_helpers.cpp CXX OutputTrajCommon.cpp CXX ParameterSet.cpp CXX PDBfile.cpp CXX PairList.cpp CXX Parallel.cpp CXX ParallelNetcdf.cpp CXX ParmFile.cpp CXX Parm_Amber.cpp CXX Parm_CharmmPsf.cpp CXX Parm_CIF.cpp CXX Parm_Gromacs.cpp CXX Parm_Mol2.cpp CXX Parm_PDB.cpp CXX Parm_SDF.cpp CXX Parm_Tinker.cpp CXX PotentialFunction.cpp CXX PotentialTerm.cpp CXX PotentialTerm_Angle.cpp CXX PotentialTerm_Bond.cpp CXX PotentialTerm_Dihedral.cpp CXX PotentialTerm_LJ_Coulomb.cpp CXX PotentialTerm_OpenMM.cpp CXX ProgressBar.cpp CXX ProgressTimer.cpp CXX PubFFT.cpp CXX ExternalFxn.cpp CXX Random.cpp CXX Range.cpp CXX RNG.cpp CXX RNG_Marsaglia.cpp CXX RNG_MersenneTwister.cpp CXX RNG_PCG32.cpp CXX RNG_Stdlib.cpp CXX RNG_Xoshiro128pp.cpp CXX RPNcalc.cpp CXX ReferenceAction.cpp CXX RemdReservoirNC.cpp CXX Residue.cpp CXX SDFfile.cpp CXX SimplexMin.cpp CXX Spline.cpp CXX SplineFxnTable.cpp CXX StringRoutines.cpp CXX StructureCheck.cpp CXX StructureMapper.cpp CXX SymmetricRmsdCalc.cpp CXX TextFormat.cpp CXX Timer.cpp CXX TinkerFile.cpp CXX TopInfo.cpp CXX Topology.cpp CXX TorsionRoutines.cpp CXX Traj_AmberCoord.cpp CXX Traj_AmberNetcdf.cpp CXX Traj_AmberRestart.cpp CXX Traj_AmberRestartNC.cpp CXX Traj_Binpos.cpp CXX Traj_CharmmCor.cpp CXX Traj_CharmmDcd.cpp CXX Traj_CharmmRestart.cpp CXX Traj_CIF.cpp CXX Traj_Conflib.cpp CXX Traj_DTR.cpp CXX Traj_GmxDump.cpp CXX Traj_GmxTng.cpp CXX Traj_GmxTrX.cpp CXX Traj_GmxXtc.cpp CXX Traj_Gro.cpp CXX Traj_Mol2File.cpp CXX Traj_NcEnsemble.cpp CXX Traj_PDBfile.cpp CXX Traj_SDF.cpp CXX Traj_SQM.cpp CXX Traj_Tinker.cpp CXX Traj_XYZ.cpp CXX TrajectoryFile.cpp CXX TrajectoryIO.cpp CXX TrajFrameCounter.cpp CXX TrajinList.cpp CXX Trajin_Multi.cpp CXX Trajin_Single.cpp CXX TrajIOarray.cpp CXX Trajout_Single.cpp CXX TrajoutList.cpp CXX Vec3.cpp CXX ViewRst.cpp CXX xoshiro128plusplus.cpp xoshiro128plusplus.cpp: In function ‘void jump()’: xoshiro128plusplus.cpp:60:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 60 | for(int i = 0; i < sizeof JUMP / sizeof *JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ xoshiro128plusplus.cpp: In function ‘void long_jump()’: xoshiro128plusplus.cpp:90:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 90 | for(int i = 0; i < sizeof LONG_JUMP / sizeof *LONG_JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CXX Action_Esander.cpp CXX Command.cpp CXX Cpptraj.cpp CXX Energy_Sander.cpp CXX ReadLine.cpp CXX main.cpp CC molsurf.c Skipping bundled READLINE build cd xdrfile && make all make[3]: Entering directory '/<>/src/xdrfile' CC xdrfile.c Skipping bundled ARPACK build cd tng && make all make[3]: Entering directory '/<>/src/tng' CC md5.c CC tng_io.c CC tng_compress.c CC xdr_seek.c CC xdrfile_trr.c CC xdrfile_xtc.c /bin/rm -f libxdrfile.a ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o make[3]: Leaving directory '/<>/src/xdrfile' CC coder.c CC warnmalloc.c CC fixpoint.c CC xtc3.c CC bwlzh.c tng_io.c: In function ‘tng_gen_data_block_add’: tng_io.c:12600:9: warning: ‘__strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-truncation] 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^ tng_io.c:12600:47: note: length computed here 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ CC xtc2.c CC widemuldiv.c CC huffmem.c CC vals16.c CC bwt.c CC mtf.c CC rle.c CC lz77.c CC dict.c CC huffman.c CC merge_sort.c /bin/rm -f libtng_io.a ar cqs libtng_io.a md5.o tng_io.o tng_compress.o coder.o warnmalloc.o fixpoint.o xtc3.o bwlzh.o xtc2.o widemuldiv.o huffmem.o vals16.o bwt.o mtf.o rle.o lz77.o dict.o huffman.o merge_sort.o make[3]: Leaving directory '/<>/src/tng' g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o -L/usr/lib/aarch64-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/aarch64-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/aarch64-linux-gnu/lib -lfftw3 -L/usr/lib/aarch64-linux-gnu/lib -lOpenMM -lnetcdf -lbz2 tng/libtng_io.a -lz xdrfile/libxdrfile.a -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro mv cpptraj "/<>/bin" make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_test -- check unittest make -j4 test "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 check unittest make[2]: Entering directory '/<>' make[2]: Nothing to be done for 'test'. cd test && make test.complete summary cd unitTests && make test.complete summary make[3]: Entering directory '/<>/unitTests' make[3]: Entering directory '/<>/test' CPPTRAJ source directory: /<>/src CPPTRAJ config.h file: /<>/config.h make[4]: Entering directory '/<>/unitTests' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. CPPTRAJ source directory: /<>/src CPPTRAJ config.h file: /<>/config.h ******************************************************************************** TEST: /<>/unitTests/NameType CPPTRAJ: NameType class unit test. make[5]: Entering directory '/<>/unitTests/NameType' g++ -Wall -O3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-3build3 -std=gnu++11 -I/<>/src -c -o main.o main.cpp -rwxr-xr-x 1 buildd buildd 157682456 Apr 1 11:01 ../bin/cpptraj -rwxr-xr-x 1 buildd buildd 157682456 Apr 1 11:01 ../bin/cpptraj make[4]: Entering directory '/<>/test' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. ******************************************************************************** TEST: /<>/test/Test_General CPPTRAJ: General tests All 15 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Parallel CPPTRAJ: Parallel tests. CPPTRAJ: Parallel test with trajectory offset All 7 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Strip CPPTRAJ: One frame strip command test CPPTRAJ: Unstrip (Lig/Rec/Complex) command test CPPTRAJ: Multi frame strip command test. CPPTRAJ: Strip topology with PDB info All 11 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_BrokenTraj CPPTRAJ: Broken Traj: Running good trajectory. CPPTRAJ: Broken Traj: Running broken trajectory. CPPTRAJ: Compressed broken trajectory test All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_TrajinOffset CPPTRAJ: Normal trajectory read with offsets. CPPTRAJ: Gzipped trajectory read with offsets CPPTRAJ: Bzip2ed trajectory read with offsets CPPTRAJ: Start argument offset All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_RemdTraj CPPTRAJ: CRD Replica Trajectory Run with offset CPPTRAJ: CRD Replica Trajectory Run CPPTRAJ: NetCDF Replica Trajectory Run test CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj CPPTRAJ: CRD Replica Trajectory Run with remdout All 8 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_trajout_framerange CPPTRAJ: Trajout Frame Range [Amber Restart] CPPTRAJ: Trajout Frame Range [Amber Coordinates] g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-3build3 -std=gnu++11 -I/<>/src -c -o NameType.o /<>/src/NameType.cpp All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_PerResRMSD CPPTRAJ: Per-Residue RMSD Test. CPPTRAJ: Per-Residue RMSD Test with averaging CPPTRAJ: Per-Residue RMSD Test with residue centering. All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_DSSP CPPTRAJ: Secstruct (DSSP) command test. CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. CPPTRAJ: Secstruct (DSSP) command with changing number of residues. CPPTRAJ: Secstruct (DSSP): SS assign output test CPPTRAJ: FtuFabI Assignment test All 10 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Center CPPTRAJ: Center command test. CPPTRAJ: Center origin command test. CPPTRAJ: Center origin mass command test. CPPTRAJ: Center reference command test. CPPTRAJ: Center point test. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Hbond CPPTRAJ: Solute Hbond test g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-3build3 -std=gnu++11 -I/<>/src -c -o CpptrajStdio.o /<>/src/CpptrajStdio.cpp CPPTRAJ: Solute Hbond test with disk caching CPPTRAJ: Solute-solvent hbond test CPPTRAJ: Hbond, no intramolecular hydrogen bonds test g++ -o a.out main.o NameType.o CpptrajStdio.o CPPTRAJ: Hbond, specified solute masks CPPTRAJ: Hbond, no angle cutoff test CPPTRAJ: Hbond, Bridge nointramol test CPPTRAJ: Hbond with imaging CPPTRAJ: Hbond, orthogonal imaging All 23 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_NCrestart CPPTRAJ: NetCDF Restart Test - TXT->NetCDF CPPTRAJ: NetCDF Restart Test - NetCDF->TXT CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Image CPPTRAJ: Orthorhombic imaged distance test. CPPTRAJ: Non-orthorhombic imaged distance test. CPPTRAJ: Orthorhombic coordinate imaging test CPPTRAJ: Nonorthorhombic coordinate imaging test make[5]: Leaving directory '/<>/unitTests/NameType' 'ZN' 'HA2' 'HA' 'HA' 'CT11' Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeName' Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeString' Unit test passed. ******************************************************************************** TEST: /<>/unitTests/ArgList CPPTRAJ: ArgList class unit test. make[5]: Entering directory '/<>/unitTests/ArgList' g++ -Wall -O3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-3build3 -std=gnu++11 -I/<>/src -c -o main.o main.cpp CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Surf CPPTRAJ: Surface calculation test CPPTRAJ: Partial Surface calculation test g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-3build3 -std=gnu++11 -I/<>/src -c -o ArgList.o /<>/src/ArgList.cpp CPPTRAJ: LCPO test with GAFF atom types All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Radgyr CPPTRAJ: Radius of gyration command test All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Mask CPPTRAJ: Mask single frame test CPPTRAJ: Mask longer command test. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Jcoupling CPPTRAJ: J-Coupling single frame test J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. Skipped test: J-Coupling extended test All 1 comparisons passed. 1 comparisons skipped. ******************************************************************************** TEST: /<>/test/Test_Diffusion CPPTRAJ: Diffusion test, no imaging. CPPTRAJ: Diffusion test, old syntax. CPPTRAJ: Diffusion test, new syntax. CPPTRAJ: Diffusion test, nonorthogonal box CPPTRAJ: STFC Diffusion Test CPPTRAJ: STFC Diffusion Test with individual distances CPPTRAJ: STFC Diffusion Test with COM CPPTRAJ: STFC Diffusion Test with second mask All 16 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Outtraj CPPTRAJ: RMSD Test with outtraj. CPPTRAJ: Outtraj Test with maxmin. All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Charmm CPPTRAJ: CHARMM PSF/DCD test CPPTRAJ: CHARMM DCD Write, step 1. CPPTRAJ: CHARMM DCD Write, step 2. CPPTRAJ: CHAMBER topology read/strip test. CPPTRAJ: Read CHARMM restart CPPTRAJ: CHARMM PSF write CPPTRAJ: CHARMM COORdinates test All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CharmmParams CPPTRAJ: Test updating topology with Charmm parameters (single residue) All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Rotdif CPPTRAJ: Rotational diffusion calculation test All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_NetcdfTraj CPPTRAJ: Convert mdcrd -> NetCDF CPPTRAJ: Convert NetCDF -> mdcrd All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Runavg CPPTRAJ: Coordinate Running Average test. CPPTRAJ: Coordinate Running Average Traj Write All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_RMSD CPPTRAJ: Basic RMSD tests CPPTRAJ: RMS coordinate rotation/rotation matrices test CPPTRAJ: RMS fit with no coordinates modification test. CPPTRAJ: RMS fit to previous test CPPTRAJ: RMS: imaging after unit cell rotation All 12 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_2DRMS CPPTRAJ: 2D RMSD Test. CPPTRAJ: 2D RMSD Test, mass-weighted. CPPTRAJ: 2D RMSD Test with reference trajectory CPPTRAJ: 2D DME Test. CPPTRAJ: 2D RMSD with reference mask test. CPPTRAJ: 2D RMSD test, no fitting. All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Mol2 CPPTRAJ: Mol2 Parm/Traj Read/Write Test. CPPTRAJ: PDB => Mol2 CPPTRAJ: Amber Top/Rst => Mol2 Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. Skipped test: Amber Top/Rst => Mol2, SYBYL atom types All 4 comparisons passed. 1 comparisons skipped. ******************************************************************************** TEST: /<>/test/Test_NAstruct CPPTRAJ: NAstruct command test. CPPTRAJ: NAstruct command test, single strand All 11 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_NAstruct_8OG CPPTRAJ: NA test (8OG) All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Average CPPTRAJ: Average Test. All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Pucker CPPTRAJ: Pucker command test CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_AtomMap CPPTRAJ: AtomMap Test CPPTRAJ: AtomMap with 'rmsfit' CPPTRAJ: Atom map charmm->amber atom order CPPTRAJ: Atom map charmm->amber atom order, by residue All 9 comparisons passed. g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-3build3 -std=gnu++11 -I/<>/src -c -o CpptrajStdio.o /<>/src/CpptrajStdio.cpp ******************************************************************************** TEST: /<>/test/Test_Datafile CPPTRAJ: Data file output precision test CPPTRAJ: Standard -> Grace Data CPPTRAJ: Grace -> Standard Data CPPTRAJ: X column format/precision test. CPPTRAJ: Data file group by name test g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-3build3 -std=gnu++11 -I/<>/src -c -o StringRoutines.o /<>/src/StringRoutines.cpp CPPTRAJ: Data file group by aspect test All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Radial CPPTRAJ: Radial test, non-orthogonal imaging CPPTRAJ: Radial test, orthogonal and no imaging All 9 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Hist CPPTRAJ: 1D/2D Histogram Analysis test CPPTRAJ: 3D histogram test. All 7 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Closest CPPTRAJ: Closest command test using first solvent atom. CPPTRAJ: Closest command test using all solvent atoms. CPPTRAJ: Closest command test, using mask center CPPTRAJ: Closest command test, using mask center and solvent mask CPPTRAJ: Closest command test, solvent mask, water oxygen only g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o All 8 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_DRMSD CPPTRAJ: Distance RMSD test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Cluster CPPTRAJ: Cluster command test, in-memory pairwise distances. CPPTRAJ: Cluster command test, read pairwise distances. CPPTRAJ: Cluster command test, read NetCDF pairwise distances. CPPTRAJ: Cluster command test, write ASCII pairwise distances. CPPTRAJ: Cluster command test, read ASCII pairwise distances. All 9 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Cluster_Sieve CPPTRAJ: Cluster, nosieve CPPTRAJ: Cluster, sieve5 CPPTRAJ: Cluster, nosieve savepairdist CPPTRAJ: Cluster, nosieve loadpairdist CPPTRAJ: Cluster, sieve5 savepairdist CPPTRAJ: Cluster, sieve5 loadpairdist CPPTRAJ: Cluster, nosieve pairwisecache none CPPTRAJ: Cluster, sieve5 pairwisecache none make[5]: Leaving directory '/<>/unitTests/ArgList' CPPTRAJ: Cluster, random Unit test passed. make[4]: Leaving directory '/<>/unitTests' make[3]: Leaving directory '/<>/unitTests' All 28 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Cluster_RandomSieve CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Cluster_DataSet CPPTRAJ: Clustering, One DataSet CPPTRAJ: Clustering, Two DataSets CPPTRAJ: Clustering, dihedral DataSet CPPTRAJ: Clustering, two dihedral DataSets CPPTRAJ: Clustering, dihedral DataSet, K-means CPPTRAJ: Clustering, two dihedral DataSets, K-means All 8 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Cluster_DBSCAN CPPTRAJ: DBSCAN test CPPTRAJ: DBSCAN automatic parameter determination test. CPPTRAJ: DBSCAN kdist map test CPPTRAJ: DBSCAN with sieve All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Cluster_Kmeans CPPTRAJ: Cpptraj Kmeans CPPTRAJ: Cpptraj Kmeans random All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Cluster_SymmRMSD CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Cluster_TrajWrites CPPTRAJ: Cluster command test, coordinate writes. CPPTRAJ: Cluster command test, coordinate writes using info file. All 8 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Cluster_Dpeaks CPPTRAJ: Density peaks clustering test All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Cluster_Nreps CPPTRAJ: Clustering with specified # reps All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_IRED CPPTRAJ: IRED vector/matrix test ******************************************************************************** TEST: /<>/test/Test_RandomizeIons CPPTRAJ: randomizeions test (original algorithm) CPPTRAJ: Randomize (around, overlap) CPPTRAJ: Randomize (around) CPPTRAJ: Randomize (overlap) CPPTRAJ: Randomize (no restrictions) All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Molsurf CPPTRAJ: Molsurf test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Corr CPPTRAJ: Correlation test All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CheckStructure CPPTRAJ: Structure Check CPPTRAJ: Structure Check with Around and Skip CPPTRAJ: Structure Check with PBC CPPTRAJ: Structure Check with Around All 8 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_RmsAvgCorr CPPTRAJ: RmsAvgCorr Reference CPPTRAJ: RmsAvgCorr First All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Contacts CPPTRAJ: Contacts test. All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Principal CPPTRAJ: Principal Test All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_ClusterDihedral CPPTRAJ: clusterdihedral test All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Vector CPPTRAJ: Basic vector tests CPPTRAJ: Test vector center with magnitude CPPTRAJ: Momentum/velocity vector test. CPPTRAJ: Force vector test. All 14 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Matrix CPPTRAJ: Matrix Tests CPPTRAJ: Generate matrix with trajectory start/stop/offset CPPTRAJ: Generate matrix with action stop/start/offset All 15 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_AtomicFluct CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. CPPTRAJ: Atomicfluct test with ADP output CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. All 13 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Grid CPPTRAJ: Dipole test CPPTRAJ: Grid test CPPTRAJ: OpenDX Grid read test CPPTRAJ: Grid with specified center test. CPPTRAJ: Grid with box center offset test. CPPTRAJ: Grid with mask center offset test. CPPTRAJ: Non-orthogonal grid test. CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test CPPTRAJ: Grid generation from 'bounds' test. All 13 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Unwrap CPPTRAJ: Unwrap non-orthogonal test CPPTRAJ: Unwrap orthogonal test All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Project CPPTRAJ: Projection All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Analyze_Modes CPPTRAJ: Modes analysis, RMS fluctuations CPPTRAJ: Modes analysis, displacements CPPTRAJ: Modes analysis, dipole correlation CPPTRAJ: Modes analysis, pseudo trajectory creation test CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Watershell CPPTRAJ: Watershell Test, non-orthorhombic imaging. CPPTRAJ: Watershell Test, orthorhombic imaging. CPPTRAJ: Watershell Test, no imaging. All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_AnalysisRunAvg CPPTRAJ: Analysis Running Average All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Volmap CPPTRAJ: VMD VolMap Algorithm test VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. Skipped test: VMD VolMap Algorithm longer tests All 2 comparisons passed. 1 comparisons skipped. ******************************************************************************** TEST: /<>/test/Test_SPAM CPPTRAJ: SPAM Test *** buffer overflow detected ***: terminated ../MasterTest.sh: line 495: 16814 Aborted (core dumped) $cpptraj_cmd >> $CPPTRAJ_OUTPUT Error: cpptraj exited with status 134 CPPTRAJ: SPAM Pure Solvent Test 1 out of 2 executions exited with an error. 2 out of 5 comparisons failed. ******************************************************************************** TEST: /<>/test/Test_LIE CPPTRAJ: LIE test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Density CPPTRAJ: Density along axis tests CPPTRAJ: Multi-frame density along axis test CPPTRAJ: Total system density test All 7 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_LipidOrder CPPTRAJ: Lipid Order Parameter Test. All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_LipidSCD CPPTRAJ: Basic lipid order parameter test CPPTRAJ: New Lipid Order Parameter Test, DOPC. All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_PairDist CPPTRAJ: PairDist Test. CPPTRAJ: Pairdist test, orthogonal imaging. CPPTRAJ: Pairdist test, nonorthogonal imaging. CPPTRAJ: Pairdist test, 2 masks. All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_ReadData CPPTRAJ: Read vector data test (no origins, origins) CPPTRAJ: Read vector data set (origins, no origins) CPPTRAJ: Read Amber output test CPPTRAJ: Read CHARMM output test CPPTRAJ: 3D data read/write test CPPTRAJ: Standard 3D data write test CPPTRAJ: Standard 3D data read test CPPTRAJ: Standard 3D data read/append test CPPTRAJ: Standard 3D data, sparse CPPTRAJ: Nonorthogonal grid standard write/read tests. CPPTRAJ: Read specific columns test. CPPTRAJ: Write non-square matrix CPPTRAJ: Read non-square matrix CPPTRAJ: Read square matrix All 15 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_GIST CPPTRAJ: GIST water-water interaction test CPPTRAJ: GIST test, orthogonal cell CPPTRAJ: GIST test, nonorthogonal cell All 11 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_GIST_Order CPPTRAJ: TIP3P water cluster test CPPTRAJ: TIP4P water cluster test CPPTRAJ: TIP5P water cluster test All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_systemVF CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_AtomicCorr CPPTRAJ: Atomic Correlation test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_AutoCorr CPPTRAJ: AutoCorr test. All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Box CPPTRAJ: Box Test (Add box info) CPPTRAJ: Box test (remove box info) CPPTRAJ: Box test (Modify box length) CPPTRAJ: Box test (auto orthogonal box, no radii) CPPTRAJ: Box test (auto orthogonal box, VDW radii) All 7 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_AtomTypeSelect CPPTRAJ: Selection by atom type test. All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_AvgRef CPPTRAJ: RMSD Test with averaged reference coordinates. All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Crank_Stat CPPTRAJ: Crankshaft test All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CreateCrd CPPTRAJ: COORDS data set creation and CRDFLUCT test. CPPTRAJ: COORDS data set creation with velocities test CPPTRAJ: TRAJ data set creation and CRDFLUCT test. CPPTRAJ: TRAJ data set creation with velocities test. CPPTRAJ: COORDS data set append test CPPTRAJ: COORDS test storing frame metadata CPPTRAJ: TRAJ test storing frame metadata All 8 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_AutoImage CPPTRAJ: AutoImage test (split DNA duplex) CPPTRAJ: AutoImage test, use anchor mask All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_LoadCrd CPPTRAJ: LoadCrd test. CPPTRAJ: LoadTraj test. CPPTRAJ: LoadTraj from trajin test. CPPTRAJ: LoadCrd append from multiple files test All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_MultiVector CPPTRAJ: Multivector test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Lifetime CPPTRAJ: Lifetime test. CPPTRAJ: Lifetime test with data set caching. CPPTRAJ: Lifetime average and cumulative average test. All 12 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_FFT CPPTRAJ: FFT test. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Timecorr CPPTRAJ: Timecorr test. All 7 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CrossCorr CPPTRAJ: CrossCorr test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_SymmRmsd CPPTRAJ: SymmRmsd CPPTRAJ: ASP symmetry-corrected RMSD test CPPTRAJ: GLU symmetry-corrected RMSD test CPPTRAJ: TYR symmetry-corrected RMSD test CPPTRAJ: Longer symmetry-corrected RMSD test. All 8 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Multidihedral CPPTRAJ: Multidihedral test CPPTRAJ: Multidihedral Nucleotide CHI test CPPTRAJ: Multidihedral protein dihedrals test CPPTRAJ: Multidihedral cyclic molecule test All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Ensemble_MREMD CPPTRAJ: M-REMD sort test. CPPTRAJ: M-REMD actions test. CPPTRAJ: M-REMD ensemble outtraj test. CPPTRAJ: M-REMD no sort, running average test CPPTRAJ: M-REMD, generate RMS data CPPTRAJ: M-REMD, meltcurve analysis All 17 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_MakeStructure CPPTRAJ: Basic makestructure test CPPTRAJ: Makestructure test with reference. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Rotate CPPTRAJ: Rotation (and inverse) of coords from matrices CPPTRAJ: Rotate with defined axis All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Integrate CPPTRAJ: Integration test. All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_NativeContacts CPPTRAJ: NativeContacts test. CPPTRAJ: NativeContacts test, save non-native contacts, residue time series CPPTRAJ: NativeContacts test, orthorhombic imaging. All 17 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CheckChiral CPPTRAJ: Check chirality test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Energy CPPTRAJ: Simple energy tests CPPTRAJ: Test kinetic energy calculation CPPTRAJ: Test total energy calculation CPPTRAJ: Test partial energy calculation All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_LESsplit CPPTRAJ: LES split/average test All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_PermuteDihedrals CPPTRAJ: PermuteDihedrals interval -120, phi psi CPPTRAJ: PermuteDihedrals, random rotations All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CCP4 CPPTRAJ: CCP4 read/write and DX conversion test. All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_DihCovar CPPTRAJ: Dihedral Covariance Matrix Test All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CurveFit CPPTRAJ: Curve fitting test. CPPTRAJ: Curve fitting multi-exponential tests. CPPTRAJ: Curve fitting, custom output range. All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Multicurve CPPTRAJ: Multicurve test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_DataSetAverage CPPTRAJ: Data set averaging and averaging over all sets test. All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_VectorMath CPPTRAJ: Vector dot/cross product test All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Esander SANDER energy tests (long) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. SKIP: SANDER energy tests (long) ******************************************************************************** TEST: /<>/test/Test_Esander_Short Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. SKIP: Energy via sander API short tests (GB/PME) ******************************************************************************** TEST: /<>/test/Test_Temperature CPPTRAJ: Temperature test. CPPTRAJ: Temperature with SHAKE on hydrogens. CPPTRAJ: Temperature with SHAKE on all atoms. CPPTRAJ: Temperature calc with extra points. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Spline CPPTRAJ: Spline test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_KDE CPPTRAJ: KDE test. CPPTRAJ: KDE with Kullback-Leibler divergence test All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Wavelet CPPTRAJ: Wavelet analysis test CPPTRAJ: Wavelet WAFEX test All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CIF CPPTRAJ: CIF read test CPPTRAJ: Generate offset traj from PDB CPPTRAJ: Generate offset traj from CIF All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_PDB CPPTRAJ: PDB format read/write test CPPTRAJ: PQR file write with various radii CPPTRAJ: PDB filter alternate atom location IDs test CPPTRAJ: Adding PDB info to topology All 10 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Align CPPTRAJ: Align Tests. CPPTRAJ: Align, unit cell rotation/imaging test. All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_VelocityAutoCorr CPPTRAJ: Velocity autocorrelation test All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_VelFrc CPPTRAJ: Test combining coordinates, velocities, and forces. CPPTRAJ: Test using velocities as coordinates. CPPTRAJ: Test writing velocities (MDVEL) CPPTRAJ: Test using forces as coordinates. CPPTRAJ: Test writing forces (MDFRC) CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_RotateDihedral CPPTRAJ: Rotate dihedral to target value. CPPTRAJ: Rotate dihedral by increment CPPTRAJ: Rotate dihedral in TRAJ data set All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_DataSetCmd CPPTRAJ: Data Set commands test All 10 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Remap CPPTRAJ: Remap Test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CompareTop CPPTRAJ: Compare topology test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Filter CPPTRAJ: Basic filter test CPPTRAJ: Data filter test. CPPTRAJ: Filter matrix test. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CombineCrd CPPTRAJ: Combine COORDS test. CPPTRAJ: Combine COORDS test with box info. CPPTRAJ: Split coords and recombine test. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_TopInfo CPPTRAJ: Topology info print test. CPPTRAJ: Topology info with reference coords test All 12 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_GromacsTrr CPPTRAJ: TRR force/velocity read -> NetCDF write test CPPTRAJ: TRR force/velocity read -> TRR write test CPPTRAJ: CRD => TRR CPPTRAJ: TRR => CRD CPPTRAJ: CRD(1-5) => TRR CPPTRAJ: CRD(6-10) => TRR CPPTRAJ: TRR (appended) => CRD CPPTRAJ: GMX: CRD with offset CPPTRAJ: GMX: TRR with offset All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_GromacsXtc CPPTRAJ: XTC read test CPPTRAJ: CRD => XTC CPPTRAJ: XTC => CRD CPPTRAJ: CRD(1-5) => XTC CPPTRAJ: CRD(6-10) => XTC CPPTRAJ: XTC (appended) => CRD CPPTRAJ: GMX: CRD with offset CPPTRAJ: GMX: XTC with offset All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_GromacsTNG CPPTRAJ: TNG read test CPPTRAJ: TNG read test (with offset) All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Ewald CPPTRAJ: Direct sum test CPPTRAJ: Ewald test (NaCl crystal) CPPTRAJ: Ewald test (trunc. oct) CPPTRAJ: Ewald test (partial system, trunc. oct) Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: Ewald test (trunc. oct), 10 frames Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: Ewald test (ortho), 10 frames All 4 comparisons passed. 2 comparisons skipped. ******************************************************************************** TEST: /<>/test/Test_LibPME CPPTRAJ: Particle mesh Ewald test (NaCl crystal) CPPTRAJ: Particle mesh Ewald test (trunc. oct) CPPTRAJ: Particle mesh Ewald test (ortho) CPPTRAJ: Particle mesh Ewald test (ortho, with mask) CPPTRAJ: PME test (partial system, trunc. oct) PME test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: PME test (trunc. oct), 10 frames All 5 comparisons passed. 1 comparisons skipped. ******************************************************************************** TEST: /<>/test/Test_LJ_PME CPPTRAJ: LJ PME test. CPPTRAJ: LJ PME kappa sweep test, 0.25 CPPTRAJ: LJ PME kappa sweep test, 0.35 CPPTRAJ: LJ PME kappa sweep test, 0.45 CPPTRAJ: LJ PME kappa sweep test, 0.5 CPPTRAJ: LJ with switch function test All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_TI CPPTRAJ: TI analysis test. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_FixImagedBonds CPPTRAJ: Fix imaged bonds test (Ortho.) CPPTRAJ: Fix imaged bonds test (Non-ortho.) All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Distance CPPTRAJ: Distance tests CPPTRAJ: Orthogonal imaged distance CPPTRAJ: Non-orthogonal imaged distance All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Volume CPPTRAJ: Volume tests All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_SetVelocity CPPTRAJ: Set Velocity test CPPTRAJ: Scale velocity test 1 out of 3 comparisons failed. ******************************************************************************** TEST: /<>/test/Test_Remlog CPPTRAJ: Replica log read/analyze test. All 7 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_AreaPerMol CPPTRAJ: Area per molecule test All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_DistBasedMask CPPTRAJ: Distance-based atom mask tests (atom, residue) CPPTRAJ: Distance-based atom mask tests (molecule) All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Calc CPPTRAJ: Calc test CPPTRAJ: Calc test with data sets CPPTRAJ: Test math functions All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CalcState CPPTRAJ: Calcstate test All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Change CPPTRAJ: Change atom and residue name tests CPPTRAJ: Change chain ID test CPPTRAJ: Change chain ID of COORDS set test All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CreateReservoir CPPTRAJ: Create RREMD NetCDF reservoir test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_FixAtomOrder CPPTRAJ: Out of order molecules test All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_LowestCurve CPPTRAJ: LowestCurve test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_MinImage CPPTRAJ: Minimum Image test. All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Regress CPPTRAJ: Linear regression test. All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Rst CPPTRAJ: Generate restraints (rst) test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Pairwise CPPTRAJ: Pairwise tests CPPTRAJ: Pairwise test, partial system All 10 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_ParmBox CPPTRAJ: Parmbox test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Solvent CPPTRAJ: Test solvent command with closest All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Translate CPPTRAJ: Translate test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_ReplicateCell CPPTRAJ: Replicate cell test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_ScaleDihedralK CPPTRAJ: Scale dihedral force constant test CPPTRAJ: Scale dihedral force constant with 'useall' All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_PhiPsi CPPTRAJ: Phipsi test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Control CPPTRAJ: Loop tests CPPTRAJ: Test set command CPPTRAJ: Test reading comma-separated list of strings CPPTRAJ: Test nested loops and variables in loops CPPTRAJ: Test loop over data set blocks CPPTRAJ: Test for filename wildcards and oversets All 13 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_InfraredSpec CPPTRAJ: Infrared spectrum calculation test All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Cphstats CPPTRAJ: Explicit pH REMD ensemble data read / sort CPPTRAJ: Constant pH stats test CPPTRAJ: Sorted implicit constant pH stats test CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats CPPTRAJ: Unsorted pH read/write test All 16 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CmdLine CPPTRAJ: Command line trajectory args test, part 1 CPPTRAJ: Command line test trajectory args test, part 2 CPPTRAJ: Command line wildcard test, part 1 CPPTRAJ: Command line wildcard test, part 2 All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_XYZformat CPPTRAJ: XYZ format write CPPTRAJ: Atom XYZ format read, test 1 CPPTRAJ: Atom XYZ format read, test 2 CPPTRAJ: Atom XYZ format read, test 3 CPPTRAJ: Atom XYZ format read, test 4 CPPTRAJ: Atom XYZ format read, test 5 CPPTRAJ: Atom XYZ format read, test 6 All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Hausdorff CPPTRAJ: Simple Hausdorff distance test. CPPTRAJ: Hausdorff distance of 2D rms output test. CPPTRAJ: Hausdorff distance of 2D rms output test. All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CatCrd CPPTRAJ: Concatenate COORDS data set test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_XtalSymm CPPTRAJ: XtalSymm Reference CPPTRAJ: XtalSymm Reimaging by Atom CPPTRAJ: XtalSymm Reimaging by Molecule All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Time CPPTRAJ: Add time to restart test CPPTRAJ: Remove time from restart test CPPTRAJ: Add time to trajectory test CPPTRAJ: Modify time info test. All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_SplitCoords CPPTRAJ: SplitCoords test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_DihedralRMS CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) CPPTRAJ: Dihedral RMSD test (to previous) CPPTRAJ: Dihedral RMS fluctuation test. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Slope CPPTRAJ: Finite difference test. All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Diagmatrix CPPTRAJ: MW covariance matrix thermo analysis test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Emin CPPTRAJ: Basic energy minimization test. CPPTRAJ: Energy minimization with angle term test. CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. CPPTRAJ: Energy minimization with nonbond term test. CPPTRAJ: OpenMM basic energy minimization tests (bonds) CPPTRAJ: OpenMM basic energy minimization tests (angles) CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) All 9 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_EvalPlateau CPPTRAJ: Evalulate plateau test All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Graft CPPTRAJ: Graft test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Flatten CPPTRAJ: Flatten test. All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Random CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs CPPTRAJ: PCG32 RNG test. CPPTRAJ: Test Stdlib RNG CPPTRAJ: Test Mersenne Twister RNG All 4 comparisons passed. make[4]: Leaving directory '/<>/test' make[3]: Leaving directory '/<>/test' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/cpptraj/ -a make -j4 install DESTDIR=/<>/cpptraj-5.1.0\+dfsg/debian/cpptraj AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>' cd src && make install make[2]: Entering directory '/<>/src' Skipping bundled READLINE build Skipping bundled ARPACK build g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o -L/usr/lib/aarch64-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/aarch64-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/aarch64-linux-gnu/lib -lfftw3 -L/usr/lib/aarch64-linux-gnu/lib -lOpenMM -lnetcdf -lbz2 tng/libtng_io.a -lz xdrfile/libxdrfile.a -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro mv cpptraj "/<>/bin" make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -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 9fe9ff4e12d77de9ac73ad9cd89850d86cafb65a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libreadline8t64 from: /lib/aarch64-linux-gnu/libreadline.so.8 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libreadline8t64 to: /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing cpptraj (in debian/cpptraj); do_strip: , oemstrip: pkgstriptranslations: processing cpptraj-dbgsym (in debian/.debhelper/cpptraj/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/cpptraj/DEBIAN/control, package cpptraj, directory debian/cpptraj pkgstripfiles: processing control file: debian/.debhelper/cpptraj/dbgsym-root/DEBIAN/control, package cpptraj-dbgsym, directory debian/.debhelper/cpptraj/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package cpptraj ... dpkg-deb: building package 'cpptraj-dbgsym' in 'debian/.debhelper/scratch-space/build-cpptraj/cpptraj-dbgsym_5.1.0+dfsg-3build3_arm64.deb'. pkgstripfiles: No PNG files. dpkg-deb: building package 'cpptraj' in '../cpptraj_5.1.0+dfsg-3build3_arm64.deb'. Renaming cpptraj-dbgsym_5.1.0+dfsg-3build3_arm64.deb to cpptraj-dbgsym_5.1.0+dfsg-3build3_arm64.ddeb dpkg-genbuildinfo --build=any -O../cpptraj_5.1.0+dfsg-3build3_arm64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../cpptraj_5.1.0+dfsg-3build3_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-04-01T11:07:56Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ cpptraj_5.1.0+dfsg-3build3_arm64.changes: ----------------------------------------- Format: 1.8 Date: Mon, 01 Apr 2024 16:39:12 +1100 Source: cpptraj Binary: cpptraj Built-For-Profiles: noudeb Architecture: arm64 Version: 5.1.0+dfsg-3build3 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: William Grant Description: cpptraj - fast, parallelized molecular dynamics trajectory data analysis Changes: cpptraj (5.1.0+dfsg-3build3) noble; urgency=medium . * No-change rebuild for CVE-2024-3094 Checksums-Sha1: 1c017a423fa9c4aed32d86586278110427b44ed0 32687408 cpptraj-dbgsym_5.1.0+dfsg-3build3_arm64.ddeb 2ca7a49cff09a92f819cada11bc9821c57dcaa3a 8630 cpptraj_5.1.0+dfsg-3build3_arm64.buildinfo bf7b8fb2bc2947d52ccf425c8aa93bac167877b0 1656038 cpptraj_5.1.0+dfsg-3build3_arm64.deb Checksums-Sha256: 40fc94a310a9f334cf1601d5b25deba8a891f61966b54ffb061c471029962aa8 32687408 cpptraj-dbgsym_5.1.0+dfsg-3build3_arm64.ddeb 27edb82be212624dd2b4121942a73b289553896995aac43227d20114d5115578 8630 cpptraj_5.1.0+dfsg-3build3_arm64.buildinfo 4b82290c4553e3142625c299d8a4dc940b26cae342b6e10b91b77e2d5afb648f 1656038 cpptraj_5.1.0+dfsg-3build3_arm64.deb Files: f8eb57afdf833ae5e49e475f833671af 32687408 debug optional cpptraj-dbgsym_5.1.0+dfsg-3build3_arm64.ddeb f1185d305067251ac05108d3886a9ce0 8630 science optional cpptraj_5.1.0+dfsg-3build3_arm64.buildinfo bcaf98116eb8fbb31dda113a209b3cf0 1656038 science optional cpptraj_5.1.0+dfsg-3build3_arm64.deb Original-Maintainer: Debichem Team /<>/cpptraj_5.1.0+dfsg-3build3_arm64.changes.new could not be renamed to /<>/cpptraj_5.1.0+dfsg-3build3_arm64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: cpptraj Binary: cpptraj cpptraj-dbgsym Architecture: arm64 Version: 5.1.0+dfsg-3build3 Checksums-Md5: f8eb57afdf833ae5e49e475f833671af 32687408 cpptraj-dbgsym_5.1.0+dfsg-3build3_arm64.ddeb bcaf98116eb8fbb31dda113a209b3cf0 1656038 cpptraj_5.1.0+dfsg-3build3_arm64.deb Checksums-Sha1: 1c017a423fa9c4aed32d86586278110427b44ed0 32687408 cpptraj-dbgsym_5.1.0+dfsg-3build3_arm64.ddeb bf7b8fb2bc2947d52ccf425c8aa93bac167877b0 1656038 cpptraj_5.1.0+dfsg-3build3_arm64.deb Checksums-Sha256: 40fc94a310a9f334cf1601d5b25deba8a891f61966b54ffb061c471029962aa8 32687408 cpptraj-dbgsym_5.1.0+dfsg-3build3_arm64.ddeb 4b82290c4553e3142625c299d8a4dc940b26cae342b6e10b91b77e2d5afb648f 1656038 cpptraj_5.1.0+dfsg-3build3_arm64.deb Build-Origin: Ubuntu Build-Architecture: arm64 Build-Date: Mon, 01 Apr 2024 11:07:54 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3ubuntu1), autopoint (= 0.21-14ubuntu1), autotools-dev (= 20220109.1), base-files (= 13ubuntu9), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu4), binutils (= 2.42-4ubuntu2), binutils-aarch64-linux-gnu (= 2.42-4ubuntu2), binutils-common (= 2.42-4ubuntu2), bsdextrautils (= 2.39.3-9ubuntu4), bsdutils (= 1:2.39.3-9ubuntu4), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3ubuntu5), cpp (= 4:13.2.0-7ubuntu1), cpp-13 (= 13.2.0-23ubuntu3), cpp-13-aarch64-linux-gnu (= 13.2.0-23ubuntu3), cpp-aarch64-linux-gnu (= 4:13.2.0-7ubuntu1), dash (= 0.5.12-6ubuntu5), debconf (= 1.5.86), debhelper (= 13.14.1ubuntu5), debianutils (= 5.17build1), debugedit (= 1:5.0-5build1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), dpkg (= 1.22.6ubuntu6), dpkg-dev (= 1.22.6ubuntu6), dwz (= 0.15-1build6), file (= 1:5.45-3build1), findutils (= 4.9.0-5), g++ (= 4:13.2.0-7ubuntu1), g++-13 (= 13.2.0-23ubuntu3), g++-13-aarch64-linux-gnu (= 13.2.0-23ubuntu3), g++-aarch64-linux-gnu (= 4:13.2.0-7ubuntu1), gcc (= 4:13.2.0-7ubuntu1), gcc-13 (= 13.2.0-23ubuntu3), gcc-13-aarch64-linux-gnu (= 13.2.0-23ubuntu3), gcc-13-base (= 13.2.0-23ubuntu3), gcc-14-base (= 14-20240330-1ubuntu2), gcc-aarch64-linux-gnu (= 4:13.2.0-7ubuntu1), gettext (= 0.21-14ubuntu1), gettext-base (= 0.21-14ubuntu1), gfortran (= 4:13.2.0-7ubuntu1), gfortran-13 (= 13.2.0-23ubuntu3), gfortran-13-aarch64-linux-gnu (= 13.2.0-23ubuntu3), gfortran-aarch64-linux-gnu (= 4:13.2.0-7ubuntu1), grep (= 3.11-4), groff-base (= 1.23.0-3build2), gzip (= 1.12-1ubuntu2), hdf5-helpers (= 1.10.10+repack-3.1ubuntu4), hostname (= 3.23+nmu2ubuntu1), icu-devtools (= 74.2-1ubuntu1), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-1), libaec-dev (= 1.1.2-1), libaec0 (= 1.1.2-1), libarchive-zip-perl (= 1.68-1), libarpack2-dev (= 3.9.1-1.1build2), libarpack2t64 (= 3.9.1-1.1build2), libasan8 (= 14-20240330-1ubuntu2), libatomic1 (= 14-20240330-1ubuntu2), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1build1), libaudit1 (= 1:3.1.2-2.1build1), libbinutils (= 2.42-4ubuntu2), libblas-dev (= 3.12.0-3), libblas3 (= 3.12.0-3), libblkid1 (= 2.39.3-9ubuntu4), libbrotli1 (= 1.1.0-2build2), libbz2-1.0 (= 1.0.8-5.1), libbz2-dev (= 1.0.8-5.1), libc-bin (= 2.39-0ubuntu8), libc-dev-bin (= 2.39-0ubuntu8), libc6 (= 2.39-0ubuntu8), libc6-dev (= 2.39-0ubuntu8), libcap-ng0 (= 0.8.4-2build2), libcap2 (= 1:2.66-5ubuntu1), libcc1-0 (= 14-20240330-1ubuntu2), libcom-err2 (= 1.47.0-2.4~exp1ubuntu3), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-4ubuntu2), libctf0 (= 2.42-4ubuntu2), libcurl3t64-gnutls (= 8.5.0-2ubuntu9), libcurl4-gnutls-dev (= 8.5.0-2ubuntu9), libcurl4t64 (= 8.5.0-2ubuntu9), libdb5.3t64 (= 5.3.28+dfsg2-6build1), libdebconfclient0 (= 0.271ubuntu3), libdebhelper-perl (= 13.14.1ubuntu5), libdpkg-perl (= 1.22.6ubuntu6), libdw1t64 (= 0.190-1.1build3), libelf1t64 (= 0.190-1.1build3), libffi8 (= 3.4.6-1), libfftw3-bin (= 3.3.10-1ubuntu3), libfftw3-dev (= 3.3.10-1ubuntu3), libfftw3-double3 (= 3.3.10-1ubuntu3), libfftw3-long3 (= 3.3.10-1ubuntu3), libfftw3-single3 (= 3.3.10-1ubuntu3), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-13-dev (= 13.2.0-23ubuntu3), libgcc-s1 (= 14-20240330-1ubuntu2), libgcrypt20 (= 1.10.3-2), libgdbm-compat4t64 (= 1.23-5.1build1), libgdbm6t64 (= 1.23-5.1build1), libgfortran-13-dev (= 13.2.0-23ubuntu3), libgfortran5 (= 14-20240330-1ubuntu2), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgnutls30t64 (= 3.8.3-1.1ubuntu3), libgomp1 (= 14-20240330-1ubuntu2), libgpg-error0 (= 1.47-3build1), libgprofng0 (= 2.42-4ubuntu2), libgssapi-krb5-2 (= 1.20.1-6ubuntu2), libhdf5-103-1t64 (= 1.10.10+repack-3.1ubuntu4), libhdf5-cpp-103-1t64 (= 1.10.10+repack-3.1ubuntu4), libhdf5-dev (= 1.10.10+repack-3.1ubuntu4), libhdf5-fortran-102t64 (= 1.10.10+repack-3.1ubuntu4), libhdf5-hl-100t64 (= 1.10.10+repack-3.1ubuntu4), libhdf5-hl-cpp-100t64 (= 1.10.10+repack-3.1ubuntu4), libhdf5-hl-fortran-100t64 (= 1.10.10+repack-3.1ubuntu4), libhogweed6t64 (= 3.9.1-2.2build1), libhwasan0 (= 14-20240330-1ubuntu2), libicu-dev (= 74.2-1ubuntu1), libicu74 (= 74.2-1ubuntu1), libidn2-0 (= 2.3.7-2), libisl23 (= 0.26-3), libitm1 (= 14-20240330-1ubuntu2), libjansson4 (= 2.14-2build2), libjpeg-dev (= 8c-2ubuntu11), libjpeg-turbo8 (= 2.1.5-2ubuntu1), libjpeg-turbo8-dev (= 2.1.5-2ubuntu1), libjpeg8 (= 8c-2ubuntu11), libjpeg8-dev (= 8c-2ubuntu11), libk5crypto3 (= 1.20.1-6ubuntu2), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.20.1-6ubuntu2), libkrb5support0 (= 1.20.1-6ubuntu2), liblapack-dev (= 3.12.0-3), liblapack3 (= 3.12.0-3), libldap2 (= 2.6.7+dfsg-1~exp1ubuntu7), liblsan0 (= 14-20240330-1ubuntu2), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.6.1+really5.4.5-1build1), libmagic-mgc (= 1:5.45-3build1), libmagic1t64 (= 1:5.45-3build1), libmd0 (= 1.1.0-2), libmount1 (= 2.39.3-9ubuntu4), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libncurses-dev (= 6.4+20240113-1ubuntu1), libncurses6 (= 6.4+20240113-1ubuntu1), libncursesw6 (= 6.4+20240113-1ubuntu1), libnetcdf-dev (= 1:4.9.2-5ubuntu3), libnetcdf19t64 (= 1:4.9.2-5ubuntu3), libnettle8t64 (= 3.9.1-2.2build1), libnghttp2-14 (= 1.59.0-1build2), libopenmm-dev (= 8.0.0+dfsg-6.1ubuntu1), libopenmm8.0t64 (= 8.0.0+dfsg-6.1ubuntu1), libp11-kit0 (= 0.25.3-4ubuntu1), libpam-modules (= 1.5.3-5ubuntu4), libpam-modules-bin (= 1.5.3-5ubuntu4), libpam-runtime (= 1.5.3-5ubuntu4), libpam0g (= 1.5.3-5ubuntu4), libpcre2-8-0 (= 10.42-4ubuntu1), libperl5.38t64 (= 5.38.2-3.2build1), libpipeline1 (= 1.5.7-2), libpsl5t64 (= 0.21.2-1.1build1), libreadline-dev (= 8.2-4build1), libreadline8t64 (= 8.2-4build1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build7), libsasl2-2 (= 2.1.28+dfsg1-5ubuntu2), libsasl2-modules-db (= 2.1.28+dfsg1-5ubuntu2), libseccomp2 (= 2.5.5-1ubuntu3), libselinux1 (= 3.5-2ubuntu2), libsframe1 (= 2.42-4ubuntu2), libsmartcols1 (= 2.39.3-9ubuntu4), libssh-4 (= 0.10.6-2build2), libssl-dev (= 3.0.13-0ubuntu3), libssl3t64 (= 3.0.13-0ubuntu3), libstdc++-13-dev (= 13.2.0-23ubuntu3), libstdc++6 (= 14-20240330-1ubuntu2), libsub-override-perl (= 0.10-1), libsystemd0 (= 255.4-1ubuntu6), libsz2 (= 1.1.2-1), libtasn1-6 (= 4.19.0-3), libtinfo6 (= 6.4+20240113-1ubuntu1), libtool (= 2.4.7-7), libtsan2 (= 14-20240330-1ubuntu2), libubsan1 (= 14-20240330-1ubuntu2), libuchardet0 (= 0.0.8-1), libudev1 (= 255.4-1ubuntu6), libunistring5 (= 1.1-2), libuuid1 (= 2.39.3-9ubuntu4), libxml2 (= 2.9.14+dfsg-1.3ubuntu3), libxml2-dev (= 2.9.14+dfsg-1.3ubuntu3), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.8.0-20.20), login (= 1:4.13+dfsg1-4ubuntu1), lto-disabled-list (= 47), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-4build1), mawk (= 1.3.4.20240123-1), ncurses-base (= 6.4+20240113-1ubuntu1), ncurses-bin (= 6.4+20240113-1ubuntu1), netcdf-bin (= 1:4.9.2-5ubuntu3), patch (= 2.7.6-7build2), perl (= 5.38.2-3.2build1), perl-base (= 5.38.2-3.2build1), perl-modules-5.38 (= 5.38.2-3.2build1), po-debconf (= 1.0.21+nmu1), readline-common (= 8.2-4build1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-2), sensible-utils (= 0.0.22), sysvinit-utils (= 3.08-6ubuntu2), tar (= 1.35+dfsg-3), util-linux (= 2.39.3-9ubuntu4), xz-utils (= 5.6.1+really5.4.5-1build1), zlib1g (= 1:1.3.dfsg-3.1ubuntu2), zlib1g-dev (= 1:1.3.dfsg-3.1ubuntu2) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1711949952" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ cpptraj_5.1.0+dfsg-3build3_arm64.deb ------------------------------------ new Debian package, version 2.0. size 1656038 bytes: control archive=857 bytes. 899 bytes, 15 lines control 328 bytes, 5 lines md5sums Package: cpptraj Version: 5.1.0+dfsg-3build3 Architecture: arm64 Maintainer: Ubuntu Developers Installed-Size: 4245 Depends: libarpack2t64 (>= 2.1), libbz2-1.0, libc6 (>= 2.38), libfftw3-double3 (>= 3.3.10), libgcc-s1 (>= 3.3.1), liblapack3 | liblapack.so.3, libnetcdf19t64 (>= 3.6.1), libopenmm8.0t64 (>= 8.0.0+dfsg), libreadline8t64 (>= 6.0), libstdc++6 (>= 13.1), zlib1g (>= 1:1.2.3.4) Section: science Priority: optional Homepage: https://github.com/Amber-MD/cpptraj Description: fast, parallelized molecular dynamics trajectory data analysis CPPTRAJ is a program designed to process and analyze molecular dynamics trajectories and relevant data sets derived from their analysis. CPPTRAJ supports many popular MD software packages including Amber, CHARMM, Gromacs, and NAMD. Original-Maintainer: Debichem Team drwxr-xr-x root/root 0 2024-04-01 05:39 ./ drwxr-xr-x root/root 0 2024-04-01 05:39 ./usr/ drwxr-xr-x root/root 0 2024-04-01 05:39 ./usr/bin/ -rwxr-xr-x root/root 4329424 2024-04-01 05:39 ./usr/bin/cpptraj drwxr-xr-x root/root 0 2024-04-01 05:39 ./usr/share/ drwxr-xr-x root/root 0 2024-04-01 05:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-04-01 05:39 ./usr/share/doc/cpptraj/ -rw-r--r-- root/root 343 2022-11-24 15:08 ./usr/share/doc/cpptraj/README.Debian -rw-r--r-- root/root 542 2024-04-01 05:39 ./usr/share/doc/cpptraj/changelog.Debian.gz -rw-r--r-- root/root 4005 2022-11-24 15:08 ./usr/share/doc/cpptraj/copyright drwxr-xr-x root/root 0 2024-04-01 05:39 ./usr/share/man/ drwxr-xr-x root/root 0 2024-04-01 05:39 ./usr/share/man/man1/ -rw-r--r-- root/root 1034 2024-04-01 05:39 ./usr/share/man/man1/cpptraj.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: 1522088 Build-Time: 1173 Distribution: noble-proposed Host Architecture: arm64 Install-Time: 22 Job: cpptraj_5.1.0+dfsg-3build3.dsc Machine Architecture: arm64 Package: cpptraj Package-Time: 1201 Source-Version: 5.1.0+dfsg-3build3 Space: 1522088 Status: successful Version: 5.1.0+dfsg-3build3 -------------------------------------------------------------------------------- Finished at 2024-04-01T11:07:56Z Build needed 00:20:01, 1522088k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-28000393 Scanning for processes to kill in build PACKAGEBUILD-28000393