https://launchpad.net/ubuntu/+source/cpptraj/5.1.0+dfsg-4/+build/28443482 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-014 5.4.0-182-generic #202-Ubuntu SMP Fri Apr 26 12:29:12 UTC 2024 s390x Buildd toolchain package versions: launchpad-buildd_237~660~ubuntu20.04.1 python3-lpbuildd_237~660~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... 29 May 10:20:49 ntpdate[1892]: adjust time server 10.211.37.1 offset 0.005900 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=oracular --arch=s390x PACKAGEBUILD-28443482 --image-type chroot /home/buildd/filecache-default/c23f799bb684944311373fdcead5a58221fa6ef7 Creating target for build PACKAGEBUILD-28443482 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=oracular --arch=s390x PACKAGEBUILD-28443482 Starting target for build PACKAGEBUILD-28443482 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=oracular --arch=s390x PACKAGEBUILD-28443482 'deb http://ftpmaster.internal/ubuntu oracular main universe' 'deb http://ftpmaster.internal/ubuntu oracular-security main universe' 'deb http://ftpmaster.internal/ubuntu oracular-updates main universe' 'deb http://ftpmaster.internal/ubuntu oracular-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-28443482 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=oracular --arch=s390x PACKAGEBUILD-28443482 Updating target for build PACKAGEBUILD-28443482 Get:1 http://ftpmaster.internal/ubuntu oracular InRelease [73.9 kB] Get:2 http://ftpmaster.internal/ubuntu oracular-security InRelease [73.9 kB] Get:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease [73.9 kB] Get:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [73.9 kB] Get:5 http://ftpmaster.internal/ubuntu oracular/main s390x Packages [1331 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/universe s390x Packages [14.5 MB] Get:8 http://ftpmaster.internal/ubuntu oracular/universe Translation-en [6052 kB] Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x Packages [130 kB] Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/main Translation-en [44.5 kB] Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x Packages [522 kB] Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe Translation-en [258 kB] Fetched 23.6 MB in 5s (4385 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 systemd-dev 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-s390x-linux-gnu cpp-s390x-linux-gnu g++-13-s390x-linux-gnu g++-s390x-linux-gnu gcc-13-s390x-linux-gnu gcc-14-base gcc-s390x-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: advancecomp apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-s390x-linux-gnu bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils 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 libassuan0 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 libgmp10 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgssapi-krb5-2 libidn2-0 libip4tc2 libisl23 libitm1 libjansson4 libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblockfile-bin liblockfile1 liblz4-1 liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libncursesw6 libnsl-dev libnsl2 libnss-nis 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 libtasn1-6 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mawk mount ncurses-base ncurses-bin openssl optipng passwd patch perl perl-base pinentry-curses procps psmisc readline-common rpcsvc-proto sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 172 upgraded, 23 newly installed, 14 to remove and 0 not upgraded. Need to get 104 MB of archives. After this operation, 60.0 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu oracular/main s390x libtirpc-common all 1.3.4+ds-1.3 [8106 B] Get:2 http://ftpmaster.internal/ubuntu oracular/main s390x libtirpc-dev s390x 1.3.4+ds-1.3 [196 kB] Get:3 http://ftpmaster.internal/ubuntu oracular/main s390x libnsl-dev s390x 1.3.0-3build3 [73.1 kB] Get:4 http://ftpmaster.internal/ubuntu oracular/main s390x libnsl2 s390x 1.3.0-3build3 [44.1 kB] Get:5 http://ftpmaster.internal/ubuntu oracular/main s390x libtirpc3t64 s390x 1.3.4+ds-1.3 [84.9 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main s390x libgssapi-krb5-2 s390x 1.20.1-6ubuntu2 [149 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/main s390x libkrb5-3 s390x 1.20.1-6ubuntu2 [360 kB] Get:8 http://ftpmaster.internal/ubuntu oracular/main s390x libk5crypto3 s390x 1.20.1-6ubuntu2 [90.3 kB] Get:9 http://ftpmaster.internal/ubuntu oracular/main s390x libkrb5support0 s390x 1.20.1-6ubuntu2 [34.7 kB] Get:10 http://ftpmaster.internal/ubuntu oracular/main s390x libargon2-1 s390x 0~20190702+dfsg-4build1 [54.1 kB] Get:11 http://ftpmaster.internal/ubuntu oracular/main s390x libblkid1 s390x 2.39.3-9ubuntu6 [128 kB] Get:12 http://ftpmaster.internal/ubuntu oracular/main s390x libpcre2-8-0 s390x 10.42-4ubuntu2 [245 kB] Get:13 http://ftpmaster.internal/ubuntu oracular/main s390x libselinux1 s390x 3.5-2ubuntu2 [84.8 kB] Get:14 http://ftpmaster.internal/ubuntu oracular/main s390x libcap2 s390x 1:2.66-5ubuntu2 [31.8 kB] Get:15 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libudev1 s390x 256~rc3-1ubuntu1 [193 kB] Get:16 http://ftpmaster.internal/ubuntu oracular/main s390x libdevmapper1.02.1 s390x 2:1.02.185-3ubuntu4 [142 kB] Get:17 http://ftpmaster.internal/ubuntu oracular/main s390x libjson-c5 s390x 0.17-1build1 [37.2 kB] Get:18 http://ftpmaster.internal/ubuntu oracular/main s390x libuuid1 s390x 2.39.3-9ubuntu6 [35.9 kB] Get:19 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libcryptsetup12 s390x 2:2.7.0-1ubuntu5 [261 kB] Get:20 http://ftpmaster.internal/ubuntu oracular/main s390x libacl1 s390x 2.3.2-2 [17.9 kB] Get:21 http://ftpmaster.internal/ubuntu oracular/main s390x libapparmor1 s390x 4.0.1-0ubuntu1 [51.4 kB] Get:22 http://ftpmaster.internal/ubuntu oracular/main s390x libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:23 http://ftpmaster.internal/ubuntu oracular/main s390x libcap-ng0 s390x 0.8.5-1 [15.7 kB] Get:24 http://ftpmaster.internal/ubuntu oracular/main s390x libaudit1 s390x 1:3.1.2-2.1build1 [48.9 kB] Get:25 http://ftpmaster.internal/ubuntu oracular/main s390x libcrypt-dev s390x 1:4.4.36-4build1 [119 kB] Get:26 http://ftpmaster.internal/ubuntu oracular/main s390x libcrypt1 s390x 1:4.4.36-4build1 [88.9 kB] Get:27 http://ftpmaster.internal/ubuntu oracular/main s390x libmount1 s390x 2.39.3-9ubuntu6 [138 kB] Get:28 http://ftpmaster.internal/ubuntu oracular/main s390x perl-modules-5.38 all 5.38.2-4 [3110 kB] Get:29 http://ftpmaster.internal/ubuntu oracular/main s390x libdb5.3t64 s390x 5.3.28+dfsg2-7 [764 kB] Get:30 http://ftpmaster.internal/ubuntu oracular/main s390x libgdbm6t64 s390x 1.23-5.1build1 [36.5 kB] Get:31 http://ftpmaster.internal/ubuntu oracular/main s390x libgdbm-compat4t64 s390x 1.23-5.1build1 [6890 B] Get:32 http://ftpmaster.internal/ubuntu oracular/main s390x libperl5.38t64 s390x 5.38.2-4 [5025 kB] Get:33 http://ftpmaster.internal/ubuntu oracular/main s390x perl s390x 5.38.2-4 [231 kB] Get:34 http://ftpmaster.internal/ubuntu oracular/main s390x perl-base s390x 5.38.2-4 [1942 kB] Get:35 http://ftpmaster.internal/ubuntu oracular/main s390x liblocale-gettext-perl s390x 1.07-7 [15.7 kB] Get:36 http://ftpmaster.internal/ubuntu oracular/main s390x libtext-iconv-perl s390x 1.7-8build3 [13.8 kB] Get:37 http://ftpmaster.internal/ubuntu oracular/main s390x libtext-charwidth-perl s390x 0.04-11build3 [9518 B] Get:38 http://ftpmaster.internal/ubuntu oracular/universe s390x libnss-nisplus s390x 1.3-5build1 [23.8 kB] Get:39 http://ftpmaster.internal/ubuntu oracular/universe s390x libnss-nis s390x 3.1-0ubuntu7 [28.3 kB] Get:40 http://ftpmaster.internal/ubuntu oracular/main s390x libc-dev-bin s390x 2.39-0ubuntu8.1 [20.2 kB] Get:41 http://ftpmaster.internal/ubuntu oracular/main s390x rpcsvc-proto s390x 1.4.2-0ubuntu7 [66.4 kB] Get:42 http://ftpmaster.internal/ubuntu oracular/main s390x libc6-dev s390x 2.39-0ubuntu8.1 [1629 kB] Get:43 http://ftpmaster.internal/ubuntu oracular/main s390x libc6 s390x 2.39-0ubuntu8.1 [2847 kB] Get:44 http://ftpmaster.internal/ubuntu oracular/main s390x libc-bin s390x 2.39-0ubuntu8.1 [654 kB] Get:45 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x openssl s390x 3.0.13-0ubuntu4 [1007 kB] Get:46 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libsystemd-shared s390x 256~rc3-1ubuntu1 [2238 kB] Get:47 http://ftpmaster.internal/ubuntu oracular/main s390x liblzma5 s390x 5.6.1+really5.4.5-1 [135 kB] Get:48 http://ftpmaster.internal/ubuntu oracular/main s390x libkmod2 s390x 31+20240202-2ubuntu7 [56.4 kB] Get:49 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libssl3t64 s390x 3.0.13-0ubuntu4 [1652 kB] Get:50 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x systemd-sysv s390x 256~rc3-1ubuntu1 [11.8 kB] Get:51 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x systemd-dev all 256~rc3-1ubuntu1 [107 kB] Get:52 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x systemd s390x 256~rc3-1ubuntu1 [3710 kB] Get:53 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libsystemd0 s390x 256~rc3-1ubuntu1 [451 kB] Get:54 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libapt-pkg6.0t64 s390x 2.9.4 [1039 kB] Get:55 http://ftpmaster.internal/ubuntu oracular/main s390x libnettle8t64 s390x 3.9.1-2.2build1 [210 kB] Get:56 http://ftpmaster.internal/ubuntu oracular/main s390x libhogweed6t64 s390x 3.9.1-2.2build1 [204 kB] Get:57 http://ftpmaster.internal/ubuntu oracular/main s390x libp11-kit0 s390x 0.25.3-4ubuntu2 [320 kB] Get:58 http://ftpmaster.internal/ubuntu oracular/main s390x libunistring5 s390x 1.2-1 [552 kB] Get:59 http://ftpmaster.internal/ubuntu oracular/main s390x libgnutls30t64 s390x 3.8.5-2ubuntu1 [954 kB] Get:60 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x apt s390x 2.9.4 [1417 kB] Get:61 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x apt-utils s390x 2.9.4 [220 kB] Get:62 http://ftpmaster.internal/ubuntu oracular/main s390x libpam-modules-bin s390x 1.5.3-7ubuntu1 [56.9 kB] Get:63 http://ftpmaster.internal/ubuntu oracular/main s390x libpam-modules s390x 1.5.3-7ubuntu1 [292 kB] Get:64 http://ftpmaster.internal/ubuntu oracular/main s390x bzip2 s390x 1.0.8-5.1 [35.5 kB] Get:65 http://ftpmaster.internal/ubuntu oracular/main s390x libbz2-1.0 s390x 1.0.8-5.1 [40.0 kB] Get:66 http://ftpmaster.internal/ubuntu oracular/main s390x gcc-14-base s390x 14.1.0-1ubuntu1 [48.4 kB] Get:67 http://ftpmaster.internal/ubuntu oracular/main s390x libgcc-s1 s390x 14.1.0-1ubuntu1 [35.8 kB] Get:68 http://ftpmaster.internal/ubuntu oracular/main s390x libgpg-error-l10n all 1.49-2 [8228 B] Get:69 http://ftpmaster.internal/ubuntu oracular/main s390x libgpg-error0 s390x 1.49-2 [75.4 kB] Get:70 http://ftpmaster.internal/ubuntu oracular/main s390x libgcrypt20 s390x 1.10.3-3 [512 kB] Get:71 http://ftpmaster.internal/ubuntu oracular/main s390x liblz4-1 s390x 1.9.4-2 [77.1 kB] Get:72 http://ftpmaster.internal/ubuntu oracular/main s390x libstdc++6 s390x 14.1.0-1ubuntu1 [907 kB] Get:73 http://ftpmaster.internal/ubuntu oracular/main s390x libxxhash0 s390x 0.8.2-2build1 [24.1 kB] Get:74 http://ftpmaster.internal/ubuntu oracular/main s390x libzstd1 s390x 1.5.5+dfsg2-2build1 [341 kB] Get:75 http://ftpmaster.internal/ubuntu oracular/main s390x zlib1g s390x 1:1.3.dfsg-3.1ubuntu2 [75.9 kB] Get:76 http://ftpmaster.internal/ubuntu oracular/main s390x libgmp10 s390x 2:6.3.0+dfsg-2ubuntu6 [337 kB] Get:77 http://ftpmaster.internal/ubuntu oracular/main s390x libffi8 s390x 3.4.6-1build1 [23.1 kB] Get:78 http://ftpmaster.internal/ubuntu oracular/main s390x libidn2-0 s390x 2.3.7-2build1 [67.3 kB] Get:79 http://ftpmaster.internal/ubuntu oracular/main s390x libtasn1-6 s390x 4.19.0-3build1 [48.5 kB] Get:80 http://ftpmaster.internal/ubuntu oracular/main s390x libdebconfclient0 s390x 0.271ubuntu3 [11.4 kB] Get:81 http://ftpmaster.internal/ubuntu oracular/main s390x base-passwd s390x 3.6.3build1 [51.5 kB] Get:82 http://ftpmaster.internal/ubuntu oracular/main s390x libassuan0 s390x 2.5.6-1build1 [38.3 kB] Get:83 http://ftpmaster.internal/ubuntu oracular/main s390x libsqlite3-0 s390x 3.45.3-1 [735 kB] Get:84 http://ftpmaster.internal/ubuntu oracular/main s390x gpg s390x 2.4.4-2ubuntu17 [589 kB] Get:85 http://ftpmaster.internal/ubuntu oracular/main s390x libreadline8t64 s390x 8.2-4build1 [171 kB] Get:86 http://ftpmaster.internal/ubuntu oracular/main s390x readline-common all 8.2-4build1 [56.5 kB] Get:87 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libncursesw6 s390x 6.5-2 [157 kB] Get:88 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libtinfo6 s390x 6.5-2 [116 kB] Get:89 http://ftpmaster.internal/ubuntu oracular/main s390x gpg-agent s390x 2.4.4-2ubuntu17 [240 kB] Get:90 http://ftpmaster.internal/ubuntu oracular/main s390x gpgconf s390x 2.4.4-2ubuntu17 [111 kB] Get:91 http://ftpmaster.internal/ubuntu oracular/main s390x pinentry-curses s390x 1.2.1-3ubuntu5 [37.6 kB] Get:92 http://ftpmaster.internal/ubuntu oracular/main s390x init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:93 http://ftpmaster.internal/ubuntu oracular/main s390x libnpth0t64 s390x 1.6-3.1build1 [8204 B] Get:94 http://ftpmaster.internal/ubuntu oracular/main s390x gpgv s390x 2.4.4-2ubuntu17 [165 kB] Get:95 http://ftpmaster.internal/ubuntu oracular/main s390x ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:96 http://ftpmaster.internal/ubuntu oracular/main s390x libseccomp2 s390x 2.5.5-1ubuntu3 [53.4 kB] Get:97 http://ftpmaster.internal/ubuntu oracular/main s390x debconf-i18n all 1.5.86ubuntu1 [205 kB] Get:98 http://ftpmaster.internal/ubuntu oracular/main s390x debconf all 1.5.86ubuntu1 [124 kB] Get:99 http://ftpmaster.internal/ubuntu oracular/main s390x libpam0g s390x 1.5.3-7ubuntu1 [69.8 kB] Get:100 http://ftpmaster.internal/ubuntu oracular/main s390x libfdisk1 s390x 2.39.3-9ubuntu6 [151 kB] Get:101 http://ftpmaster.internal/ubuntu oracular/main s390x mount s390x 2.39.3-9ubuntu6 [119 kB] Get:102 http://ftpmaster.internal/ubuntu oracular/main s390x libcom-err2 s390x 1.47.0-2.4~exp1ubuntu4 [22.9 kB] Get:103 http://ftpmaster.internal/ubuntu oracular/main s390x libkeyutils1 s390x 1.6.3-3build1 [9556 B] Get:104 http://ftpmaster.internal/ubuntu oracular/main s390x linux-libc-dev s390x 6.8.0-31.31 [1593 kB] Get:105 http://ftpmaster.internal/ubuntu oracular/main s390x base-files s390x 13.1ubuntu1 [73.8 kB] Get:106 http://ftpmaster.internal/ubuntu oracular/main s390x debianutils s390x 5.17build1 [90.2 kB] Get:107 http://ftpmaster.internal/ubuntu oracular/main s390x bash s390x 5.2.21-2ubuntu5 [835 kB] Get:108 http://ftpmaster.internal/ubuntu oracular/main s390x bsdutils s390x 1:2.39.3-9ubuntu6 [96.5 kB] Get:109 http://ftpmaster.internal/ubuntu oracular/main s390x coreutils s390x 9.4-3ubuntu6 [1483 kB] Get:110 http://ftpmaster.internal/ubuntu oracular/main s390x tar s390x 1.35+dfsg-3build1 [269 kB] Get:111 http://ftpmaster.internal/ubuntu oracular/main s390x dpkg s390x 1.22.6ubuntu10 [1274 kB] Get:112 http://ftpmaster.internal/ubuntu oracular/main s390x dash s390x 0.5.12-6ubuntu5 [95.0 kB] Get:113 http://ftpmaster.internal/ubuntu oracular/main s390x diffutils s390x 1:3.10-1build1 [188 kB] Get:114 http://ftpmaster.internal/ubuntu oracular/main s390x findutils s390x 4.9.0-5build1 [305 kB] Get:115 http://ftpmaster.internal/ubuntu oracular/main s390x grep s390x 3.11-4build1 [173 kB] Get:116 http://ftpmaster.internal/ubuntu oracular/main s390x gzip s390x 1.12-1ubuntu3 [107 kB] Get:117 http://ftpmaster.internal/ubuntu oracular/main s390x hostname s390x 3.23+nmu2ubuntu2 [11.2 kB] Get:118 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x login s390x 1:4.13+dfsg1-4ubuntu5 [202 kB] Get:119 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x ncurses-bin s390x 6.5-2 [198 kB] Get:120 http://ftpmaster.internal/ubuntu oracular/main s390x sed s390x 4.9-2build1 [198 kB] Get:121 http://ftpmaster.internal/ubuntu oracular/main s390x util-linux s390x 2.39.3-9ubuntu6 [1142 kB] Get:122 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x ncurses-base all 6.5-2 [25.8 kB] Get:123 http://ftpmaster.internal/ubuntu oracular/main s390x sysvinit-utils s390x 3.08-6ubuntu3 [34.8 kB] Get:124 http://ftpmaster.internal/ubuntu oracular/main s390x logsave s390x 1.47.0-2.4~exp1ubuntu4 [22.6 kB] Get:125 http://ftpmaster.internal/ubuntu oracular/main s390x libext2fs2t64 s390x 1.47.0-2.4~exp1ubuntu4 [234 kB] Get:126 http://ftpmaster.internal/ubuntu oracular/main s390x e2fsprogs s390x 1.47.0-2.4~exp1ubuntu4 [614 kB] Get:127 http://ftpmaster.internal/ubuntu oracular/main s390x optipng s390x 0.7.8+ds-1build2 [114 kB] Get:128 http://ftpmaster.internal/ubuntu oracular/main s390x libpng16-16t64 s390x 1.6.43-5build1 [200 kB] Get:129 http://ftpmaster.internal/ubuntu oracular/main s390x init s390x 1.66ubuntu1 [6188 B] Get:130 http://ftpmaster.internal/ubuntu oracular/main s390x libsmartcols1 s390x 2.39.3-9ubuntu6 [68.2 kB] Get:131 http://ftpmaster.internal/ubuntu oracular/main s390x uuid-runtime s390x 2.39.3-9ubuntu6 [33.4 kB] Get:132 http://ftpmaster.internal/ubuntu oracular/main s390x libattr1 s390x 1:2.5.2-1build1 [11.7 kB] Get:133 http://ftpmaster.internal/ubuntu oracular/main s390x libmd0 s390x 1.1.0-2build1 [24.6 kB] Get:134 http://ftpmaster.internal/ubuntu oracular/main s390x libpam-runtime all 1.5.3-7ubuntu1 [40.8 kB] Get:135 http://ftpmaster.internal/ubuntu oracular/main s390x libsemanage-common all 3.5-1build5 [10.1 kB] Get:136 http://ftpmaster.internal/ubuntu oracular/main s390x libsepol2 s390x 3.5-2build1 [315 kB] Get:137 http://ftpmaster.internal/ubuntu oracular/main s390x libsemanage2 s390x 3.5-1build5 [96.8 kB] Get:138 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x passwd s390x 1:4.13+dfsg1-4ubuntu5 [856 kB] Get:139 http://ftpmaster.internal/ubuntu oracular/main s390x libproc2-0 s390x 2:4.0.4-4ubuntu3 [59.8 kB] Get:140 http://ftpmaster.internal/ubuntu oracular/main s390x libss2 s390x 1.47.0-2.4~exp1ubuntu4 [17.2 kB] Get:141 http://ftpmaster.internal/ubuntu oracular/main s390x mawk s390x 1.3.4.20240123-1build1 [133 kB] Get:142 http://ftpmaster.internal/ubuntu oracular/main s390x procps s390x 2:4.0.4-4ubuntu3 [724 kB] Get:143 http://ftpmaster.internal/ubuntu oracular/main s390x sensible-utils all 0.0.22 [22.5 kB] Get:144 http://ftpmaster.internal/ubuntu oracular/main s390x ca-certificates all 20240203 [159 kB] Get:145 http://ftpmaster.internal/ubuntu oracular/main s390x krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:146 http://ftpmaster.internal/ubuntu oracular/main s390x tzdata all 2024a-4ubuntu1 [274 kB] Get:147 http://ftpmaster.internal/ubuntu oracular/main s390x bash-completion all 1:2.14.0-1 [206 kB] Get:148 http://ftpmaster.internal/ubuntu oracular/main s390x bsdextrautils s390x 2.39.3-9ubuntu6 [76.3 kB] Get:149 http://ftpmaster.internal/ubuntu oracular/main s390x libgpm2 s390x 1.20.7-11 [14.7 kB] Get:150 http://ftpmaster.internal/ubuntu oracular/main s390x libip4tc2 s390x 1.8.10-3ubuntu2 [24.2 kB] Get:151 http://ftpmaster.internal/ubuntu oracular/main s390x libjansson4 s390x 2.14-2build2 [33.2 kB] Get:152 http://ftpmaster.internal/ubuntu oracular/main s390x psmisc s390x 23.7-1build1 [178 kB] Get:153 http://ftpmaster.internal/ubuntu oracular/main s390x xz-utils s390x 5.6.1+really5.4.5-1 [269 kB] Get:154 http://ftpmaster.internal/ubuntu oracular/main s390x advancecomp s390x 2.5-1build1 [205 kB] Get:155 http://ftpmaster.internal/ubuntu oracular/main s390x libctf0 s390x 2.42-4ubuntu2 [98.4 kB] Get:156 http://ftpmaster.internal/ubuntu oracular/main s390x libctf-nobfd0 s390x 2.42-4ubuntu2 [100 kB] Get:157 http://ftpmaster.internal/ubuntu oracular/main s390x binutils-s390x-linux-gnu s390x 2.42-4ubuntu2 [2270 kB] Get:158 http://ftpmaster.internal/ubuntu oracular/main s390x libbinutils s390x 2.42-4ubuntu2 [479 kB] Get:159 http://ftpmaster.internal/ubuntu oracular/main s390x binutils s390x 2.42-4ubuntu2 [3042 B] Get:160 http://ftpmaster.internal/ubuntu oracular/main s390x binutils-common s390x 2.42-4ubuntu2 [217 kB] Get:161 http://ftpmaster.internal/ubuntu oracular/main s390x libsframe1 s390x 2.42-4ubuntu2 [14.2 kB] Get:162 http://ftpmaster.internal/ubuntu oracular/main s390x libubsan1 s390x 14.1.0-1ubuntu1 [1189 kB] Get:163 http://ftpmaster.internal/ubuntu oracular/main s390x libgomp1 s390x 14.1.0-1ubuntu1 [151 kB] Get:164 http://ftpmaster.internal/ubuntu oracular/main s390x libitm1 s390x 14.1.0-1ubuntu1 [31.1 kB] Get:165 http://ftpmaster.internal/ubuntu oracular/main s390x libatomic1 s390x 14.1.0-1ubuntu1 [9378 B] Get:166 http://ftpmaster.internal/ubuntu oracular/main s390x libasan8 s390x 14.1.0-1ubuntu1 [3003 kB] Get:167 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x g++-13 s390x 13.2.0-25ubuntu1 [15.6 kB] Get:168 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x gcc-13 s390x 13.2.0-25ubuntu1 [478 kB] Get:169 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libstdc++-13-dev s390x 13.2.0-25ubuntu1 [2534 kB] Get:170 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libgcc-13-dev s390x 13.2.0-25ubuntu1 [1004 kB] Get:171 http://ftpmaster.internal/ubuntu oracular/main s390x libcc1-0 s390x 14.1.0-1ubuntu1 [50.7 kB] Get:172 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x cpp-13 s390x 13.2.0-25ubuntu1 [1028 B] Get:173 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x gcc-13-base s390x 13.2.0-25ubuntu1 [49.9 kB] Get:174 http://ftpmaster.internal/ubuntu oracular/main s390x libisl23 s390x 0.26-3build1 [713 kB] Get:175 http://ftpmaster.internal/ubuntu oracular/main s390x libmpfr6 s390x 4.2.1-1build1 [322 kB] Get:176 http://ftpmaster.internal/ubuntu oracular/main s390x libmpc3 s390x 1.3.1-1build1 [58.4 kB] Get:177 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x gcc-13-s390x-linux-gnu s390x 13.2.0-25ubuntu1 [17.2 MB] Get:178 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x g++-13-s390x-linux-gnu s390x 13.2.0-25ubuntu1 [10.2 MB] Get:179 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x cpp-13-s390x-linux-gnu s390x 13.2.0-25ubuntu1 [8805 kB] Get:180 http://ftpmaster.internal/ubuntu oracular/main s390x g++ s390x 4:13.2.0-7ubuntu1 [1096 B] Get:181 http://ftpmaster.internal/ubuntu oracular/main s390x gcc s390x 4:13.2.0-7ubuntu1 [5014 B] Get:182 http://ftpmaster.internal/ubuntu oracular/main s390x cpp s390x 4:13.2.0-7ubuntu1 [22.4 kB] Get:183 http://ftpmaster.internal/ubuntu oracular/main s390x cpp-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [5308 B] Get:184 http://ftpmaster.internal/ubuntu oracular/main s390x gcc-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [1208 B] Get:185 http://ftpmaster.internal/ubuntu oracular/main s390x g++-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [956 B] Get:186 http://ftpmaster.internal/ubuntu oracular/main s390x dpkg-dev all 1.22.6ubuntu10 [1074 kB] Get:187 http://ftpmaster.internal/ubuntu oracular/main s390x libdpkg-perl all 1.22.6ubuntu10 [269 kB] Get:188 http://ftpmaster.internal/ubuntu oracular/main s390x patch s390x 2.7.6-7build3 [113 kB] Get:189 http://ftpmaster.internal/ubuntu oracular/main s390x make s390x 4.3-4.1build2 [196 kB] Get:190 http://ftpmaster.internal/ubuntu oracular/main s390x lto-disabled-list all 48 [12.3 kB] Get:191 http://ftpmaster.internal/ubuntu oracular/main s390x libfakeroot s390x 1.34-1 [31.9 kB] Get:192 http://ftpmaster.internal/ubuntu oracular/main s390x fakeroot s390x 1.34-1 [67.4 kB] Get:193 http://ftpmaster.internal/ubuntu oracular/main s390x liblockfile-bin s390x 1.17-1build3 [11.6 kB] Get:194 http://ftpmaster.internal/ubuntu oracular/main s390x liblockfile1 s390x 1.17-1build3 [7028 B] Get:195 http://ftpmaster.internal/ubuntu oracular/main s390x lockfile-progs s390x 0.1.19+nmu1 [8720 B] Preconfiguring packages ... Fetched 104 MB in 8s (13.0 MB/s) (Reading database ... 13395 files and directories currently installed.) Preparing to unpack .../libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) over (1.3.3+ds-1) ... Preparing to unpack .../libtirpc-dev_1.3.4+ds-1.3_s390x.deb ... Unpacking libtirpc-dev:s390x (1.3.4+ds-1.3) over (1.3.3+ds-1) ... Preparing to unpack .../libnsl-dev_1.3.0-3build3_s390x.deb ... Unpacking libnsl-dev:s390x (1.3.0-3build3) over (1.3.0-2build2) ... Preparing to unpack .../libnsl2_1.3.0-3build3_s390x.deb ... Unpacking libnsl2:s390x (1.3.0-3build3) over (1.3.0-2build2) ... dpkg: libtirpc3:s390x: dependency problems, but removing anyway as you requested: libnss-nisplus:s390x depends on libtirpc3 (>= 1.0.2). (Reading database ... 13395 files and directories currently installed.) Removing libtirpc3:s390x (1.3.3+ds-1) ... Selecting previously unselected package libtirpc3t64:s390x. (Reading database ... 13389 files and directories currently installed.) Preparing to unpack .../0-libtirpc3t64_1.3.4+ds-1.3_s390x.deb ... Adding 'diversion of /lib/s390x-linux-gnu/libtirpc.so.3 to /lib/s390x-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/s390x-linux-gnu/libtirpc.so.3.0.0 to /lib/s390x-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:s390x (1.3.4+ds-1.3) ... Preparing to unpack .../1-libgssapi-krb5-2_1.20.1-6ubuntu2_s390x.deb ... Unpacking libgssapi-krb5-2:s390x (1.20.1-6ubuntu2) over (1.20.1-3ubuntu1) ... Preparing to unpack .../2-libkrb5-3_1.20.1-6ubuntu2_s390x.deb ... Unpacking libkrb5-3:s390x (1.20.1-6ubuntu2) over (1.20.1-3ubuntu1) ... Preparing to unpack .../3-libk5crypto3_1.20.1-6ubuntu2_s390x.deb ... Unpacking libk5crypto3:s390x (1.20.1-6ubuntu2) over (1.20.1-3ubuntu1) ... Preparing to unpack .../4-libkrb5support0_1.20.1-6ubuntu2_s390x.deb ... Unpacking libkrb5support0:s390x (1.20.1-6ubuntu2) over (1.20.1-3ubuntu1) ... Preparing to unpack .../5-libargon2-1_0~20190702+dfsg-4build1_s390x.deb ... Unpacking libargon2-1:s390x (0~20190702+dfsg-4build1) over (0~20190702+dfsg-3) ... Preparing to unpack .../6-libblkid1_2.39.3-9ubuntu6_s390x.deb ... Unpacking libblkid1:s390x (2.39.3-9ubuntu6) over (2.39.1-4ubuntu2) ... Setting up libblkid1:s390x (2.39.3-9ubuntu6) ... (Reading database ... 13400 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.42-4ubuntu2_s390x.deb ... Unpacking libpcre2-8-0:s390x (10.42-4ubuntu2) over (10.42-4) ... Setting up libpcre2-8-0:s390x (10.42-4ubuntu2) ... (Reading database ... 13400 files and directories currently installed.) Preparing to unpack .../libselinux1_3.5-2ubuntu2_s390x.deb ... Unpacking libselinux1:s390x (3.5-2ubuntu2) over (3.5-1) ... Setting up libselinux1:s390x (3.5-2ubuntu2) ... (Reading database ... 13401 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.66-5ubuntu2_s390x.deb ... Unpacking libcap2:s390x (1:2.66-5ubuntu2) over (1:2.66-4ubuntu1) ... Setting up libcap2:s390x (1:2.66-5ubuntu2) ... (Reading database ... 13401 files and directories currently installed.) Preparing to unpack .../libudev1_256~rc3-1ubuntu1_s390x.deb ... Unpacking libudev1:s390x (256~rc3-1ubuntu1) over (253.5-1ubuntu6) ... Setting up libudev1:s390x (256~rc3-1ubuntu1) ... (Reading database ... 13401 files and directories currently installed.) Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.185-3ubuntu4_s390x.deb ... Unpacking libdevmapper1.02.1:s390x (2:1.02.185-3ubuntu4) over (2:1.02.185-2ubuntu1) ... Preparing to unpack .../libjson-c5_0.17-1build1_s390x.deb ... Unpacking libjson-c5:s390x (0.17-1build1) over (0.17-1) ... Preparing to unpack .../libuuid1_2.39.3-9ubuntu6_s390x.deb ... Unpacking libuuid1:s390x (2.39.3-9ubuntu6) over (2.39.1-4ubuntu2) ... Setting up libuuid1:s390x (2.39.3-9ubuntu6) ... (Reading database ... 13401 files and directories currently installed.) Preparing to unpack .../libcryptsetup12_2%3a2.7.0-1ubuntu5_s390x.deb ... Unpacking libcryptsetup12:s390x (2:2.7.0-1ubuntu5) over (2:2.6.1-4ubuntu3) ... Preparing to unpack .../libacl1_2.3.2-2_s390x.deb ... Unpacking libacl1:s390x (2.3.2-2) over (2.3.1-3) ... Setting up libacl1:s390x (2.3.2-2) ... (Reading database ... 13401 files and directories currently installed.) Preparing to unpack .../libapparmor1_4.0.1-0ubuntu1_s390x.deb ... Unpacking libapparmor1:s390x (4.0.1-0ubuntu1) over (4.0.0~alpha2-0ubuntu5) ... Preparing to unpack .../libaudit-common_1%3a3.1.2-2.1build1_all.deb ... Unpacking libaudit-common (1:3.1.2-2.1build1) over (1:3.1.1-1) ... Setting up libaudit-common (1:3.1.2-2.1build1) ... (Reading database ... 13401 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.5-1_s390x.deb ... Unpacking libcap-ng0:s390x (0.8.5-1) over (0.8.3-1build2) ... Setting up libcap-ng0:s390x (0.8.5-1) ... (Reading database ... 13401 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.1.2-2.1build1_s390x.deb ... Unpacking libaudit1:s390x (1:3.1.2-2.1build1) over (1:3.1.1-1) ... Setting up libaudit1:s390x (1:3.1.2-2.1build1) ... (Reading database ... 13401 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.36-4build1_s390x.deb ... Unpacking libcrypt-dev:s390x (1:4.4.36-4build1) over (1:4.4.36-2) ... Preparing to unpack .../libcrypt1_1%3a4.4.36-4build1_s390x.deb ... Unpacking libcrypt1:s390x (1:4.4.36-4build1) over (1:4.4.36-2) ... Setting up libcrypt1:s390x (1:4.4.36-4build1) ... (Reading database ... 13401 files and directories currently installed.) Preparing to unpack .../libmount1_2.39.3-9ubuntu6_s390x.deb ... Unpacking libmount1:s390x (2.39.3-9ubuntu6) over (2.39.1-4ubuntu2) ... Setting up libmount1:s390x (2.39.3-9ubuntu6) ... (Reading database ... 13401 files and directories currently installed.) Preparing to unpack .../perl_5.38.2-4_s390x.deb ... Unpacking perl (5.38.2-4) over (5.36.0-9ubuntu1) ... Selecting previously unselected package perl-modules-5.38. Preparing to unpack .../perl-modules-5.38_5.38.2-4_all.deb ... Unpacking perl-modules-5.38 (5.38.2-4) ... dpkg: libdb5.3:s390x: dependency problems, but removing anyway as you requested: libperl5.36:s390x depends on libdb5.3. libpam-modules:s390x depends on libdb5.3. apt-utils depends on libdb5.3. (Reading database ... 14813 files and directories currently installed.) Removing libdb5.3:s390x (5.3.28+dfsg2-2) ... Selecting previously unselected package libdb5.3t64:s390x. (Reading database ... 14807 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_s390x.deb ... Unpacking libdb5.3t64:s390x (5.3.28+dfsg2-7) ... Setting up libdb5.3t64:s390x (5.3.28+dfsg2-7) ... dpkg: libgdbm6:s390x: dependency problems, but removing anyway as you requested: libperl5.36:s390x depends on libgdbm6 (>= 1.21). libgdbm-compat4:s390x depends on libgdbm6 (>= 1.16). (Reading database ... 14813 files and directories currently installed.) Removing libgdbm6:s390x (1.23-3) ... Selecting previously unselected package libgdbm6t64:s390x. (Reading database ... 14808 files and directories currently installed.) Preparing to unpack .../libgdbm6t64_1.23-5.1build1_s390x.deb ... Unpacking libgdbm6t64:s390x (1.23-5.1build1) ... dpkg: libgdbm-compat4:s390x: dependency problems, but removing anyway as you requested: libperl5.36:s390x depends on libgdbm-compat4 (>= 1.18-3). (Reading database ... 14814 files and directories currently installed.) Removing libgdbm-compat4:s390x (1.23-3) ... Selecting previously unselected package libgdbm-compat4t64:s390x. (Reading database ... 14809 files and directories currently installed.) Preparing to unpack .../libgdbm-compat4t64_1.23-5.1build1_s390x.deb ... Unpacking libgdbm-compat4t64:s390x (1.23-5.1build1) ... Selecting previously unselected package libperl5.38t64:s390x. Preparing to unpack .../libperl5.38t64_5.38.2-4_s390x.deb ... Unpacking libperl5.38t64:s390x (5.38.2-4) ... Preparing to unpack .../perl-base_5.38.2-4_s390x.deb ... Unpacking perl-base (5.38.2-4) over (5.36.0-9ubuntu1) ... Setting up perl-base (5.38.2-4) ... (Reading database ... 15340 files and directories currently installed.) Preparing to unpack .../0-liblocale-gettext-perl_1.07-7_s390x.deb ... Unpacking liblocale-gettext-perl (1.07-7) over (1.07-6) ... Preparing to unpack .../1-libtext-iconv-perl_1.7-8build3_s390x.deb ... Unpacking libtext-iconv-perl:s390x (1.7-8build3) over (1.7-8) ... Preparing to unpack .../2-libtext-charwidth-perl_0.04-11build3_s390x.deb ... Unpacking libtext-charwidth-perl:s390x (0.04-11build3) over (0.04-11) ... Preparing to unpack .../3-libnss-nisplus_1.3-5build1_s390x.deb ... Unpacking libnss-nisplus:s390x (1.3-5build1) over (1.3-0ubuntu6) ... Preparing to unpack .../4-libnss-nis_3.1-0ubuntu7_s390x.deb ... Unpacking libnss-nis:s390x (3.1-0ubuntu7) over (3.1-0ubuntu6) ... Preparing to unpack .../5-libc-dev-bin_2.39-0ubuntu8.1_s390x.deb ... Unpacking libc-dev-bin (2.39-0ubuntu8.1) over (2.38-1ubuntu6) ... Preparing to unpack .../6-rpcsvc-proto_1.4.2-0ubuntu7_s390x.deb ... Unpacking rpcsvc-proto (1.4.2-0ubuntu7) over (1.4.2-0ubuntu6) ... Preparing to unpack .../7-libc6-dev_2.39-0ubuntu8.1_s390x.deb ... Unpacking libc6-dev:s390x (2.39-0ubuntu8.1) over (2.38-1ubuntu6) ... Preparing to unpack .../8-libc6_2.39-0ubuntu8.1_s390x.deb ... Unpacking libc6:s390x (2.39-0ubuntu8.1) over (2.38-1ubuntu6) ... Setting up libc6:s390x (2.39-0ubuntu8.1) ... (Reading database ... 15345 files and directories currently installed.) Preparing to unpack .../libc-bin_2.39-0ubuntu8.1_s390x.deb ... Unpacking libc-bin (2.39-0ubuntu8.1) over (2.38-1ubuntu6) ... Setting up libc-bin (2.39-0ubuntu8.1) ... (Reading database ... 15345 files and directories currently installed.) Preparing to unpack .../openssl_3.0.13-0ubuntu4_s390x.deb ... Unpacking openssl (3.0.13-0ubuntu4) over (3.0.10-1ubuntu2) ... Preparing to unpack .../libsystemd-shared_256~rc3-1ubuntu1_s390x.deb ... Unpacking libsystemd-shared:s390x (256~rc3-1ubuntu1) over (253.5-1ubuntu6) ... Preparing to unpack .../liblzma5_5.6.1+really5.4.5-1_s390x.deb ... Unpacking liblzma5:s390x (5.6.1+really5.4.5-1) over (5.4.1-0.2) ... Setting up liblzma5:s390x (5.6.1+really5.4.5-1) ... (Reading database ... 15344 files and directories currently installed.) Preparing to unpack .../libkmod2_31+20240202-2ubuntu7_s390x.deb ... Unpacking libkmod2:s390x (31+20240202-2ubuntu7) over (30+20230519-1ubuntu3) ... dpkg: libssl3:s390x: dependency problems, but removing anyway as you requested: systemd depends on libssl3 (>= 3.0.0). (Reading database ... 15344 files and directories currently installed.) Removing libssl3:s390x (3.0.10-1ubuntu2) ... Selecting previously unselected package libssl3t64:s390x. (Reading database ... 15333 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.0.13-0ubuntu4_s390x.deb ... Unpacking libssl3t64:s390x (3.0.13-0ubuntu4) ... Setting up libssl3t64:s390x (3.0.13-0ubuntu4) ... (Reading database ... 15346 files and directories currently installed.) Preparing to unpack .../systemd-sysv_256~rc3-1ubuntu1_s390x.deb ... Unpacking systemd-sysv (256~rc3-1ubuntu1) over (253.5-1ubuntu6) ... Preparing to unpack .../systemd-dev_256~rc3-1ubuntu1_all.deb ... Unpacking systemd-dev (256~rc3-1ubuntu1) over (253.5-1ubuntu6) ... Preparing to unpack .../systemd_256~rc3-1ubuntu1_s390x.deb ... Unpacking systemd (256~rc3-1ubuntu1) 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-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_256~rc3-1ubuntu1_s390x.deb ... Unpacking libsystemd0:s390x (256~rc3-1ubuntu1) over (253.5-1ubuntu6) ... Setting up libsystemd0:s390x (256~rc3-1ubuntu1) ... dpkg: libgnutls30:s390x: dependency problems, but removing anyway as you requested: apt depends on libgnutls30 (>= 3.7.5). (Reading database ... 15540 files and directories currently installed.) Removing libgnutls30:s390x (3.8.1-4ubuntu1) ... Removing libhogweed6:s390x (3.9.1-2) ... Removing libnettle8:s390x (3.9.1-2) ... dpkg: libapt-pkg6.0:s390x: dependency problems, but removing anyway as you requested: apt-utils depends on libapt-pkg6.0 (>= 2.7.3). apt depends on libapt-pkg6.0 (>= 2.7.3). Removing libapt-pkg6.0:s390x (2.7.3) ... Selecting previously unselected package libapt-pkg6.0t64:s390x. (Reading database ... 15469 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.9.4_s390x.deb ... Unpacking libapt-pkg6.0t64:s390x (2.9.4) ... Setting up libapt-pkg6.0t64:s390x (2.9.4) ... Selecting previously unselected package libnettle8t64:s390x. (Reading database ... 15519 files and directories currently installed.) Preparing to unpack .../libnettle8t64_3.9.1-2.2build1_s390x.deb ... Unpacking libnettle8t64:s390x (3.9.1-2.2build1) ... Setting up libnettle8t64:s390x (3.9.1-2.2build1) ... Selecting previously unselected package libhogweed6t64:s390x. (Reading database ... 15527 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.9.1-2.2build1_s390x.deb ... Unpacking libhogweed6t64:s390x (3.9.1-2.2build1) ... Setting up libhogweed6t64:s390x (3.9.1-2.2build1) ... (Reading database ... 15533 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.25.3-4ubuntu2_s390x.deb ... Unpacking libp11-kit0:s390x (0.25.3-4ubuntu2) over (0.25.0-4ubuntu1) ... Setting up libp11-kit0:s390x (0.25.3-4ubuntu2) ... Selecting previously unselected package libunistring5:s390x. (Reading database ... 15533 files and directories currently installed.) Preparing to unpack .../libunistring5_1.2-1_s390x.deb ... Unpacking libunistring5:s390x (1.2-1) ... Setting up libunistring5:s390x (1.2-1) ... Selecting previously unselected package libgnutls30t64:s390x. (Reading database ... 15538 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.5-2ubuntu1_s390x.deb ... Unpacking libgnutls30t64:s390x (3.8.5-2ubuntu1) ... Setting up libgnutls30t64:s390x (3.8.5-2ubuntu1) ... (Reading database ... 15550 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.4_s390x.deb ... Unpacking apt (2.9.4) over (2.7.3) ... Setting up apt (2.9.4) ... (Reading database ... 15550 files and directories currently installed.) Preparing to unpack .../apt-utils_2.9.4_s390x.deb ... Unpacking apt-utils (2.9.4) over (2.7.3) ... Preparing to unpack .../libpam-modules-bin_1.5.3-7ubuntu1_s390x.deb ... Unpacking libpam-modules-bin (1.5.3-7ubuntu1) over (1.5.2-6ubuntu1) ... Setting up libpam-modules-bin (1.5.3-7ubuntu1) ... (Reading database ... 15550 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.3-7ubuntu1_s390x.deb ... Unpacking libpam-modules:s390x (1.5.3-7ubuntu1) over (1.5.2-6ubuntu1) ... dpkg: warning: unable to delete old directory '/lib/s390x-linux-gnu/security': Directory not empty Setting up libpam-modules:s390x (1.5.3-7ubuntu1) ... Installing new version of config file /etc/security/namespace.init ... (Reading database ... 15550 files and directories currently installed.) Preparing to unpack .../bzip2_1.0.8-5.1_s390x.deb ... Unpacking bzip2 (1.0.8-5.1) over (1.0.8-5build1) ... dpkg: warning: old file '/bin/bzip2' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') Preparing to unpack .../libbz2-1.0_1.0.8-5.1_s390x.deb ... Unpacking libbz2-1.0:s390x (1.0.8-5.1) over (1.0.8-5build1) ... Setting up libbz2-1.0:s390x (1.0.8-5.1) ... Selecting previously unselected package gcc-14-base:s390x. (Reading database ... 15550 files and directories currently installed.) Preparing to unpack .../gcc-14-base_14.1.0-1ubuntu1_s390x.deb ... Unpacking gcc-14-base:s390x (14.1.0-1ubuntu1) ... Setting up gcc-14-base:s390x (14.1.0-1ubuntu1) ... (Reading database ... 15555 files and directories currently installed.) Preparing to unpack .../libgcc-s1_14.1.0-1ubuntu1_s390x.deb ... Unpacking libgcc-s1:s390x (14.1.0-1ubuntu1) over (13.2.0-4ubuntu3) ... Setting up libgcc-s1:s390x (14.1.0-1ubuntu1) ... (Reading database ... 15555 files and directories currently installed.) Preparing to unpack .../libgpg-error-l10n_1.49-2_all.deb ... Unpacking libgpg-error-l10n (1.49-2) over (1.47-2) ... Preparing to unpack .../libgpg-error0_1.49-2_s390x.deb ... Unpacking libgpg-error0:s390x (1.49-2) over (1.47-2) ... Setting up libgpg-error0:s390x (1.49-2) ... (Reading database ... 15555 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.10.3-3_s390x.deb ... Unpacking libgcrypt20:s390x (1.10.3-3) over (1.10.2-3ubuntu1) ... Setting up libgcrypt20:s390x (1.10.3-3) ... (Reading database ... 15555 files and directories currently installed.) Preparing to unpack .../liblz4-1_1.9.4-2_s390x.deb ... Unpacking liblz4-1:s390x (1.9.4-2) over (1.9.4-1) ... Setting up liblz4-1:s390x (1.9.4-2) ... (Reading database ... 15555 files and directories currently installed.) Preparing to unpack .../libstdc++6_14.1.0-1ubuntu1_s390x.deb ... Unpacking libstdc++6:s390x (14.1.0-1ubuntu1) over (13.2.0-4ubuntu3) ... Setting up libstdc++6:s390x (14.1.0-1ubuntu1) ... (Reading database ... 15555 files and directories currently installed.) Preparing to unpack .../libxxhash0_0.8.2-2build1_s390x.deb ... Unpacking libxxhash0:s390x (0.8.2-2build1) over (0.8.1-1) ... Setting up libxxhash0:s390x (0.8.2-2build1) ... (Reading database ... 15555 files and directories currently installed.) Preparing to unpack .../libzstd1_1.5.5+dfsg2-2build1_s390x.deb ... Unpacking libzstd1:s390x (1.5.5+dfsg2-2build1) over (1.5.5+dfsg2-1ubuntu2) ... Setting up libzstd1:s390x (1.5.5+dfsg2-2build1) ... (Reading database ... 15555 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1ubuntu2_s390x.deb ... Unpacking zlib1g:s390x (1:1.3.dfsg-3.1ubuntu2) over (1:1.2.13.dfsg-1ubuntu5) ... Setting up zlib1g:s390x (1:1.3.dfsg-3.1ubuntu2) ... (Reading database ... 15555 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.3.0+dfsg-2ubuntu6_s390x.deb ... Unpacking libgmp10:s390x (2:6.3.0+dfsg-2ubuntu6) over (2:6.3.0+dfsg-2ubuntu4) ... Setting up libgmp10:s390x (2:6.3.0+dfsg-2ubuntu6) ... (Reading database ... 15555 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.6-1build1_s390x.deb ... Unpacking libffi8:s390x (3.4.6-1build1) over (3.4.4-1) ... Setting up libffi8:s390x (3.4.6-1build1) ... (Reading database ... 15555 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.7-2build1_s390x.deb ... Unpacking libidn2-0:s390x (2.3.7-2build1) over (2.3.4-1) ... Setting up libidn2-0:s390x (2.3.7-2build1) ... (Reading database ... 15555 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.19.0-3build1_s390x.deb ... Unpacking libtasn1-6:s390x (4.19.0-3build1) over (4.19.0-3) ... Setting up libtasn1-6:s390x (4.19.0-3build1) ... (Reading database ... 15555 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.271ubuntu3_s390x.deb ... Unpacking libdebconfclient0:s390x (0.271ubuntu3) over (0.270ubuntu1) ... Setting up libdebconfclient0:s390x (0.271ubuntu3) ... (Reading database ... 15555 files and directories currently installed.) Preparing to unpack .../base-passwd_3.6.3build1_s390x.deb ... Unpacking base-passwd (3.6.3build1) over (3.6.1) ... Setting up base-passwd (3.6.3build1) ... (Reading database ... 15555 files and directories currently installed.) Preparing to unpack .../libassuan0_2.5.6-1build1_s390x.deb ... Unpacking libassuan0:s390x (2.5.6-1build1) over (2.5.6-1) ... Setting up libassuan0:s390x (2.5.6-1build1) ... (Reading database ... 15555 files and directories currently installed.) Preparing to unpack .../libsqlite3-0_3.45.3-1_s390x.deb ... Unpacking libsqlite3-0:s390x (3.45.3-1) over (3.42.0-1) ... Preparing to unpack .../gpg_2.4.4-2ubuntu17_s390x.deb ... Unpacking gpg (2.4.4-2ubuntu17) over (2.2.40-1.1ubuntu1) ... dpkg: libreadline8:s390x: dependency problems, but removing anyway as you requested: gpgconf depends on libreadline8 (>= 6.0). (Reading database ... 15555 files and directories currently installed.) Removing libreadline8:s390x (8.2-1.3) ... Selecting previously unselected package libreadline8t64:s390x. (Reading database ... 15543 files and directories currently installed.) Preparing to unpack .../libreadline8t64_8.2-4build1_s390x.deb ... Adding 'diversion of /lib/s390x-linux-gnu/libhistory.so.8 to /lib/s390x-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/s390x-linux-gnu/libhistory.so.8.2 to /lib/s390x-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/s390x-linux-gnu/libreadline.so.8 to /lib/s390x-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/s390x-linux-gnu/libreadline.so.8.2 to /lib/s390x-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:s390x (8.2-4build1) ... Preparing to unpack .../readline-common_8.2-4build1_all.deb ... Unpacking readline-common (8.2-4build1) over (8.2-1.3) ... Preparing to unpack .../libncursesw6_6.5-2_s390x.deb ... Unpacking libncursesw6:s390x (6.5-2) over (6.4+20230625-2) ... Preparing to unpack .../libtinfo6_6.5-2_s390x.deb ... Unpacking libtinfo6:s390x (6.5-2) over (6.4+20230625-2) ... Setting up libtinfo6:s390x (6.5-2) ... (Reading database ... 15563 files and directories currently installed.) Preparing to unpack .../gpg-agent_2.4.4-2ubuntu17_s390x.deb ... Unpacking gpg-agent (2.4.4-2ubuntu17) over (2.2.40-1.1ubuntu1) ... Preparing to unpack .../gpgconf_2.4.4-2ubuntu17_s390x.deb ... Unpacking gpgconf (2.4.4-2ubuntu17) over (2.2.40-1.1ubuntu1) ... Preparing to unpack .../pinentry-curses_1.2.1-3ubuntu5_s390x.deb ... Unpacking pinentry-curses (1.2.1-3ubuntu5) over (1.2.1-1ubuntu1) ... Preparing to unpack .../init-system-helpers_1.66ubuntu1_all.deb ... Unpacking init-system-helpers (1.66ubuntu1) over (1.65.2ubuntu1) ... Setting up init-system-helpers (1.66ubuntu1) ... (Reading database ... 15562 files and directories currently installed.) Removing libnpth0:s390x (1.6-3build2) ... Selecting previously unselected package libnpth0t64:s390x. (Reading database ... 15557 files and directories currently installed.) Preparing to unpack .../libnpth0t64_1.6-3.1build1_s390x.deb ... Unpacking libnpth0t64:s390x (1.6-3.1build1) ... Setting up libnpth0t64:s390x (1.6-3.1build1) ... (Reading database ... 15563 files and directories currently installed.) Preparing to unpack .../gpgv_2.4.4-2ubuntu17_s390x.deb ... Unpacking gpgv (2.4.4-2ubuntu17) over (2.2.40-1.1ubuntu1) ... Setting up gpgv (2.4.4-2ubuntu17) ... (Reading database ... 15563 files and directories currently installed.) Preparing to unpack .../ubuntu-keyring_2023.11.28.1_all.deb ... Unpacking ubuntu-keyring (2023.11.28.1) over (2021.03.26) ... Setting up ubuntu-keyring (2023.11.28.1) ... (Reading database ... 15563 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-1ubuntu3_s390x.deb ... Unpacking libseccomp2:s390x (2.5.5-1ubuntu3) over (2.5.4-1ubuntu3) ... Setting up libseccomp2:s390x (2.5.5-1ubuntu3) ... (Reading database ... 15563 files and directories currently installed.) Preparing to unpack .../debconf-i18n_1.5.86ubuntu1_all.deb ... Unpacking debconf-i18n (1.5.86ubuntu1) over (1.5.82) ... Preparing to unpack .../debconf_1.5.86ubuntu1_all.deb ... Unpacking debconf (1.5.86ubuntu1) over (1.5.82) ... Setting up debconf (1.5.86ubuntu1) ... Installing new version of config file /etc/debconf.conf ... (Reading database ... 15562 files and directories currently installed.) Preparing to unpack .../libpam0g_1.5.3-7ubuntu1_s390x.deb ... Unpacking libpam0g:s390x (1.5.3-7ubuntu1) over (1.5.2-6ubuntu1) ... Setting up libpam0g:s390x (1.5.3-7ubuntu1) ... (Reading database ... 15561 files and directories currently installed.) Preparing to unpack .../0-libfdisk1_2.39.3-9ubuntu6_s390x.deb ... Unpacking libfdisk1:s390x (2.39.3-9ubuntu6) over (2.39.1-4ubuntu2) ... Preparing to unpack .../1-mount_2.39.3-9ubuntu6_s390x.deb ... Unpacking mount (2.39.3-9ubuntu6) over (2.39.1-4ubuntu2) ... Preparing to unpack .../2-libcom-err2_1.47.0-2.4~exp1ubuntu4_s390x.deb ... Unpacking libcom-err2:s390x (1.47.0-2.4~exp1ubuntu4) over (1.47.0-2ubuntu1) ... Preparing to unpack .../3-libkeyutils1_1.6.3-3build1_s390x.deb ... Unpacking libkeyutils1:s390x (1.6.3-3build1) over (1.6.3-2) ... Preparing to unpack .../4-linux-libc-dev_6.8.0-31.31_s390x.deb ... Unpacking linux-libc-dev:s390x (6.8.0-31.31) over (6.5.0-9.9) ... Preparing to unpack .../5-base-files_13.1ubuntu1_s390x.deb ... Unpacking base-files (13.1ubuntu1) over (13ubuntu3) ... Setting up base-files (13.1ubuntu1) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Installing new version of config file /etc/update-motd.d/10-help-text ... (Reading database ... 15580 files and directories currently installed.) Preparing to unpack .../debianutils_5.17build1_s390x.deb ... Unpacking debianutils (5.17build1) over (5.8-1) ... Setting up debianutils (5.17build1) ... (Reading database ... 15579 files and directories currently installed.) Preparing to unpack .../bash_5.2.21-2ubuntu5_s390x.deb ... Unpacking bash (5.2.21-2ubuntu5) over (5.2.15-2ubuntu1) ... Setting up bash (5.2.21-2ubuntu5) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 15579 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.39.3-9ubuntu6_s390x.deb ... Unpacking bsdutils (1:2.39.3-9ubuntu6) over (1:2.39.1-4ubuntu2) ... Setting up bsdutils (1:2.39.3-9ubuntu6) ... (Reading database ... 15579 files and directories currently installed.) Removing usrmerge (35ubuntu1) ... (Reading database ... 15553 files and directories currently installed.) Preparing to unpack .../coreutils_9.4-3ubuntu6_s390x.deb ... Unpacking coreutils (9.4-3ubuntu6) over (9.1-1ubuntu2) ... Setting up coreutils (9.4-3ubuntu6) ... (Reading database ... 15558 files and directories currently installed.) Preparing to unpack .../tar_1.35+dfsg-3build1_s390x.deb ... Unpacking tar (1.35+dfsg-3build1) over (1.34+dfsg-1.2ubuntu1) ... Setting up tar (1.35+dfsg-3build1) ... (Reading database ... 15558 files and directories currently installed.) Preparing to unpack .../dpkg_1.22.6ubuntu10_s390x.deb ... Unpacking dpkg (1.22.6ubuntu10) over (1.22.0ubuntu1) ... Setting up dpkg (1.22.6ubuntu10) ... (Reading database ... 15556 files and directories currently installed.) Preparing to unpack .../dash_0.5.12-6ubuntu5_s390x.deb ... Unpacking dash (0.5.12-6ubuntu5) over (0.5.12-6ubuntu1) ... Setting up dash (0.5.12-6ubuntu5) ... (Reading database ... 15555 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.10-1build1_s390x.deb ... Unpacking diffutils (1:3.10-1build1) over (1:3.8-4) ... Setting up diffutils (1:3.10-1build1) ... (Reading database ... 15555 files and directories currently installed.) Preparing to unpack .../findutils_4.9.0-5build1_s390x.deb ... Unpacking findutils (4.9.0-5build1) over (4.9.0-5) ... Setting up findutils (4.9.0-5build1) ... (Reading database ... 15554 files and directories currently installed.) Preparing to unpack .../grep_3.11-4build1_s390x.deb ... Unpacking grep (3.11-4build1) over (3.11-2) ... Setting up grep (3.11-4build1) ... (Reading database ... 15554 files and directories currently installed.) Preparing to unpack .../gzip_1.12-1ubuntu3_s390x.deb ... Unpacking gzip (1.12-1ubuntu3) over (1.12-1ubuntu1) ... dpkg: warning: old file '/bin/uncompress' is the same as several new files! (both '/usr/bin/gunzip' and '/usr/bin/uncompress') dpkg: warning: old file '/bin/gunzip' is the same as several new files! (both '/usr/bin/gunzip' and '/usr/bin/uncompress') Setting up gzip (1.12-1ubuntu3) ... (Reading database ... 15554 files and directories currently installed.) Preparing to unpack .../hostname_3.23+nmu2ubuntu2_s390x.deb ... Unpacking hostname (3.23+nmu2ubuntu2) over (3.23+nmu1ubuntu1) ... Setting up hostname (3.23+nmu2ubuntu2) ... (Reading database ... 15554 files and directories currently installed.) Preparing to unpack .../login_1%3a4.13+dfsg1-4ubuntu5_s390x.deb ... Unpacking login (1:4.13+dfsg1-4ubuntu5) over (1:4.13+dfsg1-1ubuntu1) ... Setting up login (1:4.13+dfsg1-4ubuntu5) ... Installing new version of config file /etc/login.defs ... Installing new version of config file /etc/pam.d/login ... (Reading database ... 15554 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.5-2_s390x.deb ... Unpacking ncurses-bin (6.5-2) over (6.4+20230625-2) ... Setting up ncurses-bin (6.5-2) ... (Reading database ... 15554 files and directories currently installed.) Preparing to unpack .../sed_4.9-2build1_s390x.deb ... Unpacking sed (4.9-2build1) over (4.9-1) ... Setting up sed (4.9-2build1) ... (Reading database ... 15554 files and directories currently installed.) Preparing to unpack .../util-linux_2.39.3-9ubuntu6_s390x.deb ... Unpacking util-linux (2.39.3-9ubuntu6) over (2.39.1-4ubuntu2) ... Setting up util-linux (2.39.3-9ubuntu6) ... (Reading database ... 15556 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.5-2_all.deb ... Unpacking ncurses-base (6.5-2) over (6.4+20230625-2) ... Setting up ncurses-base (6.5-2) ... (Reading database ... 15556 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.08-6ubuntu3_s390x.deb ... Unpacking sysvinit-utils (3.08-6ubuntu3) over (3.07-1ubuntu1) ... dpkg: warning: unable to delete old directory '/lib/lsb/init-functions.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/lsb': Directory not empty dpkg: warning: unable to delete old directory '/lib/init': Directory not empty Setting up sysvinit-utils (3.08-6ubuntu3) ... (Reading database ... 15554 files and directories currently installed.) Preparing to unpack .../logsave_1.47.0-2.4~exp1ubuntu4_s390x.deb ... Unpacking logsave (1.47.0-2.4~exp1ubuntu4) over (1.47.0-2ubuntu1) ... dpkg: libext2fs2:s390x: dependency problems, but removing anyway as you requested: e2fsprogs depends on libext2fs2 (= 1.47.0-2ubuntu1). (Reading database ... 15554 files and directories currently installed.) Removing libext2fs2:s390x (1.47.0-2ubuntu1) ... Selecting previously unselected package libext2fs2t64:s390x. (Reading database ... 15547 files and directories currently installed.) Preparing to unpack .../libext2fs2t64_1.47.0-2.4~exp1ubuntu4_s390x.deb ... Adding 'diversion of /lib/s390x-linux-gnu/libe2p.so.2 to /lib/s390x-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/s390x-linux-gnu/libe2p.so.2.3 to /lib/s390x-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/s390x-linux-gnu/libext2fs.so.2 to /lib/s390x-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/s390x-linux-gnu/libext2fs.so.2.4 to /lib/s390x-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' Unpacking libext2fs2t64:s390x (1.47.0-2.4~exp1ubuntu4) ... Setting up libcom-err2:s390x (1.47.0-2.4~exp1ubuntu4) ... Setting up libext2fs2t64:s390x (1.47.0-2.4~exp1ubuntu4) ... (Reading database ... 15563 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.47.0-2.4~exp1ubuntu4_s390x.deb ... Unpacking e2fsprogs (1.47.0-2.4~exp1ubuntu4) over (1.47.0-2ubuntu1) ... dpkg: warning: unable to delete old directory '/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/udev': Directory not empty Preparing to unpack .../optipng_0.7.8+ds-1build2_s390x.deb ... Unpacking optipng (0.7.8+ds-1build2) over (0.7.7-2build1) ... (Reading database ... 15561 files and directories currently installed.) Removing libpng16-16:s390x (1.6.40-1) ... Selecting previously unselected package libpng16-16t64:s390x. (Reading database ... 15551 files and directories currently installed.) Preparing to unpack .../libpng16-16t64_1.6.43-5build1_s390x.deb ... Unpacking libpng16-16t64:s390x (1.6.43-5build1) ... Setting up libapparmor1:s390x (4.0.1-0ubuntu1) ... Setting up libargon2-1:s390x (0~20190702+dfsg-4build1) ... Setting up libdevmapper1.02.1:s390x (2:1.02.185-3ubuntu4) ... Setting up libjson-c5:s390x (0.17-1build1) ... Setting up libcryptsetup12:s390x (2:2.7.0-1ubuntu5) ... Setting up libfdisk1:s390x (2.39.3-9ubuntu6) ... Setting up libsystemd-shared:s390x (256~rc3-1ubuntu1) ... Setting up mount (2.39.3-9ubuntu6) ... Setting up systemd (256~rc3-1ubuntu1) ... Installing new version of config file /etc/systemd/journald.conf ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/pstore.conf ... Installing new version of config file /etc/systemd/sleep.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up systemd-sysv (256~rc3-1ubuntu1) ... (Reading database ... 15562 files and directories currently installed.) Preparing to unpack .../init_1.66ubuntu1_s390x.deb ... Unpacking init (1.66ubuntu1) over (1.65.2ubuntu1) ... Preparing to unpack .../libsmartcols1_2.39.3-9ubuntu6_s390x.deb ... Unpacking libsmartcols1:s390x (2.39.3-9ubuntu6) over (2.39.1-4ubuntu2) ... Setting up libsmartcols1:s390x (2.39.3-9ubuntu6) ... (Reading database ... 15563 files and directories currently installed.) Preparing to unpack .../uuid-runtime_2.39.3-9ubuntu6_s390x.deb ... Unpacking uuid-runtime (2.39.3-9ubuntu6) over (2.39.1-4ubuntu2) ... dpkg: warning: unable to delete old directory '/lib/systemd/system': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd': Directory not empty Preparing to unpack .../libattr1_1%3a2.5.2-1build1_s390x.deb ... Unpacking libattr1:s390x (1:2.5.2-1build1) over (1:2.5.1-4) ... Setting up libattr1:s390x (1:2.5.2-1build1) ... (Reading database ... 15561 files and directories currently installed.) Preparing to unpack .../libmd0_1.1.0-2build1_s390x.deb ... Unpacking libmd0:s390x (1.1.0-2build1) over (1.1.0-1) ... Setting up libmd0:s390x (1.1.0-2build1) ... (Reading database ... 15561 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.5.3-7ubuntu1_all.deb ... Unpacking libpam-runtime (1.5.3-7ubuntu1) over (1.5.2-6ubuntu1) ... Setting up libpam-runtime (1.5.3-7ubuntu1) ... (Reading database ... 15560 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.5-1build5_all.deb ... Unpacking libsemanage-common (3.5-1build5) over (3.5-1) ... Setting up libsemanage-common (3.5-1build5) ... (Reading database ... 15560 files and directories currently installed.) Preparing to unpack .../libsepol2_3.5-2build1_s390x.deb ... Unpacking libsepol2:s390x (3.5-2build1) over (3.5-1) ... Setting up libsepol2:s390x (3.5-2build1) ... (Reading database ... 15560 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.5-1build5_s390x.deb ... Unpacking libsemanage2:s390x (3.5-1build5) over (3.5-1) ... Setting up libsemanage2:s390x (3.5-1build5) ... (Reading database ... 15560 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.13+dfsg1-4ubuntu5_s390x.deb ... Unpacking passwd (1:4.13+dfsg1-4ubuntu5) over (1:4.13+dfsg1-1ubuntu1) ... Setting up passwd (1:4.13+dfsg1-4ubuntu5) ... (Reading database ... 15560 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.4-4ubuntu3_s390x.deb ... Unpacking libproc2-0:s390x (2:4.0.4-4ubuntu3) over (2:4.0.3-1ubuntu1) ... Preparing to unpack .../01-libss2_1.47.0-2.4~exp1ubuntu4_s390x.deb ... Unpacking libss2:s390x (1.47.0-2.4~exp1ubuntu4) over (1.47.0-2ubuntu1) ... Preparing to unpack .../02-mawk_1.3.4.20240123-1build1_s390x.deb ... Unpacking mawk (1.3.4.20240123-1build1) over (1.3.4.20230730-1) ... Preparing to unpack .../03-procps_2%3a4.0.4-4ubuntu3_s390x.deb ... Unpacking procps (2:4.0.4-4ubuntu3) over (2:4.0.3-1ubuntu1) ... Preparing to unpack .../04-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) over (0.0.20) ... Preparing to unpack .../05-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) over (20230311ubuntu1) ... Preparing to unpack .../06-krb5-locales_1.20.1-6ubuntu2_all.deb ... Unpacking krb5-locales (1.20.1-6ubuntu2) over (1.20.1-3ubuntu1) ... Preparing to unpack .../07-tzdata_2024a-4ubuntu1_all.deb ... Unpacking tzdata (2024a-4ubuntu1) over (2023c-9ubuntu1) ... Preparing to unpack .../08-bash-completion_1%3a2.14.0-1_all.deb ... Unpacking bash-completion (1:2.14.0-1) over (1:2.11-7) ... Preparing to unpack .../09-bsdextrautils_2.39.3-9ubuntu6_s390x.deb ... Unpacking bsdextrautils (2.39.3-9ubuntu6) over (2.39.1-4ubuntu2) ... Preparing to unpack .../10-libgpm2_1.20.7-11_s390x.deb ... Unpacking libgpm2:s390x (1.20.7-11) over (1.20.7-10build1) ... Preparing to unpack .../11-libip4tc2_1.8.10-3ubuntu2_s390x.deb ... Unpacking libip4tc2:s390x (1.8.10-3ubuntu2) over (1.8.9-2ubuntu2) ... Preparing to unpack .../12-libjansson4_2.14-2build2_s390x.deb ... Unpacking libjansson4:s390x (2.14-2build2) over (2.14-2) ... Preparing to unpack .../13-psmisc_23.7-1build1_s390x.deb ... Unpacking psmisc (23.7-1build1) over (23.6-1) ... Preparing to unpack .../14-xz-utils_5.6.1+really5.4.5-1_s390x.deb ... Unpacking xz-utils (5.6.1+really5.4.5-1) over (5.4.1-0.2) ... Preparing to unpack .../15-advancecomp_2.5-1build1_s390x.deb ... Unpacking advancecomp (2.5-1build1) over (2.5-1) ... Preparing to unpack .../16-libctf0_2.42-4ubuntu2_s390x.deb ... Unpacking libctf0:s390x (2.42-4ubuntu2) over (2.41-5ubuntu1) ... Preparing to unpack .../17-libctf-nobfd0_2.42-4ubuntu2_s390x.deb ... Unpacking libctf-nobfd0:s390x (2.42-4ubuntu2) over (2.41-5ubuntu1) ... Preparing to unpack .../18-binutils-s390x-linux-gnu_2.42-4ubuntu2_s390x.deb ... Unpacking binutils-s390x-linux-gnu (2.42-4ubuntu2) over (2.41-5ubuntu1) ... Preparing to unpack .../19-libbinutils_2.42-4ubuntu2_s390x.deb ... Unpacking libbinutils:s390x (2.42-4ubuntu2) over (2.41-5ubuntu1) ... Preparing to unpack .../20-binutils_2.42-4ubuntu2_s390x.deb ... Unpacking binutils (2.42-4ubuntu2) over (2.41-5ubuntu1) ... Preparing to unpack .../21-binutils-common_2.42-4ubuntu2_s390x.deb ... Unpacking binutils-common:s390x (2.42-4ubuntu2) over (2.41-5ubuntu1) ... Preparing to unpack .../22-libsframe1_2.42-4ubuntu2_s390x.deb ... Unpacking libsframe1:s390x (2.42-4ubuntu2) over (2.41-5ubuntu1) ... Preparing to unpack .../23-libubsan1_14.1.0-1ubuntu1_s390x.deb ... Unpacking libubsan1:s390x (14.1.0-1ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../24-libgomp1_14.1.0-1ubuntu1_s390x.deb ... Unpacking libgomp1:s390x (14.1.0-1ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../25-libitm1_14.1.0-1ubuntu1_s390x.deb ... Unpacking libitm1:s390x (14.1.0-1ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../26-libatomic1_14.1.0-1ubuntu1_s390x.deb ... Unpacking libatomic1:s390x (14.1.0-1ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../27-libasan8_14.1.0-1ubuntu1_s390x.deb ... Unpacking libasan8:s390x (14.1.0-1ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../28-g++-13_13.2.0-25ubuntu1_s390x.deb ... Unpacking g++-13 (13.2.0-25ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../29-gcc-13_13.2.0-25ubuntu1_s390x.deb ... Unpacking gcc-13 (13.2.0-25ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../30-libstdc++-13-dev_13.2.0-25ubuntu1_s390x.deb ... Unpacking libstdc++-13-dev:s390x (13.2.0-25ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../31-libgcc-13-dev_13.2.0-25ubuntu1_s390x.deb ... Unpacking libgcc-13-dev:s390x (13.2.0-25ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../32-libcc1-0_14.1.0-1ubuntu1_s390x.deb ... Unpacking libcc1-0:s390x (14.1.0-1ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../33-cpp-13_13.2.0-25ubuntu1_s390x.deb ... Unpacking cpp-13 (13.2.0-25ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../34-gcc-13-base_13.2.0-25ubuntu1_s390x.deb ... Unpacking gcc-13-base:s390x (13.2.0-25ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../35-libisl23_0.26-3build1_s390x.deb ... Unpacking libisl23:s390x (0.26-3build1) over (0.26-3) ... Preparing to unpack .../36-libmpfr6_4.2.1-1build1_s390x.deb ... Unpacking libmpfr6:s390x (4.2.1-1build1) over (4.2.1-1) ... Preparing to unpack .../37-libmpc3_1.3.1-1build1_s390x.deb ... Unpacking libmpc3:s390x (1.3.1-1build1) over (1.3.1-1) ... Selecting previously unselected package gcc-13-s390x-linux-gnu. Preparing to unpack .../38-gcc-13-s390x-linux-gnu_13.2.0-25ubuntu1_s390x.deb ... Unpacking gcc-13-s390x-linux-gnu (13.2.0-25ubuntu1) ... Selecting previously unselected package g++-13-s390x-linux-gnu. Preparing to unpack .../39-g++-13-s390x-linux-gnu_13.2.0-25ubuntu1_s390x.deb ... Unpacking g++-13-s390x-linux-gnu (13.2.0-25ubuntu1) ... Selecting previously unselected package cpp-13-s390x-linux-gnu. Preparing to unpack .../40-cpp-13-s390x-linux-gnu_13.2.0-25ubuntu1_s390x.deb ... Unpacking cpp-13-s390x-linux-gnu (13.2.0-25ubuntu1) ... Preparing to unpack .../41-g++_4%3a13.2.0-7ubuntu1_s390x.deb ... Unpacking g++ (4:13.2.0-7ubuntu1) over (4:13.2.0-1ubuntu1) ... Preparing to unpack .../42-gcc_4%3a13.2.0-7ubuntu1_s390x.deb ... Unpacking gcc (4:13.2.0-7ubuntu1) over (4:13.2.0-1ubuntu1) ... Preparing to unpack .../43-cpp_4%3a13.2.0-7ubuntu1_s390x.deb ... Unpacking cpp (4:13.2.0-7ubuntu1) over (4:13.2.0-1ubuntu1) ... Selecting previously unselected package cpp-s390x-linux-gnu. Preparing to unpack .../44-cpp-s390x-linux-gnu_4%3a13.2.0-7ubuntu1_s390x.deb ... Unpacking cpp-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Selecting previously unselected package gcc-s390x-linux-gnu. Preparing to unpack .../45-gcc-s390x-linux-gnu_4%3a13.2.0-7ubuntu1_s390x.deb ... Unpacking gcc-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Selecting previously unselected package g++-s390x-linux-gnu. Preparing to unpack .../46-g++-s390x-linux-gnu_4%3a13.2.0-7ubuntu1_s390x.deb ... Unpacking g++-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Preparing to unpack .../47-dpkg-dev_1.22.6ubuntu10_all.deb ... Unpacking dpkg-dev (1.22.6ubuntu10) over (1.22.0ubuntu1) ... Preparing to unpack .../48-libdpkg-perl_1.22.6ubuntu10_all.deb ... Unpacking libdpkg-perl (1.22.6ubuntu10) over (1.22.0ubuntu1) ... Preparing to unpack .../49-patch_2.7.6-7build3_s390x.deb ... Unpacking patch (2.7.6-7build3) over (2.7.6-7build2) ... Preparing to unpack .../50-make_4.3-4.1build2_s390x.deb ... Unpacking make (4.3-4.1build2) over (4.3-4.1build1) ... Preparing to unpack .../51-lto-disabled-list_48_all.deb ... Unpacking lto-disabled-list (48) over (43) ... Preparing to unpack .../52-libfakeroot_1.34-1_s390x.deb ... Unpacking libfakeroot:s390x (1.34-1) over (1.32.1-1) ... Preparing to unpack .../53-fakeroot_1.34-1_s390x.deb ... Unpacking fakeroot (1.34-1) over (1.32.1-1) ... Preparing to unpack .../54-liblockfile-bin_1.17-1build3_s390x.deb ... Unpacking liblockfile-bin (1.17-1build3) over (1.17-1build2) ... Preparing to unpack .../55-liblockfile1_1.17-1build3_s390x.deb ... Unpacking liblockfile1:s390x (1.17-1build3) over (1.17-1build2) ... Preparing to unpack .../56-lockfile-progs_0.1.19+nmu1_s390x.deb ... Unpacking lockfile-progs (0.1.19+nmu1) over (0.1.19build1) ... Setting up libip4tc2:s390x (1.8.10-3ubuntu2) ... Setting up libtext-iconv-perl:s390x (1.7-8build3) ... Setting up libtext-charwidth-perl:s390x (0.04-11build3) ... Setting up libkeyutils1:s390x (1.6.3-3build1) ... Setting up lto-disabled-list (48) ... Setting up apt-utils (2.9.4) ... Setting up libgpm2:s390x (1.20.7-11) ... Setting up liblockfile-bin (1.17-1build3) ... Setting up libgdbm6t64:s390x (1.23-5.1build1) ... Setting up bsdextrautils (2.39.3-9ubuntu6) ... Setting up init (1.66ubuntu1) ... Setting up libgdbm-compat4t64:s390x (1.23-5.1build1) ... Setting up psmisc (23.7-1build1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libsqlite3-0:s390x (3.45.3-1) ... Setting up binutils-common:s390x (2.42-4ubuntu2) ... Setting up linux-libc-dev:s390x (6.8.0-31.31) ... Setting up libctf-nobfd0:s390x (2.42-4ubuntu2) ... Setting up systemd-dev (256~rc3-1ubuntu1) ... Setting up krb5-locales (1.20.1-6ubuntu2) ... Setting up libgomp1:s390x (14.1.0-1ubuntu1) ... Setting up bzip2 (1.0.8-5.1) ... Setting up libsframe1:s390x (2.42-4ubuntu2) ... Setting up libfakeroot:s390x (1.34-1) ... Setting up libjansson4:s390x (2.14-2build2) ... Setting up libkrb5support0:s390x (1.20.1-6ubuntu2) ... Setting up tzdata (2024a-4ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed May 29 10:21:30 UTC 2024. Universal Time is now: Wed May 29 10:21:30 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.34-1) ... Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... Setting up gcc-13-base:s390x (13.2.0-25ubuntu1) ... Setting up make (4.3-4.1build2) ... Setting up libmpfr6:s390x (4.2.1-1build1) ... Setting up bash-completion (1:2.14.0-1) ... Installing new version of config file /etc/profile.d/bash_completion.sh ... Setting up xz-utils (5.6.1+really5.4.5-1) ... Setting up perl-modules-5.38 (5.38.2-4) ... Setting up libproc2-0:s390x (2:4.0.4-4ubuntu3) ... Setting up libpng16-16t64:s390x (1.6.43-5build1) ... Setting up libmpc3:s390x (1.3.1-1build1) ... Setting up libatomic1:s390x (14.1.0-1ubuntu1) ... Setting up patch (2.7.6-7build3) ... Setting up libss2:s390x (1.47.0-2.4~exp1ubuntu4) ... Setting up libncursesw6:s390x (6.5-2) ... Setting up libk5crypto3:s390x (1.20.1-6ubuntu2) ... Setting up logsave (1.47.0-2.4~exp1ubuntu4) ... Setting up libubsan1:s390x (14.1.0-1ubuntu1) ... Setting up advancecomp (2.5-1build1) ... Setting up sensible-utils (0.0.22) ... Setting up uuid-runtime (2.39.3-9ubuntu6) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Setting up libcrypt-dev:s390x (1:4.4.36-4build1) ... Setting up libasan8:s390x (14.1.0-1ubuntu1) ... Setting up procps (2:4.0.4-4ubuntu3) ... Installing new version of config file /etc/sysctl.conf ... Setting up mawk (1.3.4.20240123-1build1) ... Setting up libkrb5-3:s390x (1.20.1-6ubuntu2) ... Setting up liblockfile1:s390x (1.17-1build3) ... Setting up libperl5.38t64:s390x (5.38.2-4) ... Setting up libbinutils:s390x (2.42-4ubuntu2) ... Setting up libisl23:s390x (0.26-3build1) ... Setting up libc-dev-bin (2.39-0ubuntu8.1) ... Setting up openssl (3.0.13-0ubuntu4) ... Setting up libgpg-error-l10n (1.49-2) ... Setting up readline-common (8.2-4build1) ... Setting up libcc1-0:s390x (14.1.0-1ubuntu1) ... Setting up liblocale-gettext-perl (1.07-7) ... Setting up libitm1:s390x (14.1.0-1ubuntu1) ... Setting up libkmod2:s390x (31+20240202-2ubuntu7) ... Setting up libctf0:s390x (2.42-4ubuntu2) ... Setting up pinentry-curses (1.2.1-3ubuntu5) ... Setting up binutils-s390x-linux-gnu (2.42-4ubuntu2) ... Setting up debconf-i18n (1.5.86ubuntu1) ... Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu4) ... Setting up binutils (2.42-4ubuntu2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 5 removed; done. Setting up perl (5.38.2-4) ... Setting up cpp-13-s390x-linux-gnu (13.2.0-25ubuntu1) ... Setting up optipng (0.7.8+ds-1build2) ... Setting up lockfile-progs (0.1.19+nmu1) ... Setting up libgssapi-krb5-2:s390x (1.20.1-6ubuntu2) ... Setting up libdpkg-perl (1.22.6ubuntu10) ... Setting up libreadline8t64:s390x (8.2-4build1) ... Setting up libgcc-13-dev:s390x (13.2.0-25ubuntu1) ... Setting up gpgconf (2.4.4-2ubuntu17) ... Setting up libc6-dev:s390x (2.39-0ubuntu8.1) ... Setting up gpg (2.4.4-2ubuntu17) ... Setting up libstdc++-13-dev:s390x (13.2.0-25ubuntu1) ... Setting up gpg-agent (2.4.4-2ubuntu17) ... Setting up cpp-13 (13.2.0-25ubuntu1) ... Setting up cpp-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libtirpc3t64:s390x (1.3.4+ds-1.3) ... Setting up dpkg-dev (1.22.6ubuntu10) ... Setting up libtirpc-dev:s390x (1.3.4+ds-1.3) ... Setting up gcc-13-s390x-linux-gnu (13.2.0-25ubuntu1) ... Setting up gcc-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13-s390x-linux-gnu (13.2.0-25ubuntu1) ... Setting up gcc-13 (13.2.0-25ubuntu1) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libnsl2:s390x (1.3.0-3build3) ... Setting up g++-13 (13.2.0-25ubuntu1) ... Setting up g++-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libnss-nisplus:s390x (1.3-5build1) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up libnss-nis:s390x (3.1-0ubuntu7) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Setting up libnsl-dev:s390x (1.3.0-3build3) ... Processing triggers for libc-bin (2.39-0ubuntu8.1) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15784 files and directories currently installed.) Purging configuration files for libssl3:s390x (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-28443482 s390x oracular-proposed -c chroot:build-PACKAGEBUILD-28443482 --arch=s390x --dist=oracular-proposed --nolog cpptraj_5.1.0+dfsg-4.dsc Initiating build PACKAGEBUILD-28443482 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-182-generic #202-Ubuntu SMP Fri Apr 26 12:29:12 UTC 2024 s390x sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-s390x-014.buildd +==============================================================================+ | cpptraj 5.1.0+dfsg-4 (s390x) Wed, 29 May 2024 10:21:35 +0000 | +==============================================================================+ Package: cpptraj Version: 5.1.0+dfsg-4 Source Version: 5.1.0+dfsg-4 Distribution: oracular-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-28443482/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/cpptraj-eOLAzS/resolver-kJ1mjm' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- cpptraj_5.1.0+dfsg-4.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/cpptraj-eOLAzS/cpptraj-5.1.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/cpptraj-eOLAzS' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), gfortran, libarpack2-dev, libbz2-dev, libfftw3-dev, libnetcdf-dev, libreadline-dev, netcdf-bin, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), gfortran, libarpack2-dev, libbz2-dev, libfftw3-dev, libnetcdf-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 [460 B] Get:5 copy:/<>/apt_archive ./ Packages [498 B] Fetched 1915 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... 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 libkmod2 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 systemd-dev 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-s390x-linux-gnu gfortran-s390x-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 liblzma-dev libmagic-mgc libmagic1t64 libncurses-dev libncurses6 libnetcdf-dev libnetcdf19t64 libnghttp2-14 libpipeline1 libpsl5t64 libreadline-dev librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev 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-multilib gfortran-doc gfortran-13-multilib gfortran-13-doc libcoarrays-dev groff liblapack-doc libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkgconf libfftw3-doc libhdf5-doc icu-doc liblzma-doc ncurses-doc netcdf-doc readline-doc libssl-doc libtool-doc gcj-jdk pkg-config 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-s390x-linux-gnu gfortran-s390x-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 liblzma-dev libmagic-mgc libmagic1t64 libncurses-dev libncurses6 libnetcdf-dev libnetcdf19t64 libnghttp2-14 libpipeline1 libpsl5t64 libreadline-dev librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsz2 libtool libuchardet0 libxml2 libxml2-dev m4 man-db netcdf-bin po-debconf sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 87 newly installed, 0 to remove and 0 not upgraded. Need to get 66.7 MB of archives. After this operation, 247 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [712 B] Get:2 http://ftpmaster.internal/ubuntu oracular/main s390x libelf1t64 s390x 0.191-1 [69.1 kB] Get:3 http://ftpmaster.internal/ubuntu oracular/main s390x libicu74 s390x 74.2-1ubuntu3 [10.9 MB] Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libxml2 s390x 2.12.7+dfsg-2 [663 kB] Get:5 http://ftpmaster.internal/ubuntu oracular/main s390x libmagic-mgc s390x 1:5.45-3build1 [305 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main s390x libmagic1t64 s390x 1:5.45-3build1 [93.2 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/main s390x file s390x 1:5.45-3build1 [22.2 kB] Get:8 http://ftpmaster.internal/ubuntu oracular/main s390x gettext-base s390x 0.21-14ubuntu2 [39.4 kB] Get:9 http://ftpmaster.internal/ubuntu oracular/main s390x libuchardet0 s390x 0.0.8-1build1 [76.7 kB] Get:10 http://ftpmaster.internal/ubuntu oracular/main s390x groff-base s390x 1.23.0-4 [1042 kB] Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libncurses6 s390x 6.5-2 [122 kB] Get:12 http://ftpmaster.internal/ubuntu oracular/main s390x libnghttp2-14 s390x 1.61.0-1 [77.2 kB] Get:13 http://ftpmaster.internal/ubuntu oracular/main s390x libpipeline1 s390x 1.5.7-2 [25.0 kB] Get:14 http://ftpmaster.internal/ubuntu oracular/main s390x libpsl5t64 s390x 0.21.2-1.1build1 [57.7 kB] Get:15 http://ftpmaster.internal/ubuntu oracular/main s390x man-db s390x 2.12.1-1 [1250 kB] Get:16 http://ftpmaster.internal/ubuntu oracular/main s390x m4 s390x 1.4.19-4build1 [256 kB] Get:17 http://ftpmaster.internal/ubuntu oracular/main s390x autoconf all 2.71-3 [339 kB] Get:18 http://ftpmaster.internal/ubuntu oracular/main s390x autotools-dev all 20220109.1 [44.9 kB] Get:19 http://ftpmaster.internal/ubuntu oracular/main s390x automake all 1:1.16.5-1.3ubuntu1 [558 kB] Get:20 http://ftpmaster.internal/ubuntu oracular/main s390x autopoint all 0.21-14ubuntu2 [422 kB] Get:21 http://ftpmaster.internal/ubuntu oracular/main s390x libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB] Get:22 http://ftpmaster.internal/ubuntu oracular/main s390x libtool all 2.4.7-7build1 [166 kB] Get:23 http://ftpmaster.internal/ubuntu oracular/main s390x dh-autoreconf all 20 [16.1 kB] Get:24 http://ftpmaster.internal/ubuntu oracular/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] Get:25 http://ftpmaster.internal/ubuntu oracular/main s390x libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB] Get:26 http://ftpmaster.internal/ubuntu oracular/main s390x dh-strip-nondeterminism all 1.14.0-1 [5058 B] Get:27 http://ftpmaster.internal/ubuntu oracular/main s390x libdw1t64 s390x 0.191-1 [286 kB] Get:28 http://ftpmaster.internal/ubuntu oracular/main s390x debugedit s390x 1:5.0-5build2 [50.5 kB] Get:29 http://ftpmaster.internal/ubuntu oracular/main s390x dwz s390x 0.15-1build6 [122 kB] Get:30 http://ftpmaster.internal/ubuntu oracular/main s390x gettext s390x 0.21-14ubuntu2 [915 kB] Get:31 http://ftpmaster.internal/ubuntu oracular/main s390x intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:32 http://ftpmaster.internal/ubuntu oracular/main s390x po-debconf all 1.0.21+nmu1 [233 kB] Get:33 http://ftpmaster.internal/ubuntu oracular/main s390x debhelper all 13.14.1ubuntu5 [869 kB] Get:34 http://ftpmaster.internal/ubuntu oracular/main s390x libgfortran5 s390x 14.1.0-1ubuntu1 [600 kB] Get:35 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libgfortran-13-dev s390x 13.2.0-25ubuntu1 [623 kB] Get:36 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x gfortran-13-s390x-linux-gnu s390x 13.2.0-25ubuntu1 [9495 kB] Get:37 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x gfortran-13 s390x 13.2.0-25ubuntu1 [12.5 kB] Get:38 http://ftpmaster.internal/ubuntu oracular/main s390x gfortran-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [1016 B] Get:39 http://ftpmaster.internal/ubuntu oracular/main s390x gfortran s390x 4:13.2.0-7ubuntu1 [1174 B] Get:40 http://ftpmaster.internal/ubuntu oracular/universe s390x hdf5-helpers s390x 1.10.10+repack-3.1ubuntu4 [15.8 kB] Get:41 http://ftpmaster.internal/ubuntu oracular/main s390x icu-devtools s390x 74.2-1ubuntu3 [223 kB] Get:42 http://ftpmaster.internal/ubuntu oracular/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB] Get:43 http://ftpmaster.internal/ubuntu oracular/main s390x libblas3 s390x 3.12.0-3build1 [245 kB] Get:44 http://ftpmaster.internal/ubuntu oracular/main s390x liblapack3 s390x 3.12.0-3build1 [2976 kB] Get:45 http://ftpmaster.internal/ubuntu oracular/universe s390x libarpack2t64 s390x 3.9.1-1.1build2 [113 kB] Get:46 http://ftpmaster.internal/ubuntu oracular/main s390x libblas-dev s390x 3.12.0-3build1 [239 kB] Get:47 http://ftpmaster.internal/ubuntu oracular/main s390x liblapack-dev s390x 3.12.0-3build1 [5983 kB] Get:48 http://ftpmaster.internal/ubuntu oracular/universe s390x libarpack2-dev s390x 3.9.1-1.1build2 [130 kB] Get:49 http://ftpmaster.internal/ubuntu oracular/main s390x libbrotli1 s390x 1.1.0-2build2 [375 kB] Get:50 http://ftpmaster.internal/ubuntu oracular/main s390x libbz2-dev s390x 1.0.8-5.1 [39.4 kB] Get:51 http://ftpmaster.internal/ubuntu oracular/main s390x libsasl2-modules-db s390x 2.1.28+dfsg1-5ubuntu3 [21.3 kB] Get:52 http://ftpmaster.internal/ubuntu oracular/main s390x libsasl2-2 s390x 2.1.28+dfsg1-5ubuntu3 [57.8 kB] Get:53 http://ftpmaster.internal/ubuntu oracular/main s390x libldap2 s390x 2.6.7+dfsg-1~exp1ubuntu8 [203 kB] Get:54 http://ftpmaster.internal/ubuntu oracular/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-2build7 [58.4 kB] Get:55 http://ftpmaster.internal/ubuntu oracular/main s390x libssh-4 s390x 0.10.6-2build2 [189 kB] Get:56 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libcurl3t64-gnutls s390x 8.8.0-1ubuntu1 [361 kB] Get:57 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libcurl4-gnutls-dev s390x 8.8.0-1ubuntu1 [475 kB] Get:58 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libcurl4t64 s390x 8.8.0-1ubuntu1 [369 kB] Get:59 http://ftpmaster.internal/ubuntu oracular/main s390x libfftw3-double3 s390x 3.3.10-1ubuntu3 [512 kB] Get:60 http://ftpmaster.internal/ubuntu oracular/main s390x libfftw3-long3 s390x 3.3.10-1ubuntu3 [528 kB] Get:61 http://ftpmaster.internal/ubuntu oracular/main s390x libfftw3-single3 s390x 3.3.10-1ubuntu3 [481 kB] Get:62 http://ftpmaster.internal/ubuntu oracular/main s390x libfftw3-bin s390x 3.3.10-1ubuntu3 [37.5 kB] Get:63 http://ftpmaster.internal/ubuntu oracular/main s390x libfftw3-dev s390x 3.3.10-1ubuntu3 [1325 kB] Get:64 http://ftpmaster.internal/ubuntu oracular/universe s390x libsz2 s390x 1.1.3-1 [5442 B] Get:65 http://ftpmaster.internal/ubuntu oracular/universe s390x libhdf5-103-1t64 s390x 1.10.10+repack-3.1ubuntu4 [1436 kB] Get:66 http://ftpmaster.internal/ubuntu oracular/universe s390x libhdf5-cpp-103-1t64 s390x 1.10.10+repack-3.1ubuntu4 [123 kB] Get:67 http://ftpmaster.internal/ubuntu oracular/universe s390x libhdf5-fortran-102t64 s390x 1.10.10+repack-3.1ubuntu4 [92.7 kB] Get:68 http://ftpmaster.internal/ubuntu oracular/universe s390x libhdf5-hl-100t64 s390x 1.10.10+repack-3.1ubuntu4 [58.0 kB] Get:69 http://ftpmaster.internal/ubuntu oracular/universe s390x libhdf5-hl-fortran-100t64 s390x 1.10.10+repack-3.1ubuntu4 [32.3 kB] Get:70 http://ftpmaster.internal/ubuntu oracular/universe s390x libhdf5-hl-cpp-100t64 s390x 1.10.10+repack-3.1ubuntu4 [11.1 kB] Get:71 http://ftpmaster.internal/ubuntu oracular/main s390x zlib1g-dev s390x 1:1.3.dfsg-3.1ubuntu2 [904 kB] Get:72 http://ftpmaster.internal/ubuntu oracular/main s390x libjpeg-turbo8 s390x 2.1.5-2ubuntu2 [150 kB] Get:73 http://ftpmaster.internal/ubuntu oracular/main s390x libjpeg-turbo8-dev s390x 2.1.5-2ubuntu2 [284 kB] Get:74 http://ftpmaster.internal/ubuntu oracular/main s390x libjpeg8 s390x 8c-2ubuntu11 [2146 B] Get:75 http://ftpmaster.internal/ubuntu oracular/main s390x libjpeg8-dev s390x 8c-2ubuntu11 [1484 B] Get:76 http://ftpmaster.internal/ubuntu oracular/main s390x libjpeg-dev s390x 8c-2ubuntu11 [1484 B] Get:77 http://ftpmaster.internal/ubuntu oracular/universe s390x libaec-dev s390x 1.1.3-1 [23.3 kB] Get:78 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libssl-dev s390x 3.0.13-0ubuntu4 [2110 kB] Get:79 http://ftpmaster.internal/ubuntu oracular/universe s390x libhdf5-dev s390x 1.10.10+repack-3.1ubuntu4 [2908 kB] Get:80 http://ftpmaster.internal/ubuntu oracular/main s390x libicu-dev s390x 74.2-1ubuntu3 [11.9 MB] Get:81 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libncurses-dev s390x 6.5-2 [404 kB] Get:82 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x libnetcdf19t64 s390x 1:4.9.2-6 [498 kB] Get:83 http://ftpmaster.internal/ubuntu oracular/main s390x liblzma-dev s390x 5.6.1+really5.4.5-1 [184 kB] Get:84 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libxml2-dev s390x 2.12.7+dfsg-2 [73.1 kB] Get:85 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x libnetcdf-dev s390x 1:4.9.2-6 [58.0 kB] Get:86 http://ftpmaster.internal/ubuntu oracular/main s390x libreadline-dev s390x 8.2-4build1 [189 kB] Get:87 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x netcdf-bin s390x 1:4.9.2-6 [218 kB] Preconfiguring packages ... Fetched 66.7 MB in 4s (17.6 MB/s) Selecting previously unselected package libelf1t64:s390x. (Reading database ... 15784 files and directories currently installed.) Preparing to unpack .../00-libelf1t64_0.191-1_s390x.deb ... Unpacking libelf1t64:s390x (0.191-1) ... Selecting previously unselected package libicu74:s390x. Preparing to unpack .../01-libicu74_74.2-1ubuntu3_s390x.deb ... Unpacking libicu74:s390x (74.2-1ubuntu3) ... Selecting previously unselected package libxml2:s390x. Preparing to unpack .../02-libxml2_2.12.7+dfsg-2_s390x.deb ... Unpacking libxml2:s390x (2.12.7+dfsg-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3build1_s390x.deb ... Unpacking libmagic-mgc (1:5.45-3build1) ... Selecting previously unselected package libmagic1t64:s390x. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3build1_s390x.deb ... Unpacking libmagic1t64:s390x (1:5.45-3build1) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-3build1_s390x.deb ... Unpacking file (1:5.45-3build1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-14ubuntu2_s390x.deb ... Unpacking gettext-base (0.21-14ubuntu2) ... Selecting previously unselected package libuchardet0:s390x. Preparing to unpack .../07-libuchardet0_0.0.8-1build1_s390x.deb ... Unpacking libuchardet0:s390x (0.0.8-1build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-4_s390x.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package libncurses6:s390x. Preparing to unpack .../09-libncurses6_6.5-2_s390x.deb ... Unpacking libncurses6:s390x (6.5-2) ... Selecting previously unselected package libnghttp2-14:s390x. Preparing to unpack .../10-libnghttp2-14_1.61.0-1_s390x.deb ... Unpacking libnghttp2-14:s390x (1.61.0-1) ... Selecting previously unselected package libpipeline1:s390x. Preparing to unpack .../11-libpipeline1_1.5.7-2_s390x.deb ... Unpacking libpipeline1:s390x (1.5.7-2) ... Selecting previously unselected package libpsl5t64:s390x. Preparing to unpack .../12-libpsl5t64_0.21.2-1.1build1_s390x.deb ... Unpacking libpsl5t64:s390x (0.21.2-1.1build1) ... Selecting previously unselected package man-db. Preparing to unpack .../13-man-db_2.12.1-1_s390x.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../14-m4_1.4.19-4build1_s390x.deb ... Unpacking m4 (1.4.19-4build1) ... Selecting previously unselected package autoconf. Preparing to unpack .../15-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../16-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../17-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... Unpacking automake (1:1.16.5-1.3ubuntu1) ... Selecting previously unselected package autopoint. Preparing to unpack .../18-autopoint_0.21-14ubuntu2_all.deb ... Unpacking autopoint (0.21-14ubuntu2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../19-libdebhelper-perl_13.14.1ubuntu5_all.deb ... Unpacking libdebhelper-perl (13.14.1ubuntu5) ... Selecting previously unselected package libtool. Preparing to unpack .../20-libtool_2.4.7-7build1_all.deb ... Unpacking libtool (2.4.7-7build1) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../21-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../22-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../23-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../24-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libdw1t64:s390x. Preparing to unpack .../25-libdw1t64_0.191-1_s390x.deb ... Unpacking libdw1t64:s390x (0.191-1) ... Selecting previously unselected package debugedit. Preparing to unpack .../26-debugedit_1%3a5.0-5build2_s390x.deb ... Unpacking debugedit (1:5.0-5build2) ... Selecting previously unselected package dwz. Preparing to unpack .../27-dwz_0.15-1build6_s390x.deb ... Unpacking dwz (0.15-1build6) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-14ubuntu2_s390x.deb ... Unpacking gettext (0.21-14ubuntu2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.14.1ubuntu5_all.deb ... Unpacking debhelper (13.14.1ubuntu5) ... Selecting previously unselected package libgfortran5:s390x. Preparing to unpack .../32-libgfortran5_14.1.0-1ubuntu1_s390x.deb ... Unpacking libgfortran5:s390x (14.1.0-1ubuntu1) ... Selecting previously unselected package libgfortran-13-dev:s390x. Preparing to unpack .../33-libgfortran-13-dev_13.2.0-25ubuntu1_s390x.deb ... Unpacking libgfortran-13-dev:s390x (13.2.0-25ubuntu1) ... Selecting previously unselected package gfortran-13-s390x-linux-gnu. Preparing to unpack .../34-gfortran-13-s390x-linux-gnu_13.2.0-25ubuntu1_s390x.deb ... Unpacking gfortran-13-s390x-linux-gnu (13.2.0-25ubuntu1) ... Selecting previously unselected package gfortran-13. Preparing to unpack .../35-gfortran-13_13.2.0-25ubuntu1_s390x.deb ... Unpacking gfortran-13 (13.2.0-25ubuntu1) ... Selecting previously unselected package gfortran-s390x-linux-gnu. Preparing to unpack .../36-gfortran-s390x-linux-gnu_4%3a13.2.0-7ubuntu1_s390x.deb ... Unpacking gfortran-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Selecting previously unselected package gfortran. Preparing to unpack .../37-gfortran_4%3a13.2.0-7ubuntu1_s390x.deb ... Unpacking gfortran (4:13.2.0-7ubuntu1) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../38-hdf5-helpers_1.10.10+repack-3.1ubuntu4_s390x.deb ... Unpacking hdf5-helpers (1.10.10+repack-3.1ubuntu4) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../39-icu-devtools_74.2-1ubuntu3_s390x.deb ... Unpacking icu-devtools (74.2-1ubuntu3) ... Selecting previously unselected package libaec0:s390x. Preparing to unpack .../40-libaec0_1.1.3-1_s390x.deb ... Unpacking libaec0:s390x (1.1.3-1) ... Selecting previously unselected package libblas3:s390x. Preparing to unpack .../41-libblas3_3.12.0-3build1_s390x.deb ... Unpacking libblas3:s390x (3.12.0-3build1) ... Selecting previously unselected package liblapack3:s390x. Preparing to unpack .../42-liblapack3_3.12.0-3build1_s390x.deb ... Unpacking liblapack3:s390x (3.12.0-3build1) ... Selecting previously unselected package libarpack2t64:s390x. Preparing to unpack .../43-libarpack2t64_3.9.1-1.1build2_s390x.deb ... Unpacking libarpack2t64:s390x (3.9.1-1.1build2) ... Selecting previously unselected package libblas-dev:s390x. Preparing to unpack .../44-libblas-dev_3.12.0-3build1_s390x.deb ... Unpacking libblas-dev:s390x (3.12.0-3build1) ... Selecting previously unselected package liblapack-dev:s390x. Preparing to unpack .../45-liblapack-dev_3.12.0-3build1_s390x.deb ... Unpacking liblapack-dev:s390x (3.12.0-3build1) ... Selecting previously unselected package libarpack2-dev:s390x. Preparing to unpack .../46-libarpack2-dev_3.9.1-1.1build2_s390x.deb ... Unpacking libarpack2-dev:s390x (3.9.1-1.1build2) ... Selecting previously unselected package libbrotli1:s390x. Preparing to unpack .../47-libbrotli1_1.1.0-2build2_s390x.deb ... Unpacking libbrotli1:s390x (1.1.0-2build2) ... Selecting previously unselected package libbz2-dev:s390x. Preparing to unpack .../48-libbz2-dev_1.0.8-5.1_s390x.deb ... Unpacking libbz2-dev:s390x (1.0.8-5.1) ... Selecting previously unselected package libsasl2-modules-db:s390x. Preparing to unpack .../49-libsasl2-modules-db_2.1.28+dfsg1-5ubuntu3_s390x.deb ... Unpacking libsasl2-modules-db:s390x (2.1.28+dfsg1-5ubuntu3) ... Selecting previously unselected package libsasl2-2:s390x. Preparing to unpack .../50-libsasl2-2_2.1.28+dfsg1-5ubuntu3_s390x.deb ... Unpacking libsasl2-2:s390x (2.1.28+dfsg1-5ubuntu3) ... Selecting previously unselected package libldap2:s390x. Preparing to unpack .../51-libldap2_2.6.7+dfsg-1~exp1ubuntu8_s390x.deb ... Unpacking libldap2:s390x (2.6.7+dfsg-1~exp1ubuntu8) ... Selecting previously unselected package librtmp1:s390x. Preparing to unpack .../52-librtmp1_2.4+20151223.gitfa8646d.1-2build7_s390x.deb ... Unpacking librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build7) ... Selecting previously unselected package libssh-4:s390x. Preparing to unpack .../53-libssh-4_0.10.6-2build2_s390x.deb ... Unpacking libssh-4:s390x (0.10.6-2build2) ... Selecting previously unselected package libcurl3t64-gnutls:s390x. Preparing to unpack .../54-libcurl3t64-gnutls_8.8.0-1ubuntu1_s390x.deb ... Unpacking libcurl3t64-gnutls:s390x (8.8.0-1ubuntu1) ... Selecting previously unselected package libcurl4-gnutls-dev:s390x. Preparing to unpack .../55-libcurl4-gnutls-dev_8.8.0-1ubuntu1_s390x.deb ... Unpacking libcurl4-gnutls-dev:s390x (8.8.0-1ubuntu1) ... Selecting previously unselected package libcurl4t64:s390x. Preparing to unpack .../56-libcurl4t64_8.8.0-1ubuntu1_s390x.deb ... Unpacking libcurl4t64:s390x (8.8.0-1ubuntu1) ... Selecting previously unselected package libfftw3-double3:s390x. Preparing to unpack .../57-libfftw3-double3_3.3.10-1ubuntu3_s390x.deb ... Unpacking libfftw3-double3:s390x (3.3.10-1ubuntu3) ... Selecting previously unselected package libfftw3-long3:s390x. Preparing to unpack .../58-libfftw3-long3_3.3.10-1ubuntu3_s390x.deb ... Unpacking libfftw3-long3:s390x (3.3.10-1ubuntu3) ... Selecting previously unselected package libfftw3-single3:s390x. Preparing to unpack .../59-libfftw3-single3_3.3.10-1ubuntu3_s390x.deb ... Unpacking libfftw3-single3:s390x (3.3.10-1ubuntu3) ... Selecting previously unselected package libfftw3-bin. Preparing to unpack .../60-libfftw3-bin_3.3.10-1ubuntu3_s390x.deb ... Unpacking libfftw3-bin (3.3.10-1ubuntu3) ... Selecting previously unselected package libfftw3-dev:s390x. Preparing to unpack .../61-libfftw3-dev_3.3.10-1ubuntu3_s390x.deb ... Unpacking libfftw3-dev:s390x (3.3.10-1ubuntu3) ... Selecting previously unselected package libsz2:s390x. Preparing to unpack .../62-libsz2_1.1.3-1_s390x.deb ... Unpacking libsz2:s390x (1.1.3-1) ... Selecting previously unselected package libhdf5-103-1t64:s390x. Preparing to unpack .../63-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu4_s390x.deb ... Unpacking libhdf5-103-1t64:s390x (1.10.10+repack-3.1ubuntu4) ... Selecting previously unselected package libhdf5-cpp-103-1t64:s390x. Preparing to unpack .../64-libhdf5-cpp-103-1t64_1.10.10+repack-3.1ubuntu4_s390x.deb ... Unpacking libhdf5-cpp-103-1t64:s390x (1.10.10+repack-3.1ubuntu4) ... Selecting previously unselected package libhdf5-fortran-102t64:s390x. Preparing to unpack .../65-libhdf5-fortran-102t64_1.10.10+repack-3.1ubuntu4_s390x.deb ... Unpacking libhdf5-fortran-102t64:s390x (1.10.10+repack-3.1ubuntu4) ... Selecting previously unselected package libhdf5-hl-100t64:s390x. Preparing to unpack .../66-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu4_s390x.deb ... Unpacking libhdf5-hl-100t64:s390x (1.10.10+repack-3.1ubuntu4) ... Selecting previously unselected package libhdf5-hl-fortran-100t64:s390x. Preparing to unpack .../67-libhdf5-hl-fortran-100t64_1.10.10+repack-3.1ubuntu4_s390x.deb ... Unpacking libhdf5-hl-fortran-100t64:s390x (1.10.10+repack-3.1ubuntu4) ... Selecting previously unselected package libhdf5-hl-cpp-100t64:s390x. Preparing to unpack .../68-libhdf5-hl-cpp-100t64_1.10.10+repack-3.1ubuntu4_s390x.deb ... Unpacking libhdf5-hl-cpp-100t64:s390x (1.10.10+repack-3.1ubuntu4) ... Selecting previously unselected package zlib1g-dev:s390x. Preparing to unpack .../69-zlib1g-dev_1%3a1.3.dfsg-3.1ubuntu2_s390x.deb ... Unpacking zlib1g-dev:s390x (1:1.3.dfsg-3.1ubuntu2) ... Selecting previously unselected package libjpeg-turbo8:s390x. Preparing to unpack .../70-libjpeg-turbo8_2.1.5-2ubuntu2_s390x.deb ... Unpacking libjpeg-turbo8:s390x (2.1.5-2ubuntu2) ... Selecting previously unselected package libjpeg-turbo8-dev:s390x. Preparing to unpack .../71-libjpeg-turbo8-dev_2.1.5-2ubuntu2_s390x.deb ... Unpacking libjpeg-turbo8-dev:s390x (2.1.5-2ubuntu2) ... Selecting previously unselected package libjpeg8:s390x. Preparing to unpack .../72-libjpeg8_8c-2ubuntu11_s390x.deb ... Unpacking libjpeg8:s390x (8c-2ubuntu11) ... Selecting previously unselected package libjpeg8-dev:s390x. Preparing to unpack .../73-libjpeg8-dev_8c-2ubuntu11_s390x.deb ... Unpacking libjpeg8-dev:s390x (8c-2ubuntu11) ... Selecting previously unselected package libjpeg-dev:s390x. Preparing to unpack .../74-libjpeg-dev_8c-2ubuntu11_s390x.deb ... Unpacking libjpeg-dev:s390x (8c-2ubuntu11) ... Selecting previously unselected package libaec-dev:s390x. Preparing to unpack .../75-libaec-dev_1.1.3-1_s390x.deb ... Unpacking libaec-dev:s390x (1.1.3-1) ... Selecting previously unselected package libssl-dev:s390x. Preparing to unpack .../76-libssl-dev_3.0.13-0ubuntu4_s390x.deb ... Unpacking libssl-dev:s390x (3.0.13-0ubuntu4) ... Selecting previously unselected package libhdf5-dev. Preparing to unpack .../77-libhdf5-dev_1.10.10+repack-3.1ubuntu4_s390x.deb ... Unpacking libhdf5-dev (1.10.10+repack-3.1ubuntu4) ... Selecting previously unselected package libicu-dev:s390x. Preparing to unpack .../78-libicu-dev_74.2-1ubuntu3_s390x.deb ... Unpacking libicu-dev:s390x (74.2-1ubuntu3) ... Selecting previously unselected package libncurses-dev:s390x. Preparing to unpack .../79-libncurses-dev_6.5-2_s390x.deb ... Unpacking libncurses-dev:s390x (6.5-2) ... Selecting previously unselected package libnetcdf19t64:s390x. Preparing to unpack .../80-libnetcdf19t64_1%3a4.9.2-6_s390x.deb ... Unpacking libnetcdf19t64:s390x (1:4.9.2-6) ... Selecting previously unselected package liblzma-dev:s390x. Preparing to unpack .../81-liblzma-dev_5.6.1+really5.4.5-1_s390x.deb ... Unpacking liblzma-dev:s390x (5.6.1+really5.4.5-1) ... Selecting previously unselected package libxml2-dev:s390x. Preparing to unpack .../82-libxml2-dev_2.12.7+dfsg-2_s390x.deb ... Unpacking libxml2-dev:s390x (2.12.7+dfsg-2) ... Selecting previously unselected package libnetcdf-dev. Preparing to unpack .../83-libnetcdf-dev_1%3a4.9.2-6_s390x.deb ... Unpacking libnetcdf-dev (1:4.9.2-6) ... Selecting previously unselected package libreadline-dev:s390x. Preparing to unpack .../84-libreadline-dev_8.2-4build1_s390x.deb ... Unpacking libreadline-dev:s390x (8.2-4build1) ... Selecting previously unselected package netcdf-bin. Preparing to unpack .../85-netcdf-bin_1%3a4.9.2-6_s390x.deb ... Unpacking netcdf-bin (1:4.9.2-6) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../86-sbuild-build-depends-main-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:s390x (1.5.7-2) ... Setting up libfftw3-single3:s390x (3.3.10-1ubuntu3) ... Setting up hdf5-helpers (1.10.10+repack-3.1ubuntu4) ... Setting up libmagic-mgc (1:5.45-3build1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.14.1ubuntu5) ... Setting up libbrotli1:s390x (1.1.0-2build2) ... Setting up libmagic1t64:s390x (1:5.45-3build1) ... Setting up libpsl5t64:s390x (0.21.2-1.1build1) ... Setting up libnghttp2-14:s390x (1.61.0-1) ... Setting up libfftw3-long3:s390x (3.3.10-1ubuntu3) ... Setting up gettext-base (0.21-14ubuntu2) ... Setting up m4 (1.4.19-4build1) ... Setting up file (1:5.45-3build1) ... Setting up libaec0:s390x (1.1.3-1) ... Setting up libelf1t64:s390x (0.191-1) ... Setting up libdw1t64:s390x (0.191-1) ... Setting up libsasl2-modules-db:s390x (2.1.28+dfsg1-5ubuntu3) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:s390x (3.12.0-3build1) ... update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build7) ... Setting up libncurses6:s390x (6.5-2) ... Setting up libssl-dev:s390x (3.0.13-0ubuntu4) ... Setting up autopoint (0.21-14ubuntu2) ... Setting up libjpeg-turbo8:s390x (2.1.5-2ubuntu2) ... Setting up libfftw3-double3:s390x (3.3.10-1ubuntu3) ... Setting up libsasl2-2:s390x (2.1.28+dfsg1-5ubuntu3) ... Setting up libssh-4:s390x (0.10.6-2build2) ... Setting up libgfortran5:s390x (14.1.0-1ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:s390x (5.6.1+really5.4.5-1) ... Setting up libicu74:s390x (74.2-1ubuntu3) ... Setting up zlib1g-dev:s390x (1:1.3.dfsg-3.1ubuntu2) ... Setting up dwz (0.15-1build6) ... Setting up libuchardet0:s390x (0.0.8-1build1) ... Setting up debugedit (1:5.0-5build2) ... Setting up libgfortran-13-dev:s390x (13.2.0-25ubuntu1) ... Setting up libxml2:s390x (2.12.7+dfsg-2) ... Setting up libldap2:s390x (2.6.7+dfsg-1~exp1ubuntu8) ... Setting up libblas-dev:s390x (3.12.0-3build1) ... update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so to provide /usr/lib/s390x-linux-gnu/libblas.so (libblas.so-s390x-linux-gnu) in auto mode Setting up libsz2:s390x (1.1.3-1) ... Setting up libbz2-dev:s390x (1.0.8-5.1) ... Setting up libjpeg8:s390x (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 (1.14.0-1) ... Setting up libjpeg-turbo8-dev:s390x (2.1.5-2ubuntu2) ... Setting up liblapack3:s390x (3.12.0-3build1) ... update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode Setting up libncurses-dev:s390x (6.5-2) ... Setting up gettext (0.21-14ubuntu2) ... Setting up libarpack2t64:s390x (3.9.1-1.1build2) ... Setting up libcurl4t64:s390x (8.8.0-1ubuntu1) ... Setting up libtool (2.4.7-7build1) ... Setting up libfftw3-bin (3.3.10-1ubuntu3) ... Setting up libaec-dev:s390x (1.1.3-1) ... Setting up libcurl3t64-gnutls:s390x (8.8.0-1ubuntu1) ... Setting up libreadline-dev:s390x (8.2-4build1) ... Setting up libcurl4-gnutls-dev:s390x (8.8.0-1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up liblapack-dev:s390x (3.12.0-3build1) ... update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so to provide /usr/lib/s390x-linux-gnu/liblapack.so (liblapack.so-s390x-linux-gnu) in auto mode Setting up icu-devtools (74.2-1ubuntu3) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-4) ... Setting up gfortran-13-s390x-linux-gnu (13.2.0-25ubuntu1) ... Setting up libjpeg8-dev:s390x (8c-2ubuntu11) ... Setting up libhdf5-103-1t64:s390x (1.10.10+repack-3.1ubuntu4) ... Setting up libfftw3-dev:s390x (3.3.10-1ubuntu3) ... Setting up libicu-dev:s390x (74.2-1ubuntu3) ... Setting up libhdf5-hl-100t64:s390x (1.10.10+repack-3.1ubuntu4) ... Setting up libnetcdf19t64:s390x (1:4.9.2-6) ... Setting up libarpack2-dev:s390x (3.9.1-1.1build2) ... Setting up gfortran-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhdf5-cpp-103-1t64:s390x (1.10.10+repack-3.1ubuntu4) ... Setting up libjpeg-dev:s390x (8c-2ubuntu11) ... Setting up libhdf5-fortran-102t64:s390x (1.10.10+repack-3.1ubuntu4) ... Setting up man-db (2.12.1-1) ... 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 netcdf-bin (1:4.9.2-6) ... Setting up libxml2-dev:s390x (2.12.7+dfsg-2) ... Setting up gfortran-13 (13.2.0-25ubuntu1) ... Setting up libhdf5-hl-cpp-100t64:s390x (1.10.10+repack-3.1ubuntu4) ... Setting up libhdf5-hl-fortran-100t64:s390x (1.10.10+repack-3.1ubuntu4) ... Setting up debhelper (13.14.1ubuntu5) ... 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 libhdf5-dev (1.10.10+repack-3.1ubuntu4) ... update-alternatives: using /usr/lib/s390x-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/s390x-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libnetcdf-dev (1:4.9.2-6) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.39-0ubuntu8.1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (s390x included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-182-generic #202-Ubuntu SMP Fri Apr 26 12:29:12 UTC 2024 s390x (s390x) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu10 g++-13_13.2.0-25ubuntu1 gcc-13_13.2.0-25ubuntu1 libc6-dev_2.39-0ubuntu8.1 libstdc++-13-dev_13.2.0-25ubuntu1 libstdc++6_14.1.0-1ubuntu1 linux-libc-dev_6.8.0-31.31 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1build1 apt_2.9.4 apt-utils_2.9.4 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu2 autotools-dev_20220109.1 base-files_13.1ubuntu1 base-passwd_3.6.3build1 bash_5.2.21-2ubuntu5 bash-completion_1:2.14.0-1 binutils_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 binutils-s390x-linux-gnu_2.42-4ubuntu2 bsdextrautils_2.39.3-9ubuntu6 bsdutils_1:2.39.3-9ubuntu6 build-essential_12.10ubuntu1 bzip2_1.0.8-5.1 ca-certificates_20240203 coreutils_9.4-3ubuntu6 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-25ubuntu1 cpp-13-s390x-linux-gnu_13.2.0-25ubuntu1 cpp-s390x-linux-gnu_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu5 debconf_1.5.86ubuntu1 debconf-i18n_1.5.86ubuntu1 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build2 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1build1 dpkg_1.22.6ubuntu10 dpkg-dev_1.22.6ubuntu10 dwz_0.15-1build6 e2fsprogs_1.47.0-2.4~exp1ubuntu4 fakeroot_1.34-1 file_1:5.45-3build1 findutils_4.9.0-5build1 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-25ubuntu1 g++-13-s390x-linux-gnu_13.2.0-25ubuntu1 g++-s390x-linux-gnu_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-25ubuntu1 gcc-13-base_13.2.0-25ubuntu1 gcc-13-s390x-linux-gnu_13.2.0-25ubuntu1 gcc-14-base_14.1.0-1ubuntu1 gcc-s390x-linux-gnu_4:13.2.0-7ubuntu1 gettext_0.21-14ubuntu2 gettext-base_0.21-14ubuntu2 gfortran_4:13.2.0-7ubuntu1 gfortran-13_13.2.0-25ubuntu1 gfortran-13-s390x-linux-gnu_13.2.0-25ubuntu1 gfortran-s390x-linux-gnu_4:13.2.0-7ubuntu1 gpg_2.4.4-2ubuntu17 gpg-agent_2.4.4-2ubuntu17 gpgconf_2.4.4-2ubuntu17 gpgv_2.4.4-2ubuntu17 grep_3.11-4build1 groff-base_1.23.0-4 gzip_1.12-1ubuntu3 hdf5-helpers_1.10.10+repack-3.1ubuntu4 hostname_3.23+nmu2ubuntu2 icu-devtools_74.2-1ubuntu3 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-6ubuntu2 libacl1_2.3.2-2 libaec-dev_1.1.3-1 libaec0_1.1.3-1 libapparmor1_4.0.1-0ubuntu1 libapt-pkg6.0t64_2.9.4 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4build1 libarpack2-dev_3.9.1-1.1build2 libarpack2t64_3.9.1-1.1build2 libasan8_14.1.0-1ubuntu1 libassuan0_2.5.6-1build1 libatomic1_14.1.0-1ubuntu1 libattr1_1:2.5.2-1build1 libaudit-common_1:3.1.2-2.1build1 libaudit1_1:3.1.2-2.1build1 libbinutils_2.42-4ubuntu2 libblas-dev_3.12.0-3build1 libblas3_3.12.0-3build1 libblkid1_2.39.3-9ubuntu6 libbrotli1_1.1.0-2build2 libbz2-1.0_1.0.8-5.1 libbz2-dev_1.0.8-5.1 libc-bin_2.39-0ubuntu8.1 libc-dev-bin_2.39-0ubuntu8.1 libc6_2.39-0ubuntu8.1 libc6-dev_2.39-0ubuntu8.1 libcap-ng0_0.8.5-1 libcap2_1:2.66-5ubuntu2 libcc1-0_14.1.0-1ubuntu1 libcom-err2_1.47.0-2.4~exp1ubuntu4 libcrypt-dev_1:4.4.36-4build1 libcrypt1_1:4.4.36-4build1 libcryptsetup12_2:2.7.0-1ubuntu5 libctf-nobfd0_2.42-4ubuntu2 libctf0_2.42-4ubuntu2 libcurl3t64-gnutls_8.8.0-1ubuntu1 libcurl4-gnutls-dev_8.8.0-1ubuntu1 libcurl4t64_8.8.0-1ubuntu1 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.271ubuntu3 libdebhelper-perl_13.14.1ubuntu5 libdevmapper1.02.1_2:1.02.185-3ubuntu4 libdpkg-perl_1.22.6ubuntu10 libdw1t64_0.191-1 libelf1t64_0.191-1 libext2fs2t64_1.47.0-2.4~exp1ubuntu4 libfakeroot_1.34-1 libfdisk1_2.39.3-9ubuntu6 libffi8_3.4.6-1build1 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_1.14.0-1 libgcc-13-dev_13.2.0-25ubuntu1 libgcc-s1_14.1.0-1ubuntu1 libgcrypt20_1.10.3-3 libgdbm-compat4t64_1.23-5.1build1 libgdbm6t64_1.23-5.1build1 libgfortran-13-dev_13.2.0-25ubuntu1 libgfortran5_14.1.0-1ubuntu1 libgmp10_2:6.3.0+dfsg-2ubuntu6 libgnutls30t64_3.8.5-2ubuntu1 libgomp1_14.1.0-1ubuntu1 libgpg-error-l10n_1.49-2 libgpg-error0_1.49-2 libgpm2_1.20.7-11 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 libicu-dev_74.2-1ubuntu3 libicu74_74.2-1ubuntu3 libidn2-0_2.3.7-2build1 libip4tc2_1.8.10-3ubuntu2 libisl23_0.26-3build1 libitm1_14.1.0-1ubuntu1 libjansson4_2.14-2build2 libjpeg-dev_8c-2ubuntu11 libjpeg-turbo8_2.1.5-2ubuntu2 libjpeg-turbo8-dev_2.1.5-2ubuntu2 libjpeg8_8c-2ubuntu11 libjpeg8-dev_8c-2ubuntu11 libjson-c5_0.17-1build1 libk5crypto3_1.20.1-6ubuntu2 libkeyutils1_1.6.3-3build1 libkmod2_31+20240202-2ubuntu7 libkrb5-3_1.20.1-6ubuntu2 libkrb5support0_1.20.1-6ubuntu2 liblapack-dev_3.12.0-3build1 liblapack3_3.12.0-3build1 libldap2_2.6.7+dfsg-1~exp1ubuntu8 liblocale-gettext-perl_1.07-7 liblockfile-bin_1.17-1build3 liblockfile1_1.17-1build3 liblz4-1_1.9.4-2 liblzma-dev_5.6.1+really5.4.5-1 liblzma5_5.6.1+really5.4.5-1 libmagic-mgc_1:5.45-3build1 libmagic1t64_1:5.45-3build1 libmd0_1.1.0-2build1 libmount1_2.39.3-9ubuntu6 libmpc3_1.3.1-1build1 libmpfr6_4.2.1-1build1 libncurses-dev_6.5-2 libncurses6_6.5-2 libncursesw6_6.5-2 libnetcdf-dev_1:4.9.2-6 libnetcdf19t64_1:4.9.2-6 libnettle8t64_3.9.1-2.2build1 libnghttp2-14_1.61.0-1 libnpth0t64_1.6-3.1build1 libnsl-dev_1.3.0-3build3 libnsl2_1.3.0-3build3 libnss-nis_3.1-0ubuntu7 libnss-nisplus_1.3-5build1 libp11-kit0_0.25.3-4ubuntu2 libpam-modules_1.5.3-7ubuntu1 libpam-modules-bin_1.5.3-7ubuntu1 libpam-runtime_1.5.3-7ubuntu1 libpam0g_1.5.3-7ubuntu1 libpcre2-8-0_10.42-4ubuntu2 libperl5.36_5.36.0-9ubuntu1 libperl5.38t64_5.38.2-4 libpipeline1_1.5.7-2 libpng16-16t64_1.6.43-5build1 libproc2-0_2:4.0.4-4ubuntu3 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+dfsg1-5ubuntu3 libsasl2-modules-db_2.1.28+dfsg1-5ubuntu3 libseccomp2_2.5.5-1ubuntu3 libselinux1_3.5-2ubuntu2 libsemanage-common_3.5-1build5 libsemanage2_3.5-1build5 libsepol2_3.5-2build1 libsframe1_2.42-4ubuntu2 libsmartcols1_2.39.3-9ubuntu6 libsqlite3-0_3.45.3-1 libss2_1.47.0-2.4~exp1ubuntu4 libssh-4_0.10.6-2build2 libssl-dev_3.0.13-0ubuntu4 libssl3t64_3.0.13-0ubuntu4 libstdc++-13-dev_13.2.0-25ubuntu1 libstdc++6_14.1.0-1ubuntu1 libsystemd-shared_256~rc3-1ubuntu1 libsystemd0_256~rc3-1ubuntu1 libsz2_1.1.3-1 libtasn1-6_4.19.0-3build1 libtext-charwidth-perl_0.04-11build3 libtext-iconv-perl_1.7-8build3 libtext-wrapi18n-perl_0.06-10 libtinfo6_6.5-2 libtirpc-common_1.3.4+ds-1.3 libtirpc-dev_1.3.4+ds-1.3 libtirpc3t64_1.3.4+ds-1.3 libtool_2.4.7-7build1 libubsan1_14.1.0-1ubuntu1 libuchardet0_0.0.8-1build1 libudev1_256~rc3-1ubuntu1 libunistring2_1.0-2 libunistring5_1.2-1 libuuid1_2.39.3-9ubuntu6 libxml2_2.12.7+dfsg-2 libxml2-dev_2.12.7+dfsg-2 libxxhash0_0.8.2-2build1 libzstd1_1.5.5+dfsg2-2build1 linux-libc-dev_6.8.0-31.31 lockfile-progs_0.1.19+nmu1 login_1:4.13+dfsg1-4ubuntu5 logsave_1.47.0-2.4~exp1ubuntu4 lto-disabled-list_48 m4_1.4.19-4build1 make_4.3-4.1build2 man-db_2.12.1-1 mawk_1.3.4.20240123-1build1 mount_2.39.3-9ubuntu6 ncurses-base_6.5-2 ncurses-bin_6.5-2 netcdf-bin_1:4.9.2-6 openssl_3.0.13-0ubuntu4 optipng_0.7.8+ds-1build2 passwd_1:4.13+dfsg1-4ubuntu5 patch_2.7.6-7build3 perl_5.38.2-4 perl-base_5.38.2-4 perl-modules-5.36_5.36.0-9ubuntu1 perl-modules-5.38_5.38.2-4 pinentry-curses_1.2.1-3ubuntu5 pkgbinarymangler_154 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.4-4ubuntu3 psmisc_23.7-1build1 readline-common_8.2-4build1 rpcsvc-proto_1.4.2-0ubuntu7 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2build1 sensible-utils_0.0.22 systemd_256~rc3-1ubuntu1 systemd-dev_256~rc3-1ubuntu1 systemd-sysv_256~rc3-1ubuntu1 sysvinit-utils_3.08-6ubuntu3 tar_1.35+dfsg-3build1 tzdata_2024a-4ubuntu1 ubuntu-keyring_2023.11.28.1 util-linux_2.39.3-9ubuntu6 uuid-runtime_2.39.3-9ubuntu6 xz-utils_5.6.1+really5.4.5-1 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-4 Maintainer: Debichem Team 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 armhf mips64el ppc64el riscv64], libreadline-dev, netcdf-bin Package-List: cpptraj deb science optional arch=any Checksums-Sha1: b326e493769758a5e5e29173898e049c6a60e9a2 28363024 cpptraj_5.1.0+dfsg.orig.tar.xz 01a62f884bc2739ce8f799c62b3e260f8205b82c 6084 cpptraj_5.1.0+dfsg-4.debian.tar.xz Checksums-Sha256: 89e279bbb5d35db4d2599fa98322bb8c4b876ce6117f8896e75520a3da1182f3 28363024 cpptraj_5.1.0+dfsg.orig.tar.xz 0e96d529626c3f73247201aa16e7b8c8afba853694be1a331a3ae73a5fe4bf3c 6084 cpptraj_5.1.0+dfsg-4.debian.tar.xz Files: bf932a3aed87ad43645613135c712505 28363024 cpptraj_5.1.0+dfsg.orig.tar.xz 6e26922e03d8c1c199dfd28f36581cba 6084 cpptraj_5.1.0+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmZCJuQSHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKHhmEP/igOOwHV5yAXVBSlVNtYT+DL2jzFwcLP /LYplbd5pvvDm9Aw8+6fAj7aDwFLhCQJg9/MR+Xu90VQ7ymrdWRRnqX0RcwggbPs JGGG0RRU0NrZnbyxTKD1Z/H6w1NkenykJpnoOrkBlFMZJc9kCAdWnLwKFSxcg2Xl SX11O3s7QwLrjlqcCF2gXy3eWGjKJHLiW0WN+O+j3PNYd5QcnrfvtFvV4lUoTv6q 9UFvejofK1hkx1ysw/P/V2DlAawOzX0BVzRBU9xCwXAXFv0lu5JJWdD66NWaCb0N ja6vW2eZTvs5Ble8s1AoF0EevpTh6PICJ75e6T/PIS2AH/DbBmCo6ATEbpnALd3Z pj4D1HTrBlaRw60ZlyqKK4iqKd35KmSJRDT1Fa2YilCBInJDd1fZQHgEVPj2WF7S DsyS59VonzRUmCznTxKPFybDCmUdVveN6jpxWpcYjYg+cO/L5rPXERwU28jDpCuK QWZz+AK0tzQLm05TFV4Qg7QJFgn/mIOPYF1HQgsGtJ/V0RNSBd+/NeKWGF1qSX7y +eERIOK+8DrYjOebe24bRUs/lR1Vx+HTxpAQw47+VZBvogGbyDfp1AiElZvb0Ia4 pQ5omJd6jxqbHFP0HdxVwMZYDPFJlkYN5O1sHQTFq+3wYzEhmvIzE0tV9fqCOBKw gP/0H6lIFBch =XQSu -----END PGP SIGNATURE----- gpgv: Signature made Mon May 13 14:42:44 2024 UTC gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./cpptraj_5.1.0+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting cpptraj in /<> dpkg-source: info: unpacking cpptraj_5.1.0+dfsg.orig.tar.xz dpkg-source: info: unpacking cpptraj_5.1.0+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series 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-28443482 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-28443482 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-28443482 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-4 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture s390x 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/s390x-linux-gnu --with-fftw3=/usr/lib/s390x-linux-gnu --with-readline=/usr/lib/s390x-linux-gnu arpack specified: /usr/lib/s390x-linux-gnu fftw3 specified: /usr/lib/s390x-linux-gnu readline specified: /usr/lib/s390x-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 vmdplugin disabled due to nonfree source. Configuration summary: Build type: Serial Options: netcdf bzlib tng zlib arpack lapack blas fftw3 readline xdrfile Target platform: Linux, 32-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 CXX Action_HydrogenBond.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:76:23: 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:76:57: 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_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 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: CXX Analysis_Corr.cpp /usr/include/c++/13/bits/stl_vector.h:809:23: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] 809 | { _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:809:23: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] 809 | { _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; | ^~~~~~~ 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) | ~~~~~~~~~~~~~~~~~^~~~~~~~ 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_Analyze.cpp CXX Exec_Calc.cpp CXX Exec_CatCrd.cpp CXX Exec_Change.cpp CXX Exec_ClusterMap.cpp CXX Exec_CombineCoords.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.204402]’ 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.204401]’ 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.204400]’ 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.204387.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.204386.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.204385.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_Commands.cpp CXX Exec_CompareTop.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_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 CXX Action_Esander.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 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 CC xdr_seek.c CC xdrfile_trr.c CC xdrfile_xtc.c Skipping bundled ARPACK build cd tng && make all make[3]: Entering directory '/<>/src/tng' CC md5.c CC tng_io.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 tng_compress.c CC coder.c CC warnmalloc.c CC fixpoint.c CC xtc3.c CC bwlzh.c CC xtc2.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 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/s390x-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/s390x-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/s390x-linux-gnu/lib -lfftw3 -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 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. ******************************************************************************** TEST: /<>/unitTests/NameType CPPTRAJ: NameType class unit test. make[5]: Entering directory '/<>/unitTests/NameType' g++ -Wall -O3 -g -O2 -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-4 -std=gnu++11 -I/<>/src -c -o main.o main.cpp -rwxr-xr-x 1 buildd buildd 159404920 May 29 10:27 ../bin/cpptraj -rwxr-xr-x 1 buildd buildd 159404920 May 29 10:27 ../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 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -Wall -O3 -g -O2 -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-4 -std=gnu++11 -I/<>/src -c -o NameType.o /<>/src/NameType.cpp 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 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -Wall -O3 -g -O2 -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-4 -std=gnu++11 -I/<>/src -c -o CpptrajStdio.o /<>/src/CpptrajStdio.cpp All 8 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_trajout_framerange CPPTRAJ: Trajout Frame Range [Amber Restart] CPPTRAJ: Trajout Frame Range [Amber Coordinates] All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_PerResRMSD CPPTRAJ: Per-Residue RMSD Test. g++ -o a.out main.o NameType.o CpptrajStdio.o 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 CPPTRAJ: Solute Hbond test with disk caching CPPTRAJ: Solute-solvent hbond test CPPTRAJ: Hbond, no intramolecular hydrogen bonds test CPPTRAJ: Hbond, specified solute masks 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 -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-4 -std=gnu++11 -I/<>/src -c -o main.o main.cpp CPPTRAJ: Hbond, no angle cutoff test CPPTRAJ: Hbond, Bridge nointramol 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 -Wall -O3 -g -O2 -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-4 -std=gnu++11 -I/<>/src -c -o ArgList.o /<>/src/ArgList.cpp 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 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 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. g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -Wall -O3 -g -O2 -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-4 -std=gnu++11 -I/<>/src -c -o CpptrajStdio.o /<>/src/CpptrajStdio.cpp ******************************************************************************** TEST: /<>/test/Test_Outtraj CPPTRAJ: RMSD Test with outtraj. g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -Wall -O3 -g -O2 -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-4 -std=gnu++11 -I/<>/src -c -o StringRoutines.o /<>/src/StringRoutines.cpp 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 g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o CPPTRAJ: AtomMap with 'rmsfit' CPPTRAJ: Atom map charmm->amber atom order CPPTRAJ: Atom map charmm->amber atom order, by residue All 9 comparisons passed. ******************************************************************************** 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 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 make[5]: Leaving directory '/<>/unitTests/ArgList' Unit test passed. make[4]: Leaving directory '/<>/unitTests' make[3]: Leaving directory '/<>/unitTests' 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 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 CPPTRAJ: Cluster, random 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: 16901 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. Error: Mode 33554432; currently only mode 2 for CCP4 files is supported. Error: reading datafile fav8.guv.O.1.ccp4 Error: Could not read data file 'fav8.guv.O.1.ccp4'. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: cpptraj exited with status 1 1 out of 1 executions exited with an error. 2 out of 2 comparisons failed. ******************************************************************************** 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 Error: # atoms in TRX file (0) does not match # atoms in parm nvt.protein.mol2 (1960) Error: Could not set up 'nvt.2frame.trr' for reading. Error: Could not set up input trajectory 'nvt.2frame.trr'. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: cpptraj exited with status 1 CPPTRAJ: TRR force/velocity read -> TRR write test Error: # atoms in TRX file (0) does not match # atoms in parm nvt.protein.mol2 (1960) Error: Could not set up 'nvt.2frame.trr' for reading. Error: Could not set up input trajectory 'nvt.2frame.trr'. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: cpptraj exited with status 1 CPPTRAJ: CRD => TRR CPPTRAJ: TRR => CRD Error: # atoms in TRX file (0) does not match # atoms in parm tz2.truncoct.parm7 (5827) Error: Could not set up 'mop.trr' for reading. Error: Could not set up input trajectory 'mop.trr'. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: cpptraj exited with status 1 CPPTRAJ: CRD(1-5) => TRR CPPTRAJ: CRD(6-10) => TRR CPPTRAJ: TRR (appended) => CRD Error: # atoms in TRX file (0) does not match # atoms in parm tz2.truncoct.parm7 (5827) Error: Could not set up 'mop.trr' for reading. Error: Could not set up input trajectory 'mop.trr'. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: cpptraj exited with status 1 CPPTRAJ: GMX: CRD with offset CPPTRAJ: GMX: TRR with offset Error: # atoms in TRX file (0) does not match # atoms in parm tz2.truncoct.parm7 (5827) Error: Could not set up 'mop.trr' for reading. Error: Could not set up input trajectory 'mop.trr'. 1 errors encountered reading input. Error: Error(s) occurred during execution. Error: cpptraj exited with status 1 5 out of 9 executions exited with an error. 5 out of 5 comparisons failed. ******************************************************************************** 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 TNG library: General info block contents corrupt. Hashes do not match. tng_io.c: 2370 TNG library: Molecules block contents corrupt. Hashes do not match. tng_io.c: 3277 TNG library: Data block contents corrupt (PARTIAL CHARGES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (ATOM MASSES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Frame set block contents corrupt (first frame 0). Hashes do not match. tng_io.c: 3701 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: General info block contents corrupt. Hashes do not match. tng_io.c: 2370 TNG library: Molecules block contents corrupt. Hashes do not match. tng_io.c: 3277 TNG library: Data block contents corrupt (PARTIAL CHARGES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (ATOM MASSES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Frame set block contents corrupt (first frame 0). Hashes do not match. tng_io.c: 3701 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Frame set block contents corrupt (first frame 0). Hashes do not match. tng_io.c: 3701 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Frame set block contents corrupt (first frame 0). Hashes do not match. tng_io.c: 3701 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Frame set block contents corrupt (first frame 0). Hashes do not match. tng_io.c: 3701 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 CPPTRAJ: TNG read test (with offset) TNG library: General info block contents corrupt. Hashes do not match. tng_io.c: 2370 TNG library: Molecules block contents corrupt. Hashes do not match. tng_io.c: 3277 TNG library: Data block contents corrupt (PARTIAL CHARGES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (ATOM MASSES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Frame set block contents corrupt (first frame 0). Hashes do not match. tng_io.c: 3701 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: General info block contents corrupt. Hashes do not match. tng_io.c: 2370 TNG library: Molecules block contents corrupt. Hashes do not match. tng_io.c: 3277 TNG library: Data block contents corrupt (PARTIAL CHARGES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (ATOM MASSES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Frame set block contents corrupt (first frame 0). Hashes do not match. tng_io.c: 3701 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Frame set block contents corrupt (first frame 0). Hashes do not match. tng_io.c: 3701 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Frame set block contents corrupt (first frame 0). Hashes do not match. tng_io.c: 3701 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Frame set block contents corrupt (first frame 0). Hashes do not match. tng_io.c: 3701 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: General info block contents corrupt. Hashes do not match. tng_io.c: 2370 TNG library: Molecules block contents corrupt. Hashes do not match. tng_io.c: 3277 TNG library: Data block contents corrupt (PARTIAL CHARGES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (ATOM MASSES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Frame set block contents corrupt (first frame 0). Hashes do not match. tng_io.c: 3701 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: General info block contents corrupt. Hashes do not match. tng_io.c: 2370 TNG library: Molecules block contents corrupt. Hashes do not match. tng_io.c: 3277 TNG library: Data block contents corrupt (PARTIAL CHARGES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (ATOM MASSES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Frame set block contents corrupt (first frame 0). Hashes do not match. tng_io.c: 3701 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Frame set block contents corrupt (first frame 0). Hashes do not match. tng_io.c: 3701 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Frame set block contents corrupt (first frame 0). Hashes do not match. tng_io.c: 3701 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Frame set block contents corrupt (first frame 0). Hashes do not match. tng_io.c: 3701 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (LAMBDAS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (POSITIONS). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (FORCES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (VELOCITIES). Hashes do not match. tng_io.c: 6445 TNG library: Data block contents corrupt (BOX SHAPE). Hashes do not match. tng_io.c: 6445 6 out of 6 comparisons failed. ******************************************************************************** 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. OpenMM basic energy minimization tests requires OpenMM. Cpptraj was compiled without OpenMM support. Skipped test: OpenMM basic energy minimization tests All 4 comparisons passed. 1 comparisons skipped. ******************************************************************************** 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 '/<>' /usr/bin/make -C test summary make[2]: Entering directory '/<>/test' -rwxr-xr-x 1 buildd buildd 159404920 May 29 10:27 ../bin/cpptraj ===================== TEST SUMMARY ====================== 832 out of 855 comparisons OK (16 failed, 0 warnings, 7 skipped). 468 out of 475 program executions completed. 165 out of 173 tests completed with no issues. 2 tests skipped. ========================================================= make[2]: *** [Makefile:662: summary] Error 23 make[2]: Leaving directory '/<>/test' make[1]: *** [debian/rules:17: override_dh_auto_test] Error 2 make[1]: Leaving directory '/<>' make: *** [debian/rules:10: binary-arch] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2024-05-29T10:28:13Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build Type: any Build-Space: 1449412 Build-Time: 382 Distribution: oracular-proposed Fail-Stage: build Host Architecture: s390x Install-Time: 11 Job: cpptraj_5.1.0+dfsg-4.dsc Machine Architecture: s390x Package: cpptraj Package-Time: 398 Source-Version: 5.1.0+dfsg-4 Space: 1449412 Status: attempted Version: 5.1.0+dfsg-4 -------------------------------------------------------------------------------- Finished at 2024-05-29T10:28:13Z Build needed 00:06:38, 1449412k disk space E: Build failure (dpkg-buildpackage died) RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=oracular --arch=s390x PACKAGEBUILD-28443482 Scanning for processes to kill in build PACKAGEBUILD-28443482