https://launchpad.net/ubuntu/+source/cpptraj/5.1.0+dfsg-3build1/+build/26342895 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-101 5.4.0-152-generic #169-Ubuntu SMP Tue Jun 6 22:23:09 UTC 2023 x86_64 Buildd toolchain package versions: launchpad-buildd_233~634~ubuntu20.04.1 python3-lpbuildd_233~634~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. Syncing the system clock with the buildd NTP service... 27 Jun 18:06:56 ntpdate[1842]: adjust time server 10.131.248.1 offset -0.001279 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26342895 --image-type chroot /home/buildd/filecache-default/1fc1752c0976ad9eb0e621fd063fde252dab04e3 Creating target for build PACKAGEBUILD-26342895 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26342895 Starting target for build PACKAGEBUILD-26342895 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26342895 'deb http://ftpmaster.internal/ubuntu mantic main universe' 'deb http://ftpmaster.internal/ubuntu mantic-security main universe' 'deb http://ftpmaster.internal/ubuntu mantic-updates main universe' 'deb http://ftpmaster.internal/ubuntu mantic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-26342895 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26342895 Updating target for build PACKAGEBUILD-26342895 Get:1 http://ftpmaster.internal/ubuntu mantic InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu mantic-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu mantic-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu mantic-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main amd64 Packages [1400 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main Translation-en [515 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/universe amd64 Packages [15.1 MB] Get:8 http://ftpmaster.internal/ubuntu mantic/universe Translation-en [5937 kB] Get:9 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 Packages [65.9 kB] Get:10 http://ftpmaster.internal/ubuntu mantic-proposed/main Translation-en [25.4 kB] Get:11 http://ftpmaster.internal/ubuntu mantic-proposed/universe amd64 Packages [422 kB] Get:12 http://ftpmaster.internal/ubuntu mantic-proposed/universe Translation-en [166 kB] Fetched 24.2 MB in 3s (8036 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-13-base libproc2-0 The following packages will be upgraded: adduser advancecomp apt base-files bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils ca-certificates coreutils cpp cpp-12 dash debconf diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-12 gcc gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv grep hostname libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libext2fs2 libfakeroot libfdisk1 libgcc-12-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgprofng0 libgssapi-krb5-2 libisl23 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblsan0 liblzma5 libmd0 libmount1 libmpfr6 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libpng16-16 libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libtsan2 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev logsave lsb-base lto-disabled-list mawk mount ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.36 pkgbinarymangler procps readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tar tzdata usrmerge util-linux util-linux-extra xz-utils zlib1g 139 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 111 MB of archives. After this operation, 286 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu mantic/main amd64 libcrypt-dev amd64 1:4.4.35-1 [112 kB] Get:2 http://ftpmaster.internal/ubuntu mantic/main amd64 libc6-dev amd64 2.37-0ubuntu2 [2092 kB] Get:3 http://ftpmaster.internal/ubuntu mantic/main amd64 libc-dev-bin amd64 2.37-0ubuntu2 [20.0 kB] Get:4 http://ftpmaster.internal/ubuntu mantic/main amd64 libcrypt1 amd64 1:4.4.35-1 [82.1 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main amd64 linux-libc-dev amd64 6.3.0-7.7 [1544 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main amd64 libc6 amd64 2.37-0ubuntu2 [3179 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/main amd64 libc-bin amd64 2.37-0ubuntu2 [669 kB] Get:8 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-13-base amd64 13.1.0-6ubuntu1 [42.0 kB] Get:9 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcc-s1 amd64 13.1.0-6ubuntu1 [62.5 kB] Get:10 http://ftpmaster.internal/ubuntu mantic/main amd64 base-files amd64 13ubuntu1 [74.0 kB] Get:11 http://ftpmaster.internal/ubuntu mantic/main amd64 bash amd64 5.2.15-2ubuntu1 [795 kB] Get:12 http://ftpmaster.internal/ubuntu mantic/main amd64 bsdutils amd64 1:2.38.1-5ubuntu2 [91.5 kB] Get:13 http://ftpmaster.internal/ubuntu mantic/main amd64 coreutils amd64 9.1-1ubuntu2 [1407 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main amd64 liblzma5 amd64 5.4.1-0.2 [125 kB] Get:15 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcrypt20 amd64 1.10.1-3ubuntu1 [529 kB] Get:16 http://ftpmaster.internal/ubuntu mantic/main amd64 libstdc++6 amd64 13.1.0-6ubuntu1 [772 kB] Get:17 http://ftpmaster.internal/ubuntu mantic/main amd64 libacl1 amd64 2.3.1-3 [16.4 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main amd64 libapparmor1 amd64 3.0.8-1ubuntu3 [46.3 kB] Get:19 http://ftpmaster.internal/ubuntu mantic/main amd64 libaudit-common all 1:3.0.9-1 [5142 B] Get:20 http://ftpmaster.internal/ubuntu mantic/main amd64 libcap-ng0 amd64 0.8.3-1build2 [15.3 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main amd64 libaudit1 amd64 1:3.0.9-1 [46.0 kB] Get:22 http://ftpmaster.internal/ubuntu mantic/main amd64 libblkid1 amd64 2.38.1-5ubuntu2 [111 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main amd64 libcap2 amd64 1:2.66-4ubuntu1 [29.4 kB] Get:24 http://ftpmaster.internal/ubuntu mantic/main amd64 libperl5.36 amd64 5.36.0-7ubuntu1 [4834 kB] Get:25 http://ftpmaster.internal/ubuntu mantic/main amd64 perl amd64 5.36.0-7ubuntu1 [235 kB] Get:26 http://ftpmaster.internal/ubuntu mantic/main amd64 perl-base amd64 5.36.0-7ubuntu1 [1784 kB] Get:27 http://ftpmaster.internal/ubuntu mantic/main amd64 perl-modules-5.36 all 5.36.0-7ubuntu1 [2984 kB] Get:28 http://ftpmaster.internal/ubuntu mantic/main amd64 libdb5.3 amd64 5.3.28+dfsg2-1 [742 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/main amd64 zlib1g amd64 1:1.2.13.dfsg-1ubuntu4 [61.2 kB] Get:30 http://ftpmaster.internal/ubuntu mantic/main amd64 debconf all 1.5.82 [125 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main amd64 libssl3 amd64 3.0.9-1ubuntu1 [1901 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main amd64 libzstd1 amd64 1.5.4+dfsg2-5 [292 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main amd64 libkmod2 amd64 30+20221128-1ubuntu1 [49.5 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main amd64 libpcre2-8-0 amd64 10.42-1 [228 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main amd64 libselinux1 amd64 3.4-1build4 [78.1 kB] Get:36 http://ftpmaster.internal/ubuntu mantic/main amd64 libmount1 amd64 2.38.1-5ubuntu2 [121 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam0g amd64 1.5.2-6ubuntu1 [65.9 kB] Get:38 http://ftpmaster.internal/ubuntu mantic/main amd64 libseccomp2 amd64 2.5.4-1ubuntu3 [49.1 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/main amd64 systemd-sysv amd64 252.5-2ubuntu3 [11.5 kB] Get:40 http://ftpmaster.internal/ubuntu mantic/main amd64 systemd amd64 252.5-2ubuntu3 [3002 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/main amd64 libsystemd-shared amd64 252.5-2ubuntu3 [1832 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main amd64 libargon2-1 amd64 0~20190702+dfsg-3 [20.3 kB] Get:43 http://ftpmaster.internal/ubuntu mantic/main amd64 libudev1 amd64 252.5-2ubuntu3 [150 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/main amd64 libdevmapper1.02.1 amd64 2:1.02.185-2ubuntu1 [139 kB] Get:45 http://ftpmaster.internal/ubuntu mantic/main amd64 libuuid1 amd64 2.38.1-5ubuntu2 [32.7 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main amd64 libcryptsetup12 amd64 2:2.6.1-4ubuntu1 [243 kB] Get:47 http://ftpmaster.internal/ubuntu mantic/main amd64 libfdisk1 amd64 2.38.1-5ubuntu2 [144 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/main amd64 libp11-kit0 amd64 0.24.1-2ubuntu1 [248 kB] Get:49 http://ftpmaster.internal/ubuntu mantic/main amd64 mount amd64 2.38.1-5ubuntu2 [114 kB] Get:50 http://ftpmaster.internal/ubuntu mantic/main amd64 libsystemd0 amd64 252.5-2ubuntu3 [389 kB] Get:51 http://ftpmaster.internal/ubuntu mantic/main amd64 libapt-pkg6.0 amd64 2.7.1 [930 kB] Get:52 http://ftpmaster.internal/ubuntu mantic/main amd64 tar amd64 1.34+dfsg-1.2ubuntu1 [293 kB] Get:53 http://ftpmaster.internal/ubuntu mantic/main amd64 dpkg amd64 1.21.22ubuntu1 [1393 kB] Get:54 http://ftpmaster.internal/ubuntu mantic/main amd64 dash amd64 0.5.12-2ubuntu1 [88.2 kB] Get:55 http://ftpmaster.internal/ubuntu mantic/main amd64 diffutils amd64 1:3.8-4 [176 kB] Get:56 http://ftpmaster.internal/ubuntu mantic/main amd64 findutils amd64 4.9.0-4ubuntu1 [299 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main amd64 grep amd64 3.8-5 [160 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/main amd64 hostname amd64 3.23+nmu1ubuntu1 [11.0 kB] Get:59 http://ftpmaster.internal/ubuntu mantic/main amd64 ncurses-bin amd64 6.4-4 [185 kB] Get:60 http://ftpmaster.internal/ubuntu mantic/main amd64 sed amd64 4.9-1 [193 kB] Get:61 http://ftpmaster.internal/ubuntu mantic/main amd64 libsmartcols1 amd64 2.38.1-5ubuntu2 [59.5 kB] Get:62 http://ftpmaster.internal/ubuntu mantic/main amd64 util-linux-extra amd64 2.38.1-5ubuntu2 [83.8 kB] Get:63 http://ftpmaster.internal/ubuntu mantic/main amd64 util-linux amd64 2.38.1-5ubuntu2 [1075 kB] Get:64 http://ftpmaster.internal/ubuntu mantic/main amd64 ncurses-base all 6.4-4 [23.3 kB] Get:65 http://ftpmaster.internal/ubuntu mantic/main amd64 sysvinit-utils amd64 3.06-4ubuntu1 [33.0 kB] Get:66 http://ftpmaster.internal/ubuntu mantic/main amd64 lsb-base all 11.6 [4606 B] Get:67 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 adduser all 3.134ubuntu1 [136 kB] Get:68 http://ftpmaster.internal/ubuntu mantic/main amd64 gpgv amd64 2.2.40-1.1ubuntu1 [140 kB] Get:69 http://ftpmaster.internal/ubuntu mantic/main amd64 libgnutls30 amd64 3.7.9-2ubuntu1 [999 kB] Get:70 http://ftpmaster.internal/ubuntu mantic/main amd64 apt amd64 2.7.1 [1359 kB] Get:71 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam-modules-bin amd64 1.5.2-6ubuntu1 [47.3 kB] Get:72 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam-modules amd64 1.5.2-6ubuntu1 [284 kB] Get:73 http://ftpmaster.internal/ubuntu mantic/main amd64 logsave amd64 1.47.0-1ubuntu1 [14.2 kB] Get:74 http://ftpmaster.internal/ubuntu mantic/main amd64 libext2fs2 amd64 1.47.0-1ubuntu1 [212 kB] Get:75 http://ftpmaster.internal/ubuntu mantic/main amd64 e2fsprogs amd64 1.47.0-1ubuntu1 [598 kB] Get:76 http://ftpmaster.internal/ubuntu mantic/main amd64 libattr1 amd64 1:2.5.1-4 [12.4 kB] Get:77 http://ftpmaster.internal/ubuntu mantic/main amd64 libdebconfclient0 amd64 0.267ubuntu1 [7892 B] Get:78 http://ftpmaster.internal/ubuntu mantic/main amd64 libmd0 amd64 1.1.0-1 [26.9 kB] Get:79 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam-runtime all 1.5.2-6ubuntu1 [41.5 kB] Get:80 http://ftpmaster.internal/ubuntu mantic/main amd64 libsemanage-common all 3.4-1build4 [9852 B] Get:81 http://ftpmaster.internal/ubuntu mantic/main amd64 libsepol2 amd64 3.4-2.1 [301 kB] Get:82 http://ftpmaster.internal/ubuntu mantic/main amd64 libsemanage2 amd64 3.4-1build4 [92.7 kB] Get:83 http://ftpmaster.internal/ubuntu mantic/main amd64 libncurses6 amd64 6.4-4 [112 kB] Get:84 http://ftpmaster.internal/ubuntu mantic/main amd64 libncursesw6 amd64 6.4-4 [147 kB] Get:85 http://ftpmaster.internal/ubuntu mantic/main amd64 libtinfo6 amd64 6.4-4 [103 kB] Get:86 http://ftpmaster.internal/ubuntu mantic/main amd64 usrmerge all 35ubuntu1 [58.2 kB] Get:87 http://ftpmaster.internal/ubuntu mantic/main amd64 libcom-err2 amd64 1.47.0-1ubuntu1 [14.5 kB] Get:88 http://ftpmaster.internal/ubuntu mantic/main amd64 libproc2-0 amd64 2:4.0.3-1ubuntu1 [55.9 kB] Get:89 http://ftpmaster.internal/ubuntu mantic/main amd64 libss2 amd64 1.47.0-1ubuntu1 [16.8 kB] Get:90 http://ftpmaster.internal/ubuntu mantic/main amd64 mawk amd64 1.3.4.20230525-1 [113 kB] Get:91 http://ftpmaster.internal/ubuntu mantic/main amd64 procps amd64 2:4.0.3-1ubuntu1 [609 kB] Get:92 http://ftpmaster.internal/ubuntu mantic/main amd64 sensible-utils all 0.0.20 [19.6 kB] Get:93 http://ftpmaster.internal/ubuntu mantic/main amd64 openssl amd64 3.0.9-1ubuntu1 [1189 kB] Get:94 http://ftpmaster.internal/ubuntu mantic/main amd64 ca-certificates all 20230311ubuntu1 [152 kB] Get:95 http://ftpmaster.internal/ubuntu mantic/main amd64 libgssapi-krb5-2 amd64 1.20.1-2 [142 kB] Get:96 http://ftpmaster.internal/ubuntu mantic/main amd64 libkrb5-3 amd64 1.20.1-2 [346 kB] Get:97 http://ftpmaster.internal/ubuntu mantic/main amd64 libkrb5support0 amd64 1.20.1-2 [32.7 kB] Get:98 http://ftpmaster.internal/ubuntu mantic/main amd64 libk5crypto3 amd64 1.20.1-2 [81.1 kB] Get:99 http://ftpmaster.internal/ubuntu mantic/main amd64 readline-common all 8.2-1.3 [55.7 kB] Get:100 http://ftpmaster.internal/ubuntu mantic/main amd64 libreadline8 amd64 8.2-1.3 [151 kB] Get:101 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libsqlite3-0 amd64 3.42.0-1 [668 kB] Get:102 http://ftpmaster.internal/ubuntu mantic/main amd64 tzdata all 2023c-4exp1ubuntu1 [271 kB] Get:103 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libpng16-16 amd64 1.6.40-1 [186 kB] Get:104 http://ftpmaster.internal/ubuntu mantic/main amd64 xz-utils amd64 5.4.1-0.2 [270 kB] Get:105 http://ftpmaster.internal/ubuntu mantic/main amd64 advancecomp amd64 2.5-1 [180 kB] Get:106 http://ftpmaster.internal/ubuntu mantic/main amd64 libgprofng0 amd64 2.40.50.20230622-1ubuntu1 [902 kB] Get:107 http://ftpmaster.internal/ubuntu mantic/main amd64 libctf0 amd64 2.40.50.20230622-1ubuntu1 [97.1 kB] Get:108 http://ftpmaster.internal/ubuntu mantic/main amd64 libctf-nobfd0 amd64 2.40.50.20230622-1ubuntu1 [99.7 kB] Get:109 http://ftpmaster.internal/ubuntu mantic/main amd64 binutils-x86-64-linux-gnu amd64 2.40.50.20230622-1ubuntu1 [2524 kB] Get:110 http://ftpmaster.internal/ubuntu mantic/main amd64 libbinutils amd64 2.40.50.20230622-1ubuntu1 [631 kB] Get:111 http://ftpmaster.internal/ubuntu mantic/main amd64 binutils amd64 2.40.50.20230622-1ubuntu1 [18.7 kB] Get:112 http://ftpmaster.internal/ubuntu mantic/main amd64 binutils-common amd64 2.40.50.20230622-1ubuntu1 [252 kB] Get:113 http://ftpmaster.internal/ubuntu mantic/main amd64 libisl23 amd64 0.26-3 [741 kB] Get:114 http://ftpmaster.internal/ubuntu mantic/main amd64 libmpfr6 amd64 4.2.0-1 [352 kB] Get:115 http://ftpmaster.internal/ubuntu mantic/main amd64 g++-12 amd64 12.3.0-3ubuntu1 [12.1 MB] Get:116 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-12 amd64 12.3.0-3ubuntu1 [21.6 MB] Get:117 http://ftpmaster.internal/ubuntu mantic/main amd64 cpp-12 amd64 12.3.0-3ubuntu1 [10.7 MB] Get:118 http://ftpmaster.internal/ubuntu mantic/main amd64 libubsan1 amd64 13.1.0-6ubuntu1 [1104 kB] Get:119 http://ftpmaster.internal/ubuntu mantic/main amd64 libstdc++-12-dev amd64 12.3.0-3ubuntu1 [2180 kB] Get:120 http://ftpmaster.internal/ubuntu mantic/main amd64 libgomp1 amd64 13.1.0-6ubuntu1 [142 kB] Get:121 http://ftpmaster.internal/ubuntu mantic/main amd64 libitm1 amd64 13.1.0-6ubuntu1 [29.5 kB] Get:122 http://ftpmaster.internal/ubuntu mantic/main amd64 libatomic1 amd64 13.1.0-6ubuntu1 [10.4 kB] Get:123 http://ftpmaster.internal/ubuntu mantic/main amd64 libasan8 amd64 13.1.0-6ubuntu1 [2827 kB] Get:124 http://ftpmaster.internal/ubuntu mantic/main amd64 liblsan0 amd64 13.1.0-6ubuntu1 [1203 kB] Get:125 http://ftpmaster.internal/ubuntu mantic/main amd64 libquadmath0 amd64 13.1.0-6ubuntu1 [153 kB] Get:126 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcc-12-dev amd64 12.3.0-3ubuntu1 [2575 kB] Get:127 http://ftpmaster.internal/ubuntu mantic/main amd64 libtsan2 amd64 13.1.0-6ubuntu1 [2599 kB] Get:128 http://ftpmaster.internal/ubuntu mantic/main amd64 libcc1-0 amd64 13.1.0-6ubuntu1 [48.1 kB] Get:129 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-12-base amd64 12.3.0-3ubuntu1 [42.7 kB] Get:130 http://ftpmaster.internal/ubuntu mantic/main amd64 g++ amd64 4:12.2.0-3ubuntu1 [1120 B] Get:131 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc amd64 4:12.2.0-3ubuntu1 [5160 B] Get:132 http://ftpmaster.internal/ubuntu mantic/main amd64 cpp amd64 4:12.2.0-3ubuntu1 [27.8 kB] Get:133 http://ftpmaster.internal/ubuntu mantic/main amd64 dpkg-dev all 1.21.22ubuntu1 [1118 kB] Get:134 http://ftpmaster.internal/ubuntu mantic/main amd64 libdpkg-perl all 1.21.22ubuntu1 [247 kB] Get:135 http://ftpmaster.internal/ubuntu mantic/main amd64 lto-disabled-list all 41 [12.4 kB] Get:136 http://ftpmaster.internal/ubuntu mantic/main amd64 libfakeroot amd64 1.31-1.2 [32.0 kB] Get:137 http://ftpmaster.internal/ubuntu mantic/main amd64 fakeroot amd64 1.31-1.2 [60.1 kB] Get:138 http://ftpmaster.internal/ubuntu mantic/main amd64 gpg amd64 2.2.40-1.1ubuntu1 [523 kB] Get:139 http://ftpmaster.internal/ubuntu mantic/main amd64 gpgconf amd64 2.2.40-1.1ubuntu1 [96.3 kB] Get:140 http://ftpmaster.internal/ubuntu mantic/main amd64 gpg-agent amd64 2.2.40-1.1ubuntu1 [216 kB] Get:141 http://ftpmaster.internal/ubuntu mantic/main amd64 pkgbinarymangler all 153 [16.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 111 MB in 1s (110 MB/s) (Reading database ... 13093 files and directories currently installed.) 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Setting up libc6-dev:amd64 (2.37-0ubuntu2) ... Setting up gpg (2.2.40-1.1ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.40.50.20230622-1ubuntu1) ... Setting up gpg-agent (2.2.40-1.1ubuntu1) ... Setting up libstdc++-12-dev:amd64 (12.3.0-3ubuntu1) ... Setting up systemd (252.5-2ubuntu3) ... Installing new version of config file /etc/systemd/logind.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 binutils (2.40.50.20230622-1ubuntu1) ... Setting up dpkg-dev (1.21.22ubuntu1) ... Setting up gcc-12 (12.3.0-3ubuntu1) ... Setting up g++-12 (12.3.0-3ubuntu1) ... Setting up systemd-sysv (252.5-2ubuntu3) ... Setting up gcc (4:12.2.0-3ubuntu1) ... Setting up g++ (4:12.2.0-3ubuntu1) ... Processing triggers for libc-bin (2.37-0ubuntu2) ... Processing triggers for debianutils (5.7-0.4) ... Processing triggers for ca-certificates (20230311ubuntu1) ... 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-26342895 amd64 mantic-proposed -c chroot:build-PACKAGEBUILD-26342895 --arch=amd64 --dist=mantic-proposed --nolog -A cpptraj_5.1.0+dfsg-3build1.dsc Initiating build PACKAGEBUILD-26342895 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-152-generic #169-Ubuntu SMP Tue Jun 6 22:23:09 UTC 2023 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-101.buildd +==============================================================================+ | cpptraj 5.1.0+dfsg-3build1 (amd64) Tue, 27 Jun 2023 18:07:24 +0000 | +==============================================================================+ Package: cpptraj Version: 5.1.0+dfsg-3build1 Source Version: 5.1.0+dfsg-3build1 Distribution: mantic-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-26342895/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/cpptraj-HmGFtp/resolver-jmEsP0' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- cpptraj_5.1.0+dfsg-3build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/cpptraj-HmGFtp/cpptraj-5.1.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/cpptraj-HmGFtp' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), gfortran, libarpack2-dev, libbz2-dev, libfftw3-dev, libnetcdf-dev, libopenmm-dev, libreadline-dev, netcdf-bin, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), gfortran, libarpack2-dev, libbz2-dev, libfftw3-dev, libnetcdf-dev, libopenmm-dev, libreadline-dev, netcdf-bin, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [448 B] Get:5 copy:/<>/apt_archive ./ Packages [505 B] Fetched 1910 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 additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-12 groff-base hdf5-helpers icu-devtools intltool-debian libaec-dev libaec0 libarchive-zip-perl libarpack2 libarpack2-dev libblas-dev libblas3 libbrotli1 libbz2-dev libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdw1 libelf1 libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-quad3 libfftw3-single3 libfile-stripnondeterminism-perl libgfortran-12-dev libgfortran5 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libicu-dev libicu72 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libldap2 libmagic-mgc libmagic1 libncurses-dev libnetcdf-dev libnetcdf19 libnghttp2-14 libopenmm-dev libopenmm8.0 libpipeline1 libpsl5 libreadline-dev librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsub-override-perl libsz2 libtool libuchardet0 libxml2 libxml2-dev m4 man-db netcdf-bin po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-multilib gfortran-doc gfortran-12-multilib gfortran-12-doc libcoarrays-dev groff liblapack-doc libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config libfftw3-doc libhdf5-doc icu-doc ncurses-doc netcdf-doc readline-doc libssl-doc libtool-doc gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libldap-common pkg-config publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-12 groff-base hdf5-helpers icu-devtools intltool-debian libaec-dev libaec0 libarchive-zip-perl libarpack2 libarpack2-dev libblas-dev libblas3 libbrotli1 libbz2-dev libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdw1 libelf1 libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-quad3 libfftw3-single3 libfile-stripnondeterminism-perl libgfortran-12-dev libgfortran5 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libicu-dev libicu72 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libldap2 libmagic-mgc libmagic1 libncurses-dev libnetcdf-dev libnetcdf19 libnghttp2-14 libopenmm-dev libopenmm8.0 libpipeline1 libpsl5 libreadline-dev librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsub-override-perl libsz2 libtool libuchardet0 libxml2 libxml2-dev m4 man-db netcdf-bin po-debconf sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 88 newly installed, 0 to remove and 0 not upgraded. Need to get 70.9 MB of archives. After this operation, 279 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [718 B] Get:2 http://ftpmaster.internal/ubuntu mantic/main amd64 libelf1 amd64 0.188-2.1 [53.4 kB] Get:3 http://ftpmaster.internal/ubuntu mantic/main amd64 libicu72 amd64 72.1-3ubuntu2 [10.8 MB] Get:4 http://ftpmaster.internal/ubuntu mantic/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [764 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main amd64 bsdextrautils amd64 2.38.1-5ubuntu2 [71.0 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main amd64 libmagic-mgc amd64 1:5.44-3 [293 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/main amd64 libmagic1 amd64 1:5.44-3 [85.6 kB] Get:8 http://ftpmaster.internal/ubuntu mantic/main amd64 file amd64 1:5.44-3 [21.8 kB] Get:9 http://ftpmaster.internal/ubuntu mantic/main amd64 gettext-base amd64 0.21-12 [38.0 kB] Get:10 http://ftpmaster.internal/ubuntu mantic/main amd64 libuchardet0 amd64 0.0.7-1build2 [76.9 kB] Get:11 http://ftpmaster.internal/ubuntu mantic/main amd64 groff-base amd64 1.22.4-10 [937 kB] Get:12 http://ftpmaster.internal/ubuntu mantic/main amd64 libnghttp2-14 amd64 1.54.0-1 [72.7 kB] Get:13 http://ftpmaster.internal/ubuntu mantic/main amd64 libpipeline1 amd64 1.5.7-1 [23.3 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main amd64 libpsl5 amd64 0.21.2-1 [59.0 kB] Get:15 http://ftpmaster.internal/ubuntu mantic/main amd64 man-db amd64 2.11.2-2 [1220 kB] Get:16 http://ftpmaster.internal/ubuntu mantic/main amd64 m4 amd64 1.4.19-3 [243 kB] Get:17 http://ftpmaster.internal/ubuntu mantic/main amd64 autoconf all 2.71-3 [339 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:19 http://ftpmaster.internal/ubuntu mantic/main amd64 automake all 1:1.16.5-1.3 [558 kB] Get:20 http://ftpmaster.internal/ubuntu mantic/main amd64 autopoint all 0.21-12 [422 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main amd64 libdebhelper-perl all 13.11.4ubuntu3 [66.1 kB] Get:22 http://ftpmaster.internal/ubuntu mantic/main amd64 libtool all 2.4.7-5 [166 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main amd64 dh-autoreconf all 20 [16.1 kB] Get:24 http://ftpmaster.internal/ubuntu mantic/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:25 http://ftpmaster.internal/ubuntu mantic/main amd64 libsub-override-perl all 0.09-4 [8706 B] Get:26 http://ftpmaster.internal/ubuntu mantic/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:27 http://ftpmaster.internal/ubuntu mantic/main amd64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:28 http://ftpmaster.internal/ubuntu mantic/main amd64 libdw1 amd64 0.188-2.1 [251 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/main amd64 debugedit amd64 1:5.0-5 [46.1 kB] Get:30 http://ftpmaster.internal/ubuntu mantic/main amd64 dwz amd64 0.15-1 [112 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main amd64 gettext amd64 0.21-12 [866 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main amd64 debhelper all 13.11.4ubuntu3 [925 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main amd64 libgfortran5 amd64 13.1.0-6ubuntu1 [891 kB] Get:36 http://ftpmaster.internal/ubuntu mantic/main amd64 libgfortran-12-dev amd64 12.3.0-3ubuntu1 [926 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main amd64 gfortran-12 amd64 12.3.0-3ubuntu1 [11.2 MB] Get:38 http://ftpmaster.internal/ubuntu mantic/main amd64 gfortran amd64 4:12.2.0-3ubuntu1 [1184 B] Get:39 http://ftpmaster.internal/ubuntu mantic/universe amd64 hdf5-helpers amd64 1.10.8+repack1-1ubuntu1 [13.9 kB] Get:40 http://ftpmaster.internal/ubuntu mantic/main amd64 icu-devtools amd64 72.1-3ubuntu2 [210 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/universe amd64 libaec0 amd64 1.0.6-1 [20.1 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main amd64 libblas3 amd64 3.11.0-2 [244 kB] Get:43 http://ftpmaster.internal/ubuntu mantic/main amd64 liblapack3 amd64 3.11.0-2 [2659 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/universe amd64 libarpack2 amd64 3.8.0-3 [106 kB] Get:45 http://ftpmaster.internal/ubuntu mantic/main amd64 libblas-dev amd64 3.11.0-2 [170 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main amd64 liblapack-dev amd64 3.11.0-2 [5073 kB] Get:47 http://ftpmaster.internal/ubuntu mantic/universe amd64 libarpack2-dev amd64 3.8.0-3 [122 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/main amd64 libbrotli1 amd64 1.0.9-2build8 [309 kB] Get:49 http://ftpmaster.internal/ubuntu mantic/main amd64 libbz2-dev amd64 1.0.8-5build1 [32.5 kB] Get:50 http://ftpmaster.internal/ubuntu mantic/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-1 [20.0 kB] Get:51 http://ftpmaster.internal/ubuntu mantic/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-1 [55.6 kB] Get:52 http://ftpmaster.internal/ubuntu mantic/main amd64 libldap2 amd64 2.6.3+dfsg-1~exp1ubuntu2 [184 kB] Get:53 http://ftpmaster.internal/ubuntu mantic/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build4 [58.2 kB] Get:54 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libssh-4 amd64 0.10.5-2 [187 kB] Get:55 http://ftpmaster.internal/ubuntu mantic/main amd64 libcurl3-gnutls amd64 7.88.1-10ubuntu1 [301 kB] Get:56 http://ftpmaster.internal/ubuntu mantic/main amd64 libcurl4 amd64 7.88.1-10ubuntu1 [307 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main amd64 libcurl4-gnutls-dev amd64 7.88.1-10ubuntu1 [402 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/main amd64 libfftw3-double3 amd64 3.3.10-1ubuntu1 [835 kB] Get:59 http://ftpmaster.internal/ubuntu mantic/main amd64 libfftw3-long3 amd64 3.3.10-1ubuntu1 [368 kB] Get:60 http://ftpmaster.internal/ubuntu mantic/main amd64 libfftw3-quad3 amd64 3.3.10-1ubuntu1 [655 kB] Get:61 http://ftpmaster.internal/ubuntu mantic/main amd64 libfftw3-single3 amd64 3.3.10-1ubuntu1 [869 kB] Get:62 http://ftpmaster.internal/ubuntu mantic/main amd64 libfftw3-bin amd64 3.3.10-1ubuntu1 [39.0 kB] Get:63 http://ftpmaster.internal/ubuntu mantic/main amd64 libfftw3-dev amd64 3.3.10-1ubuntu1 [2372 kB] Get:64 http://ftpmaster.internal/ubuntu mantic/universe amd64 libsz2 amd64 1.0.6-1 [5354 B] Get:65 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhdf5-103-1 amd64 1.10.8+repack1-1ubuntu1 [1301 kB] Get:66 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhdf5-cpp-103-1 amd64 1.10.8+repack1-1ubuntu1 [122 kB] Get:67 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhdf5-fortran-102 amd64 1.10.8+repack1-1ubuntu1 [85.4 kB] Get:68 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhdf5-hl-100 amd64 1.10.8+repack1-1ubuntu1 [56.0 kB] Get:69 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhdf5-hl-fortran-100 amd64 1.10.8+repack1-1ubuntu1 [32.0 kB] Get:70 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhdf5-hl-cpp-100 amd64 1.10.8+repack1-1ubuntu1 [10.8 kB] Get:71 http://ftpmaster.internal/ubuntu mantic/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1ubuntu4 [895 kB] Get:72 http://ftpmaster.internal/ubuntu mantic/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB] Get:73 http://ftpmaster.internal/ubuntu mantic/main amd64 libjpeg-turbo8-dev amd64 2.1.5-2ubuntu1 [294 kB] Get:74 http://ftpmaster.internal/ubuntu mantic/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] Get:75 http://ftpmaster.internal/ubuntu mantic/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B] Get:76 http://ftpmaster.internal/ubuntu mantic/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B] Get:77 http://ftpmaster.internal/ubuntu mantic/universe amd64 libaec-dev amd64 1.0.6-1 [17.9 kB] Get:78 http://ftpmaster.internal/ubuntu mantic/main amd64 libssl-dev amd64 3.0.9-1ubuntu1 [2375 kB] Get:79 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhdf5-dev amd64 1.10.8+repack1-1ubuntu1 [2801 kB] Get:80 http://ftpmaster.internal/ubuntu mantic/main amd64 libicu-dev amd64 72.1-3ubuntu2 [11.8 MB] Get:81 http://ftpmaster.internal/ubuntu mantic/main amd64 libncurses-dev amd64 6.4-4 [383 kB] Get:82 http://ftpmaster.internal/ubuntu mantic/universe amd64 libnetcdf19 amd64 1:4.9.2-1 [469 kB] Get:83 http://ftpmaster.internal/ubuntu mantic/main amd64 libxml2-dev amd64 2.9.14+dfsg-1.2 [786 kB] Get:84 http://ftpmaster.internal/ubuntu mantic/universe amd64 libnetcdf-dev amd64 1:4.9.2-1 [57.9 kB] Get:85 http://ftpmaster.internal/ubuntu mantic-proposed/universe amd64 libopenmm8.0 amd64 8.0.0+dfsg-2 [997 kB] Get:86 http://ftpmaster.internal/ubuntu mantic-proposed/universe amd64 libopenmm-dev amd64 8.0.0+dfsg-2 [333 kB] Get:87 http://ftpmaster.internal/ubuntu mantic/main amd64 libreadline-dev amd64 8.2-1.3 [167 kB] Get:88 http://ftpmaster.internal/ubuntu mantic/universe amd64 netcdf-bin amd64 1:4.9.2-1 [208 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 70.9 MB in 1s (132 MB/s) Selecting previously unselected package libelf1:amd64. (Reading database ... 12590 files and directories currently installed.) Preparing to unpack .../00-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../01-libicu72_72.1-3ubuntu2_amd64.deb ... Unpacking libicu72:amd64 (72.1-3ubuntu2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../02-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../03-bsdextrautils_2.38.1-5ubuntu2_amd64.deb ... Unpacking bsdextrautils (2.38.1-5ubuntu2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../05-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... 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Setting up libnghttp2-14:amd64 (1.54.0-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libfftw3-long3:amd64 (3.3.10-1ubuntu1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libreadline-dev:amd64 (8.2-1.3) ... Setting up libaec0:amd64 (1.0.6-1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libfftw3-quad3:amd64 (3.3.10-1ubuntu1) ... Setting up libssl-dev:amd64 (3.0.9-1ubuntu1) ... Setting up autopoint (0.21-12) ... Setting up icu-devtools (72.1-3ubuntu2) ... Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ... Setting up libfftw3-double3:amd64 (3.3.10-1ubuntu1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-1) ... Setting up libssh-4:amd64 (0.10.5-2) ... Setting up libgfortran5:amd64 (13.1.0-6ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1ubuntu4) ... Setting up libuchardet0:amd64 (0.0.7-1build2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libopenmm8.0 (8.0.0+dfsg-2) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libicu-dev:amd64 (72.1-3ubuntu2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up libldap2:amd64 (2.6.3+dfsg-1~exp1ubuntu2) ... Setting up libblas-dev:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libsz2:amd64 (1.0.6-1) ... Setting up libbz2-dev:amd64 (1.0.8-5build1) ... Setting up libjpeg8:amd64 (8c-2ubuntu11) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libdw1:amd64 (0.188-2.1) ... Setting up libjpeg-turbo8-dev:amd64 (2.1.5-2ubuntu1) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libfftw3-bin (3.3.10-1ubuntu1) ... Setting up libaec-dev:amd64 (1.0.6-1) ... Setting up libarpack2:amd64 (3.8.0-3) ... Setting up libcurl3-gnutls:amd64 (7.88.1-10ubuntu1) ... Setting up libgfortran-12-dev:amd64 (12.3.0-3ubuntu1) ... Setting up libcurl4-gnutls-dev:amd64 (7.88.1-10ubuntu1) ... Setting up libopenmm-dev (8.0.0+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up gfortran-12 (12.3.0-3ubuntu1) ... Setting up libxml2-dev:amd64 (2.9.14+dfsg-1.2) ... Setting up liblapack-dev:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up debugedit (1:5.0-5) ... Setting up libcurl4:amd64 (7.88.1-10ubuntu1) ... Setting up libjpeg8-dev:amd64 (8c-2ubuntu11) ... Setting up libfftw3-dev:amd64 (3.3.10-1ubuntu1) ... Setting up libarpack2-dev:amd64 (3.8.0-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libjpeg-dev:amd64 (8c-2ubuntu11) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up gfortran (4:12.2.0-3ubuntu1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libhdf5-103-1:amd64 (1.10.8+repack1-1ubuntu1) ... Setting up libhdf5-cpp-103-1:amd64 (1.10.8+repack1-1ubuntu1) ... Setting up libhdf5-hl-100:amd64 (1.10.8+repack1-1ubuntu1) ... Setting up debhelper (13.11.4ubuntu3) ... Setting up libhdf5-hl-cpp-100:amd64 (1.10.8+repack1-1ubuntu1) ... Setting up libhdf5-fortran-102:amd64 (1.10.8+repack1-1ubuntu1) ... Setting up libnetcdf19:amd64 (1:4.9.2-1) ... Setting up libhdf5-hl-fortran-100:amd64 (1.10.8+repack1-1ubuntu1) ... Setting up netcdf-bin (1:4.9.2-1) ... Setting up libhdf5-dev (1.10.8+repack1-1ubuntu1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libnetcdf-dev (1:4.9.2-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.37-0ubuntu2) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-152-generic #169-Ubuntu SMP Tue Jun 6 22:23:09 UTC 2023 amd64 (x86_64) Toolchain package versions: binutils_2.40.50.20230622-1ubuntu1 dpkg-dev_1.21.22ubuntu1 g++-12_12.3.0-3ubuntu1 gcc-12_12.3.0-3ubuntu1 libc6-dev_2.37-0ubuntu2 libstdc++-12-dev_12.3.0-3ubuntu1 libstdc++6_13.1.0-6ubuntu1 linux-libc-dev_6.3.0-7.7 Package versions: adduser_3.134ubuntu1 advancecomp_2.5-1 apt_2.7.1 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-12 autotools-dev_20220109.1 base-files_13ubuntu1 base-passwd_3.6.1 bash_5.2.15-2ubuntu1 binutils_2.40.50.20230622-1ubuntu1 binutils-common_2.40.50.20230622-1ubuntu1 binutils-x86-64-linux-gnu_2.40.50.20230622-1ubuntu1 bsdextrautils_2.38.1-5ubuntu2 bsdutils_1:2.38.1-5ubuntu2 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 coreutils_9.1-1ubuntu2 cpp_4:12.2.0-3ubuntu1 cpp-12_12.3.0-3ubuntu1 dash_0.5.12-2ubuntu1 debconf_1.5.82 debhelper_13.11.4ubuntu3 debianutils_5.7-0.4 debugedit_1:5.0-5 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dpkg_1.21.22ubuntu1 dpkg-dev_1.21.22ubuntu1 dwz_0.15-1 e2fsprogs_1.47.0-1ubuntu1 fakeroot_1.31-1.2 file_1:5.44-3 findutils_4.9.0-4ubuntu1 g++_4:12.2.0-3ubuntu1 g++-12_12.3.0-3ubuntu1 gcc_4:12.2.0-3ubuntu1 gcc-12_12.3.0-3ubuntu1 gcc-12-base_12.3.0-3ubuntu1 gcc-13-base_13.1.0-6ubuntu1 gettext_0.21-12 gettext-base_0.21-12 gfortran_4:12.2.0-3ubuntu1 gfortran-12_12.3.0-3ubuntu1 gpg_2.2.40-1.1ubuntu1 gpg-agent_2.2.40-1.1ubuntu1 gpgconf_2.2.40-1.1ubuntu1 gpgv_2.2.40-1.1ubuntu1 grep_3.8-5 groff-base_1.22.4-10 gzip_1.12-1ubuntu1 hdf5-helpers_1.10.8+repack1-1ubuntu1 hostname_3.23+nmu1ubuntu1 icu-devtools_72.1-3ubuntu2 init_1.65.2 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libaec-dev_1.0.6-1 libaec0_1.0.6-1 libapparmor1_3.0.8-1ubuntu3 libapt-pkg6.0_2.7.1 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-3 libarpack2_3.8.0-3 libarpack2-dev_3.8.0-3 libasan8_13.1.0-6ubuntu1 libassuan0_2.5.5-5 libatomic1_13.1.0-6ubuntu1 libattr1_1:2.5.1-4 libaudit-common_1:3.0.9-1 libaudit1_1:3.0.9-1 libbinutils_2.40.50.20230622-1ubuntu1 libblas-dev_3.11.0-2 libblas3_3.11.0-2 libblkid1_2.38.1-5ubuntu2 libbrotli1_1.0.9-2build8 libbz2-1.0_1.0.8-5build1 libbz2-dev_1.0.8-5build1 libc-bin_2.37-0ubuntu2 libc-dev-bin_2.37-0ubuntu2 libc6_2.37-0ubuntu2 libc6-dev_2.37-0ubuntu2 libcap-ng0_0.8.3-1build2 libcap2_1:2.66-4ubuntu1 libcc1-0_13.1.0-6ubuntu1 libcom-err2_1.47.0-1ubuntu1 libcrypt-dev_1:4.4.35-1 libcrypt1_1:4.4.35-1 libcryptsetup12_2:2.6.1-4ubuntu1 libctf-nobfd0_2.40.50.20230622-1ubuntu1 libctf0_2.40.50.20230622-1ubuntu1 libcurl3-gnutls_7.88.1-10ubuntu1 libcurl4_7.88.1-10ubuntu1 libcurl4-gnutls-dev_7.88.1-10ubuntu1 libdb5.3_5.3.28+dfsg2-1 libdebconfclient0_0.267ubuntu1 libdebhelper-perl_13.11.4ubuntu3 libdevmapper1.02.1_2:1.02.185-2ubuntu1 libdpkg-perl_1.21.22ubuntu1 libdw1_0.188-2.1 libelf1_0.188-2.1 libext2fs2_1.47.0-1ubuntu1 libfakeroot_1.31-1.2 libfdisk1_2.38.1-5ubuntu2 libffi8_3.4.4-1 libfftw3-bin_3.3.10-1ubuntu1 libfftw3-dev_3.3.10-1ubuntu1 libfftw3-double3_3.3.10-1ubuntu1 libfftw3-long3_3.3.10-1ubuntu1 libfftw3-quad3_3.3.10-1ubuntu1 libfftw3-single3_3.3.10-1ubuntu1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-3ubuntu1 libgcc-s1_13.1.0-6ubuntu1 libgcrypt20_1.10.1-3ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran-12-dev_12.3.0-3ubuntu1 libgfortran5_13.1.0-6ubuntu1 libgmp10_2:6.2.1+dfsg1-1.1ubuntu1 libgnutls30_3.7.9-2ubuntu1 libgomp1_13.1.0-6ubuntu1 libgpg-error0_1.46-1 libgprofng0_2.40.50.20230622-1ubuntu1 libgssapi-krb5-2_1.20.1-2 libhdf5-103-1_1.10.8+repack1-1ubuntu1 libhdf5-cpp-103-1_1.10.8+repack1-1ubuntu1 libhdf5-dev_1.10.8+repack1-1ubuntu1 libhdf5-fortran-102_1.10.8+repack1-1ubuntu1 libhdf5-hl-100_1.10.8+repack1-1ubuntu1 libhdf5-hl-cpp-100_1.10.8+repack1-1ubuntu1 libhdf5-hl-fortran-100_1.10.8+repack1-1ubuntu1 libhogweed6_3.8.1-2 libicu-dev_72.1-3ubuntu2 libicu72_72.1-3ubuntu2 libidn2-0_2.3.3-1build1 libip4tc2_1.8.7-1ubuntu7 libisl23_0.26-3 libitm1_13.1.0-6ubuntu1 libjansson4_2.14-2 libjpeg-dev_8c-2ubuntu11 libjpeg-turbo8_2.1.5-2ubuntu1 libjpeg-turbo8-dev_2.1.5-2ubuntu1 libjpeg8_8c-2ubuntu11 libjpeg8-dev_8c-2ubuntu11 libjson-c5_0.16-2 libk5crypto3_1.20.1-2 libkeyutils1_1.6.3-2 libkmod2_30+20221128-1ubuntu1 libkrb5-3_1.20.1-2 libkrb5support0_1.20.1-2 liblapack-dev_3.11.0-2 liblapack3_3.11.0-2 libldap2_2.6.3+dfsg-1~exp1ubuntu2 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblsan0_13.1.0-6ubuntu1 liblz4-1_1.9.4-1 liblzma5_5.4.1-0.2 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libsmartcols1_2.38.1-5ubuntu2 libsqlite3-0_3.42.0-1 libss2_1.47.0-1ubuntu1 libssh-4_0.10.5-2 libssl-dev_3.0.9-1ubuntu1 libssl3_3.0.9-1ubuntu1 libstdc++-12-dev_12.3.0-3ubuntu1 libstdc++6_13.1.0-6ubuntu1 libsub-override-perl_0.09-4 libsystemd-shared_252.5-2ubuntu3 libsystemd0_252.5-2ubuntu3 libsz2_1.0.6-1 libtasn1-6_4.19.0-2 libtinfo6_6.4-4 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libtsan2_13.1.0-6ubuntu1 libubsan1_13.1.0-6ubuntu1 libuchardet0_0.0.7-1build2 libudev1_252.5-2ubuntu3 libunistring2_1.0-2 libuuid1_2.38.1-5ubuntu2 libxml2_2.9.14+dfsg-1.2 libxml2-dev_2.9.14+dfsg-1.2 libxxhash0_0.8.1-1 libzstd1_1.5.4+dfsg2-5 linux-libc-dev_6.3.0-7.7 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-1ubuntu1 logsave_1.47.0-1ubuntu1 lsb-base_11.6 lto-disabled-list_41 m4_1.4.19-3 make_4.3-4.1build1 man-db_2.11.2-2 mawk_1.3.4.20230525-1 mount_2.38.1-5ubuntu2 ncurses-base_6.4-4 ncurses-bin_6.4-4 netcdf-bin_1:4.9.2-1 openssl_3.0.9-1ubuntu1 optipng_0.7.7-2build1 passwd_1:4.13+dfsg1-1ubuntu1 patch_2.7.6-7build2 perl_5.36.0-7ubuntu1 perl-base_5.36.0-7ubuntu1 perl-modules-5.36_5.36.0-7ubuntu1 pinentry-curses_1.2.1-1ubuntu1 pkgbinarymangler_153 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.3-1ubuntu1 readline-common_8.2-1.3 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 systemd_252.5-2ubuntu3 systemd-sysv_252.5-2ubuntu3 sysvinit-utils_3.06-4ubuntu1 tar_1.34+dfsg-1.2ubuntu1 tzdata_2023c-4exp1ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_35ubuntu1 util-linux_2.38.1-5ubuntu2 util-linux-extra_2.38.1-5ubuntu2 xz-utils_5.4.1-0.2 zlib1g_1:1.2.13.dfsg-1ubuntu4 zlib1g-dev_1:1.2.13.dfsg-1ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: cpptraj Binary: cpptraj Architecture: any Version: 5.1.0+dfsg-3build1 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 ppc64el], libreadline-dev, netcdf-bin Package-List: cpptraj deb science optional arch=any Checksums-Sha1: b326e493769758a5e5e29173898e049c6a60e9a2 28363024 cpptraj_5.1.0+dfsg.orig.tar.xz 2d35c58536b417bf106e0a76c130851502c04e8e 6064 cpptraj_5.1.0+dfsg-3build1.debian.tar.xz Checksums-Sha256: 89e279bbb5d35db4d2599fa98322bb8c4b876ce6117f8896e75520a3da1182f3 28363024 cpptraj_5.1.0+dfsg.orig.tar.xz 8191c01e2dced7ae6e751f8f00201b5740c184739edb6754ee398836aad5bc1d 6064 cpptraj_5.1.0+dfsg-3build1.debian.tar.xz Files: bf932a3aed87ad43645613135c712505 28363024 cpptraj_5.1.0+dfsg.orig.tar.xz fbbdae5a01fea1876c370911fd95a944 6064 cpptraj_5.1.0+dfsg-3build1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEETQvhLw5HdtiqzpaW5mx3Wuv+bH0FAmSbJK0ACgkQ5mx3Wuv+ bH1Oqg//X68VhXh+yjGF8DOFdIMqTEWY8BkkwvGKSiT7kKG6Pzdn+/lyTbc/w0X8 Voi/MBgLr6p0ZqPBsb+zqKZzgAV8fHOz3UlkkY0U37fk1KicEonKQ0xGC9nkzlV3 0ChOy8ylQJuP0MCTs4T3WCx5WM5JCPXcROPjcSsnZfPMX6OiZp1A27Ixn/Fr0Ijh SVj71zlAl/0dBQfjnnSow/0j7GjyWio3BkB3sp0/wCChGopVtzMrlGG8qvkLXGU/ VgV6tRZj7SA1oEc27gUmE/ytUs0HPxQTvZpHusXvT8PGGGzaCNh0plTt1ckWMC76 Icf7qM4WnUHcyMgUo658O7p3bLZYfPxbDMiHNhSk4ubs3uS3zf65m71hldNyAUis ebyulqfRcvyOwKYUotUyofxFjyVjk7NQfEvwhjGQZXOjpOkU6JjWgSbipsGOdrrE RsFmOniqM5apx2RZk+H0ucRytUIjEHCEibUaPkM1ucgm7+ZfZrEyIz29Nglu0ywO OYVmNwhzKvltOgHwxQijQLkBQ/iEiupEUSq6cBmNqM4IAmY6uFevGrc4wwoDgKmP 1yTyJTpMp2jnAJy1ivHfjXSQiPnJ1gm2LOZ7PWpQy3i+mbtVBcpltMh6j+umd7M7 wkXDoToag4Y7i1FteSwvY1gUfQsiBas/byuD0FBisBpFbhXBXUM= =xQps -----END PGP SIGNATURE----- gpgv: Signature made Tue Jun 27 18:04:29 2023 UTC gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./cpptraj_5.1.0+dfsg-3build1.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-3build1.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-26342895 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-26342895 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-26342895 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-3build1 dpkg-buildpackage: info: source distribution mantic dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 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 dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' ./configure gnu --with-arpack=/usr/lib/x86_64-linux-gnu --with-fftw3=/usr/lib/x86_64-linux-gnu --with-readline=/usr/lib/x86_64-linux-gnu --with-openmm=/usr/lib/x86_64-linux-gnu arpack specified: /usr/lib/x86_64-linux-gnu fftw3 specified: /usr/lib/x86_64-linux-gnu readline specified: /usr/lib/x86_64-linux-gnu openmm specified: /usr/lib/x86_64-linux-gnu Testing C++ compiler: OK Testing C compiler: OK Testing basic C++11 support: OK Testing system headers for C++11 support: OK Warning: Compilation of sanderlib requires AMBERHOME to be set Warning: if --with-sanderlib not specified. Checking BZLIB: OK Checking ZLIB: OK Checking NetCDF: OK Checking LAPACK/BLAS: OK Checking ARPACK: OK Checking FFTW3: OK Checking Readline: OK Checking OpenMM: OK vmdplugin disabled due to nonfree source. Configuration summary: Build type: Serial Options: netcdf bzlib tng zlib arpack lapack blas fftw3 readline xdrfile openmm Target platform: Linux, 64-bit. gnu compilers in use. C++11 support enabled. PME support enabled. Compiler optimizations are on. Cleaning source directory. -------------------------------------------------------------------------------- An environment resource file for CPPTRAJ has been created: /<>/cpptraj.sh You may 'source' this file to set up your environment for CPPTRAJ. -------------------------------------------------------------------------------- CPPTRAJ configuration complete. make[1]: Leaving directory '/<>' dh_auto_build make -j4 make[1]: Entering directory '/<>' cd src && make install make[2]: Entering directory '/<>/src' CXX SpaceGroup.cpp CXX ActionList.cpp CXX ActionFrameCounter.cpp CXX ActionTopWriter.cpp CXX Action_Align.cpp CXX Action_Angle.cpp CXX Action_AreaPerMol.cpp CXX Action_AtomMap.cpp CXX Action_AtomicCorr.cpp CXX Action_AtomicFluct.cpp CXX Action_AutoImage.cpp CXX Action_Average.cpp CXX Action_Bounds.cpp CXX Action_Box.cpp CXX Action_Center.cpp CXX Action_Channel.cpp CXX Action_CheckChirality.cpp CXX Action_CheckStructure.cpp CXX Action_Closest.cpp CXX Action_ClusterDihedral.cpp CXX Action_Contacts.cpp CXX Action_CreateCrd.cpp CXX Action_CreateReservoir.cpp CXX Action_DNAionTracker.cpp CXX Action_DSSP.cpp CXX Action_Density.cpp CXX Action_Diffusion.cpp CXX Action_Dihedral.cpp CXX Action_DihedralRMS.cpp CXX Action_Dipole.cpp CXX Action_Distance.cpp CXX Action_DistRmsd.cpp CXX Action_Energy.cpp In file included from Ewald_ParticleMesh.h:5, from Action_Energy.cpp:4: helpme_standalone.h:2323: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2323 | #pragma omp parallel for num_threads(nThreads) | helpme_standalone.h:2343: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 2343 | #pragma omp parallel for num_threads(nThreads) | helpme_standalone.h:3014: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3014 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) | helpme_standalone.h:3120: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3120 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) | helpme_standalone.h:3247: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3247 | #pragma omp parallel for num_threads(nThreads) | helpme_standalone.h:3701: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3701 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:3739: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3739 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:3802: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3802 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:3840: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 3840 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:4044: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4044 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:4052: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 4052 | #pragma omp for | helpme_standalone.h:4097: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4097 | #pragma omp parallel for num_threads(nThreads_) | helpme_standalone.h:4145: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4145 | #pragma omp parallel for num_threads(nThreads_) | helpme_standalone.h:4172: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4172 | #pragma omp parallel for num_threads(nThreads_) | helpme_standalone.h:4224: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4224 | #pragma omp parallel for num_threads(nThreads_) | helpme_standalone.h:4228: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4228 | #pragma omp parallel for num_threads(nThreads_) | helpme_standalone.h:4275: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4275 | #pragma omp parallel for num_threads(nThreads_) | helpme_standalone.h:4388: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4388 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) | helpme_standalone.h:4419: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) | helpme_standalone.h:4503: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4503 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:4510: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 4510 | #pragma omp for | CXX Action_FilterByData.cpp CXX Action_FixAtomOrder.cpp CXX Action_FixImagedBonds.cpp CXX Action_GIST.cpp CXX Action_Grid.cpp CXX Action_GridFreeEnergy.cpp In file included from Matrix_3x3.h:3, from Box.h:3, from Frame.h:5, from Topology.h:10, from DataSet_Coords.h:4, from DataSet_Coords_REF.h:3, from ReferenceFrame.h:3, from DataSetList.h:4, from DataFile.h:4, from DataFileList.h:3, from ActionState.h:3, from Action.h:5, from Action_GIST.h:3, from Action_GIST.cpp:3: In member function ‘Vec3::operator-(Vec3 const&) const’, inlined from ‘Action_GIST::Order(Frame const&)’ at Action_GIST.cpp:814:31: Vec3.h:76:57: 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: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:76:23: 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]; | ^~~ 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]; | ^~~ CXX Action_HydrogenBond.cpp CXX Action_Image.cpp CXX Action_InfraredSpectrum.cpp CXX Action_Jcoupling.cpp CXX Action_LESsplit.cpp CXX Action_LIE.cpp CXX Action_LipidOrder.cpp CXX Action_MakeStructure.cpp CXX Action_Mask.cpp CXX Action_Matrix.cpp CXX Action_MinImage.cpp CXX Action_Molsurf.cpp CXX Action_MultiDihedral.cpp In file included from Action_Matrix.cpp:2: In member function ‘Action_Matrix::matrix_res::matrix_res(Action_Matrix::matrix_res const&)’, inlined from ‘std::__new_allocator::construct(Action_Matrix::matrix_res*, Action_Matrix::matrix_res const&)void’ at /usr/include/c++/12/bits/new_allocator.h:175:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, Action_Matrix::matrix_res*, Action_Matrix::matrix_res const&)void’ at /usr/include/c++/12/bits/alloc_traits.h:516:17, inlined from ‘std::vector >::push_back(Action_Matrix::matrix_res const&)’ at /usr/include/c++/12/bits/stl_vector.h:1281:30, inlined from ‘Action_Matrix::MaskToMatResArray(Topology const&, AtomMask const&) const’ at Action_Matrix.cpp:245:25: Action_Matrix.h:56:12: warning: ‘MEM[(const struct matrix_res &)&blank_res].resnum_’ may be used uninitialized [-Wmaybe-uninitialized] 56 | struct matrix_res { | ^~~~~~~~~~ Action_Matrix.cpp: In member function ‘Action_Matrix::MaskToMatResArray(Topology const&, AtomMask const&) const’: Action_Matrix.cpp:239:14: note: ‘blank_res’ declared here 239 | matrix_res blank_res; | ^~~~~~~~~ CXX Action_MultiVector.cpp CXX Action_NAstruct.cpp CXX Action_NativeContacts.cpp CXX Action_NMRrst.cpp CXX Action_OrderParameter.cpp CXX Action_Outtraj.cpp CXX Action_PairDist.cpp CXX Action_Pairwise.cpp CXX Action_Principal.cpp CXX Action_Projection.cpp CXX Action_Pucker.cpp CXX Action_Radgyr.cpp CXX Action_Radial.cpp CXX Action_RandomizeIons.cpp CXX Action_Remap.cpp CXX Action_ReplicateCell.cpp CXX Action_Rmsd.cpp CXX Action_Rotate.cpp CXX Action_RunningAvg.cpp CXX Action_STFC_Diffusion.cpp CXX Action_Scale.cpp CXX Action_SetVelocity.cpp CXX Action_Spam.cpp CXX Action_Strip.cpp CXX Action_Surf.cpp CXX Action_SymmetricRmsd.cpp CXX Action_Temperature.cpp CXX Action_Time.cpp CXX Action_Translate.cpp CXX Action_Unstrip.cpp CXX Action_Unwrap.cpp CXX Action_Vector.cpp CXX Action_VelocityAutoCorr.cpp CXX Action_Volmap.cpp CXX Action_Volume.cpp CXX Action_Watershell.cpp CXX Action_XtalSymm.cpp CXX AnalysisList.cpp CXX Analysis_AmdBias.cpp CXX Analysis_AutoCorr.cpp CXX Analysis_Average.cpp CXX Analysis_Clustering.cpp CXX Analysis_Corr.cpp CXX Analysis_ConstantPHStats.cpp In file included from /usr/include/c++/12/vector:64, from ArgList.h:3, from Action.h:4, from Action_XtalSymm.h:3, from Action_XtalSymm.cpp:1: In member function ‘std::vector >::assign(unsigned long, Vec3 const&)’, inlined from ‘Action_XtalSymm::Init(ArgList&, ActionInit&, int)’ at Action_XtalSymm.cpp:57:12: /usr/include/c++/12/bits/stl_vector.h:804:23: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] 804 | { _M_fill_assign(__n, __val); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function ‘Action_XtalSymm::Init(ArgList&, ActionInit&, int)’: /usr/include/c++/12/bits/vector.tcc:264:5: note: by argument 3 of type ‘const struct value_type &’ to ‘std::vector >::_M_fill_assign(unsigned long, Vec3 const&)’ declared here 264 | 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++/12/bits/stl_vector.h:804:23: warning: ‘’ may be used uninitialized [-Wmaybe-uninitialized] 804 | { _M_fill_assign(__n, __val); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function ‘Action_XtalSymm::Init(ArgList&, ActionInit&, int)’: /usr/include/c++/12/bits/vector.tcc:264:5: note: by argument 3 of type ‘const struct value_type &’ to ‘std::vector >::_M_fill_assign(unsigned long, Vec3 const&)’ declared here 264 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ Action_XtalSymm.cpp:58:33: note: ‘’ declared here 58 | RefT_.assign(nCopyTotal, Vec3()); | ^ 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 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_) | CXX Ewald_Regular.cpp helpme_standalone.h:4503: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 4503 | #pragma omp parallel num_threads(nThreads_) | helpme_standalone.h:4510: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas] 4510 | #pragma omp for | CXX ExclusionArray.cpp CXX Exec_AddMissingRes.cpp helpme_standalone.h: In instantiation of ‘std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]’: helpme_standalone.h:3898:50: required from ‘void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]’ Ewald_ParticleMesh.cpp:187:32: required from here helpme_standalone.h:1010:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 1010 | for (int val = 0; val < nRows_; ++val) eigenPairs.push_back({eigenValues[val][0], unsortedEigenVectors[val]}); | ~~~~^~~~~~~~ helpme_standalone.h:1013:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 1013 | for (int val = 0; val < nRows_; ++val) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of ‘void helpme::PMEInstance >::sanityChecks(int, const RealMat&, const RealMat&, int) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]’: helpme_standalone.h:5018:9: required from ‘Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]’ Ewald_ParticleMesh.cpp:190:42: required from here helpme_standalone.h:3198:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 3198 | if (parameters.nCols() != (nCartesian(parameterAngMom) - cartesianOffset)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of ‘void helpme::PMEInstance >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]’: helpme_standalone.h:5019:9: required from ‘Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]’ Ewald_ParticleMesh.cpp:190:42: required from here helpme_standalone.h:3746:45: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 3746 | for (size_t row = threadID; row < gridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~ helpme_standalone.h:3753:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 3753 | for (int atom = 0; atom < nAtoms; ++atom) { | ~~~~~^~~~~~~~ helpme_standalone.h:3761:61: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 3761 | if (cGridIterator.size() && thisAtomsThread == threadID) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~ helpme_standalone.h:3750:25: warning: unused variable ‘gridIteratorC’ [-Wunused-variable] 3750 | const auto &gridIteratorC = threadedGridIteratorC_[threadID]; | ^~~~~~~~~~~~~ helpme_standalone.h:3794:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 3794 | for (int atom = splineCache_.size(); atom < newSize; ++atom) | ~~~~~^~~~~~~~~ helpme_standalone.h:3810:47: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 3810 | for (size_t cRow = threadID; cRow < gridDimensionC_; cRow += nThreads_) { | ~~~~~^~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of ‘Real* helpme::PMEInstance >::spreadParameters(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]’: helpme_standalone.h:5020:25: required from ‘Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]’ Ewald_ParticleMesh.cpp:190:42: required from here helpme_standalone.h:3708:45: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 3708 | for (size_t row = threadID; row < myGridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of ‘helpme::PMEInstance >::Complex* helpme::PMEInstance >::forwardTransform(Real*) [with Real = double; typename std::enable_if::value, int>::type = 0; Complex = std::complex]’: helpme_standalone.h:5023:32: required from ‘Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]’ Ewald_ParticleMesh.cpp:190:42: required from here helpme_standalone.h:4004:28: warning: variable ‘realCBA’ set but not used [-Wunused-but-set-variable] 4004 | Real *__restrict__ realCBA; | ^~~~~~~ CXX Exec_Analyze.cpp helpme_standalone.h: In instantiation of ‘void helpme::Matrix::assertSymmetric(const Real&) const [with Real = double]’: helpme_standalone.h:1000:9: required from ‘std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]’ helpme_standalone.h:3898:50: required from ‘void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]’ Ewald_ParticleMesh.cpp:187:32: required from here helpme_standalone.h:796:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 796 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of ‘void helpme::JacobiCyclicDiagonalization(Real*, Real*, const Real*, int) [with Real = double]’: helpme_standalone.h:1006:42: required from ‘std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]’ helpme_standalone.h:3898:50: required from ‘void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]’ Ewald_ParticleMesh.cpp:187:32: required from here helpme_standalone.h:213:20: warning: variable ‘cos_2phi’ set but not used [-Wunused-but-set-variable] 213 | Real sin_2phi, cos_2phi, cot_2phi; | ^~~~~~~~ helpme_standalone.h: In instantiation of ‘helpme::Matrix helpme::Matrix::applyOperation(const std::function&) const [with Real = double]’: helpme_standalone.h:785:26: required from ‘helpme::Matrix helpme::Matrix::inverse() const [with Real = double]’ helpme_standalone.h:3910:44: required from ‘void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]’ Ewald_ParticleMesh.cpp:187:32: required from here helpme_standalone.h:824:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 824 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of ‘void helpme::BSpline::update(short int, Real, short int, short int) [with Real = double]’: helpme_standalone.h:3829:47: required from ‘void helpme::PMEInstance >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]’ helpme_standalone.h:5019:9: required from ‘Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]’ Ewald_ParticleMesh.cpp:190:42: required from here helpme_standalone.h:2208:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2208 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:2208:72: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘short int’ [-Wsign-compare] 2208 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~ 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_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.212790]’ 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.212789]’ 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.212788]’ 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.212775.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.212774.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.212773.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(); | ^~~~~~~~~ helpme_standalone.h: In member function ‘helpme::PMEInstance::computeERec(int, helpme::Matrix const&, helpme::Matrix const&)’: helpme_standalone.h:5031:16: warning: ‘energy’ may be used uninitialized [-Wmaybe-uninitialized] 5031 | return energy; | ^~~~~~ helpme_standalone.h:5021:14: note: ‘energy’ was declared here 5021 | Real energy; | ^~~~~~ CXX Exec_Commands.cpp CXX Exec_CompareTop.cpp CXX Exec_CrdAction.cpp CXX Exec_CrdOut.cpp CXX Exec_CreateSet.cpp CXX Exec_DataFile.cpp CXX Exec_DataFilter.cpp CXX Exec_DataSetCmd.cpp CXX Exec_Emin.cpp CXX Exec_Flatten.cpp CXX Exec_GenerateAmberRst.cpp CXX Exec_Graft.cpp CXX Exec_Help.cpp CXX Exec_LoadCrd.cpp CXX Exec_LoadTraj.cpp CXX Exec_ParallelAnalysis.cpp CXX Exec_ParmBox.cpp CXX Exec_ParmSolvent.cpp CXX Exec_ParmStrip.cpp CXX Exec_ParmWrite.cpp CXX Exec_PermuteDihedrals.cpp CXX Exec_Precision.cpp CXX Exec_PrepareForLeap.cpp CXX Exec_PrintData.cpp CXX Exec_Random.cpp CXX Exec_ReadData.cpp CXX Exec_ReadEnsembleData.cpp CXX Exec_ReadInput.cpp CXX Exec_RotateDihedral.cpp CXX Exec_RunAnalysis.cpp CXX Exec_ScaleDihedralK.cpp CXX Exec_Set.cpp CXX Exec_SequenceAlign.cpp CXX Exec_Show.cpp CXX Exec_SortEnsembleData.cpp CXX Exec_SplitCoords.cpp CXX Exec_System.cpp CXX Exec_Top.cpp CXX Exec_Traj.cpp CXX Exec_UpdateParameters.cpp CXX Exec_ViewRst.cpp CXX File_TempName.cpp CXX FileIO_Bzip2.cpp CXX FileIO_Gzip.cpp CXX FileIO_Mpi.cpp CXX FileIO_MpiShared.cpp CXX FileIO_Std.cpp CXX FileName.cpp CXX FileType.cpp CXX FileTypes.cpp CXX ForLoop.cpp CXX ForLoop_dataSetBlocks.cpp CXX ForLoop_integer.cpp CXX ForLoop_list.cpp CXX ForLoop_mask.cpp CXX ForLoop_overSets.cpp CXX Frame.cpp CXX GridAction.cpp CXX HistBin.cpp CXX Hungarian.cpp CXX ImageRoutines.cpp CXX Image_List_Mask.cpp CXX Image_List_Pair.cpp CXX Image_List_Unit.cpp CXX InputTrajCommon.cpp CXX KDE.cpp CXX MapAtom.cpp CXX MaskArray.cpp CXX MaskToken.cpp CXX Matrix_3x3.cpp CXX MdOpts.cpp CXX MetaData.cpp CXX Minimize_SteepestDescent.cpp CXX Mol.cpp CXX Mol2File.cpp CXX NameType.cpp CXX NC_Cmatrix.cpp CXX NC_Routines.cpp CXX NetcdfFile.cpp CXX OMM_helpers.cpp CXX OutputTrajCommon.cpp CXX ParameterSet.cpp CXX PDBfile.cpp CXX PairList.cpp CXX Parallel.cpp CXX ParallelNetcdf.cpp CXX ParmFile.cpp CXX Parm_Amber.cpp CXX Parm_CharmmPsf.cpp CXX Parm_CIF.cpp CXX Parm_Gromacs.cpp CXX Parm_Mol2.cpp CXX Parm_PDB.cpp CXX Parm_SDF.cpp CXX Parm_Tinker.cpp CXX PotentialFunction.cpp CXX PotentialTerm.cpp CXX PotentialTerm_Angle.cpp CXX PotentialTerm_Bond.cpp CXX PotentialTerm_Dihedral.cpp CXX PotentialTerm_LJ_Coulomb.cpp CXX PotentialTerm_OpenMM.cpp CXX ProgressBar.cpp CXX ProgressTimer.cpp CXX PubFFT.cpp CXX ExternalFxn.cpp CXX Random.cpp CXX Range.cpp CXX RNG.cpp CXX RNG_Marsaglia.cpp CXX RNG_MersenneTwister.cpp CXX RNG_PCG32.cpp CXX RNG_Stdlib.cpp CXX RNG_Xoshiro128pp.cpp CXX RPNcalc.cpp CXX ReferenceAction.cpp CXX RemdReservoirNC.cpp CXX Residue.cpp CXX SDFfile.cpp CXX SimplexMin.cpp CXX Spline.cpp CXX SplineFxnTable.cpp CXX StringRoutines.cpp CXX StructureCheck.cpp CXX StructureMapper.cpp CXX SymmetricRmsdCalc.cpp CXX TextFormat.cpp CXX Timer.cpp CXX TinkerFile.cpp CXX TopInfo.cpp CXX Topology.cpp CXX TorsionRoutines.cpp CXX Traj_AmberCoord.cpp CXX Traj_AmberNetcdf.cpp CXX Traj_AmberRestart.cpp CXX Traj_AmberRestartNC.cpp CXX Traj_Binpos.cpp CXX Traj_CharmmCor.cpp CXX Traj_CharmmDcd.cpp CXX Traj_CharmmRestart.cpp CXX Traj_CIF.cpp CXX Traj_Conflib.cpp CXX Traj_DTR.cpp CXX Traj_GmxDump.cpp CXX Traj_GmxTng.cpp CXX Traj_GmxTrX.cpp CXX Traj_GmxXtc.cpp CXX Traj_Gro.cpp CXX Traj_Mol2File.cpp CXX Traj_NcEnsemble.cpp CXX Traj_PDBfile.cpp CXX Traj_SDF.cpp CXX Traj_SQM.cpp CXX Traj_Tinker.cpp CXX Traj_XYZ.cpp CXX TrajectoryFile.cpp CXX TrajectoryIO.cpp CXX TrajFrameCounter.cpp CXX TrajinList.cpp CXX Trajin_Multi.cpp CXX Trajin_Single.cpp CXX TrajIOarray.cpp CXX Trajout_Single.cpp CXX TrajoutList.cpp CXX Vec3.cpp CXX ViewRst.cpp CXX xoshiro128plusplus.cpp xoshiro128plusplus.cpp: In function ‘void jump()’: xoshiro128plusplus.cpp:60:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 60 | for(int i = 0; i < sizeof JUMP / sizeof *JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ xoshiro128plusplus.cpp: In function ‘void long_jump()’: xoshiro128plusplus.cpp:90:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 90 | for(int i = 0; i < sizeof LONG_JUMP / sizeof *LONG_JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CXX Action_Esander.cpp CXX Command.cpp CXX Cpptraj.cpp CXX Energy_Sander.cpp CXX ReadLine.cpp CXX main.cpp CC molsurf.c Skipping bundled READLINE build cd xdrfile && make all make[3]: Entering directory '/<>/src/xdrfile' CC xdrfile.c Skipping bundled ARPACK build cd tng && make all make[3]: Entering directory '/<>/src/tng' CC md5.c CC tng_io.c CC xdr_seek.c CC xdrfile_trr.c CC xdrfile_xtc.c CC tng_compress.c /bin/rm -f libxdrfile.a ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o make[3]: Leaving directory '/<>/src/xdrfile' CC coder.c CC warnmalloc.c CC fixpoint.c CC xtc3.c tng_io.c: In function ‘tng_gen_data_block_add’: tng_io.c:12600:9: warning: ‘strncpy’ 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 bwlzh.c CC xtc2.c CC widemuldiv.c CC huffmem.c CC vals16.c CC bwt.c CC mtf.c CC rle.c CC lz77.c CC dict.c CC huffman.c CC merge_sort.c /bin/rm -f libtng_io.a ar cqs libtng_io.a md5.o tng_io.o tng_compress.o coder.o warnmalloc.o fixpoint.o xtc3.o bwlzh.o xtc2.o widemuldiv.o huffmem.o vals16.o bwt.o mtf.o rle.o lz77.o dict.o huffman.o merge_sort.o make[3]: Leaving directory '/<>/src/tng' g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o -L/usr/lib/x86_64-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/x86_64-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/x86_64-linux-gnu/lib -lfftw3 -L/usr/lib/x86_64-linux-gnu/lib -lOpenMM -lnetcdf -lbz2 tng/libtng_io.a -lz xdrfile/libxdrfile.a -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro mv cpptraj "/<>/bin" make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_test -- check unittest make -j4 test "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 check unittest make[2]: Entering directory '/<>' make[2]: Nothing to be done for 'test'. cd test && make test.complete summary cd unitTests && make test.complete summary make[3]: Entering directory '/<>/unitTests' make[3]: Entering directory '/<>/test' CPPTRAJ source directory: /<>/src CPPTRAJ config.h file: /<>/config.h make[4]: Entering directory '/<>/unitTests' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. CPPTRAJ source directory: /<>/src CPPTRAJ config.h file: /<>/config.h ******************************************************************************** TEST: /<>/unitTests/NameType CPPTRAJ: NameType class unit test. make[5]: Entering directory '/<>/unitTests/NameType' g++ -Wall -O3 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-3build1 -std=gnu++11 -I/<>/src -c -o main.o main.cpp -rwxr-xr-x 1 buildd buildd 160795432 Jun 27 18:11 ../bin/cpptraj make[4]: Entering directory '/<>/test' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. -rwxr-xr-x 1 buildd buildd 160795432 Jun 27 18:11 ../bin/cpptraj ******************************************************************************** TEST: /<>/test/Test_General CPPTRAJ: General tests All 15 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Parallel CPPTRAJ: Parallel tests. CPPTRAJ: Parallel test with trajectory offset All 7 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Strip CPPTRAJ: One frame strip command test CPPTRAJ: Unstrip (Lig/Rec/Complex) command test CPPTRAJ: Multi frame strip command test. CPPTRAJ: Strip topology with PDB info All 11 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_BrokenTraj CPPTRAJ: Broken Traj: Running good trajectory. CPPTRAJ: Broken Traj: Running broken trajectory. CPPTRAJ: Compressed broken trajectory test All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_TrajinOffset CPPTRAJ: Normal trajectory read with offsets. CPPTRAJ: Gzipped trajectory read with offsets CPPTRAJ: Bzip2ed trajectory read with offsets CPPTRAJ: Start argument offset All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_RemdTraj CPPTRAJ: CRD Replica Trajectory Run with offset CPPTRAJ: CRD Replica Trajectory Run CPPTRAJ: NetCDF Replica Trajectory Run test CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-3build1 -std=gnu++11 -I/<>/src -c -o NameType.o /<>/src/NameType.cpp CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj CPPTRAJ: CRD Replica Trajectory Run with remdout All 8 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_trajout_framerange CPPTRAJ: Trajout Frame Range [Amber Restart] CPPTRAJ: Trajout Frame Range [Amber Coordinates] All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_PerResRMSD CPPTRAJ: Per-Residue RMSD Test. CPPTRAJ: Per-Residue RMSD Test with averaging CPPTRAJ: Per-Residue RMSD Test with residue centering. All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_DSSP CPPTRAJ: Secstruct (DSSP) command test. CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. CPPTRAJ: Secstruct (DSSP) command with changing number of residues. CPPTRAJ: Secstruct (DSSP): SS assign output test CPPTRAJ: FtuFabI Assignment test All 10 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Center CPPTRAJ: Center command test. g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-3build1 -std=gnu++11 -I/<>/src -c -o CpptrajStdio.o /<>/src/CpptrajStdio.cpp CPPTRAJ: Center origin command test. CPPTRAJ: Center origin mass command test. CPPTRAJ: Center reference command test. CPPTRAJ: Center point test. All 5 comparisons passed. g++ -o a.out main.o NameType.o CpptrajStdio.o ******************************************************************************** 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 CPPTRAJ: Hbond, no angle cutoff test CPPTRAJ: Hbond, Bridge nointramol test CPPTRAJ: Hbond with imaging CPPTRAJ: Hbond, orthogonal imaging All 23 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_NCrestart CPPTRAJ: NetCDF Restart Test - TXT->NetCDF CPPTRAJ: NetCDF Restart Test - NetCDF->TXT CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Image CPPTRAJ: Orthorhombic imaged distance test. CPPTRAJ: Non-orthorhombic imaged distance test. CPPTRAJ: Orthorhombic coordinate imaging test 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: Nonorthorhombic coordinate imaging test CPPTRAJ: ArgList class unit test. make[5]: Entering directory '/<>/unitTests/ArgList' g++ -Wall -O3 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-3build1 -std=gnu++11 -I/<>/src -c -o main.o main.cpp CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Surf CPPTRAJ: Surface calculation test CPPTRAJ: Partial Surface calculation test g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-3build1 -std=gnu++11 -I/<>/src -c -o ArgList.o /<>/src/ArgList.cpp CPPTRAJ: LCPO test with GAFF atom types All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Radgyr CPPTRAJ: Radius of gyration command test All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Mask CPPTRAJ: Mask single frame test CPPTRAJ: Mask longer command test. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Jcoupling CPPTRAJ: J-Coupling single frame test J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. Skipped test: J-Coupling extended test All 1 comparisons passed. 1 comparisons skipped. ******************************************************************************** TEST: /<>/test/Test_Diffusion CPPTRAJ: Diffusion test, no imaging. CPPTRAJ: Diffusion test, old syntax. CPPTRAJ: Diffusion test, new syntax. CPPTRAJ: Diffusion test, nonorthogonal box CPPTRAJ: STFC Diffusion Test CPPTRAJ: STFC Diffusion Test with individual distances CPPTRAJ: STFC Diffusion Test with COM CPPTRAJ: STFC Diffusion Test with second mask All 16 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Outtraj CPPTRAJ: RMSD Test with outtraj. CPPTRAJ: Outtraj Test with maxmin. All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Charmm CPPTRAJ: CHARMM PSF/DCD test CPPTRAJ: CHARMM DCD Write, step 1. CPPTRAJ: CHARMM DCD Write, step 2. CPPTRAJ: CHAMBER topology read/strip test. CPPTRAJ: Read CHARMM restart CPPTRAJ: CHARMM PSF write CPPTRAJ: CHARMM COORdinates test All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CharmmParams CPPTRAJ: Test updating topology with Charmm parameters (single residue) All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Rotdif CPPTRAJ: Rotational diffusion calculation test All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_NetcdfTraj CPPTRAJ: Convert mdcrd -> NetCDF CPPTRAJ: Convert NetCDF -> mdcrd All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Runavg CPPTRAJ: Coordinate Running Average test. CPPTRAJ: Coordinate Running Average Traj Write All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_RMSD CPPTRAJ: Basic RMSD tests CPPTRAJ: RMS coordinate rotation/rotation matrices test CPPTRAJ: RMS fit with no coordinates modification test. CPPTRAJ: RMS fit to previous test CPPTRAJ: RMS: imaging after unit cell rotation All 12 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_2DRMS CPPTRAJ: 2D RMSD Test. CPPTRAJ: 2D RMSD Test, mass-weighted. CPPTRAJ: 2D RMSD Test with reference trajectory CPPTRAJ: 2D DME Test. CPPTRAJ: 2D RMSD with reference mask test. CPPTRAJ: 2D RMSD test, no fitting. All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Mol2 CPPTRAJ: Mol2 Parm/Traj Read/Write Test. CPPTRAJ: PDB => Mol2 CPPTRAJ: Amber Top/Rst => Mol2 Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. Skipped test: Amber Top/Rst => Mol2, SYBYL atom types All 4 comparisons passed. 1 comparisons skipped. ******************************************************************************** TEST: /<>/test/Test_NAstruct CPPTRAJ: NAstruct command test. CPPTRAJ: NAstruct command test, single strand All 11 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_NAstruct_8OG CPPTRAJ: NA test (8OG) All 3 comparisons passed. g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-3build1 -std=gnu++11 -I/<>/src -c -o CpptrajStdio.o /<>/src/CpptrajStdio.cpp ******************************************************************************** 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. g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/cpptraj-5.1.0+dfsg-3build1 -std=gnu++11 -I/<>/src -c -o StringRoutines.o /<>/src/StringRoutines.cpp ******************************************************************************** TEST: /<>/test/Test_AtomMap CPPTRAJ: AtomMap Test CPPTRAJ: AtomMap with 'rmsfit' CPPTRAJ: Atom map charmm->amber atom order CPPTRAJ: Atom map charmm->amber atom order, by residue All 9 comparisons passed. ******************************************************************************** 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 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 g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o 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 make[5]: Leaving directory '/<>/unitTests/ArgList' Unit test passed. make[4]: Leaving directory '/<>/unitTests' make[3]: Leaving directory '/<>/unitTests' 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 CPPTRAJ: SPAM Pure Solvent Test All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_LIE CPPTRAJ: LIE test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Density CPPTRAJ: Density along axis tests CPPTRAJ: Multi-frame density along axis test CPPTRAJ: Total system density test All 7 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_LipidOrder CPPTRAJ: Lipid Order Parameter Test. All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_LipidSCD CPPTRAJ: Basic lipid order parameter test CPPTRAJ: New Lipid Order Parameter Test, DOPC. All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_PairDist CPPTRAJ: PairDist Test. CPPTRAJ: Pairdist test, orthogonal imaging. CPPTRAJ: Pairdist test, nonorthogonal imaging. CPPTRAJ: Pairdist test, 2 masks. All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_ReadData CPPTRAJ: Read vector data test (no origins, origins) CPPTRAJ: Read vector data set (origins, no origins) CPPTRAJ: Read Amber output test CPPTRAJ: Read CHARMM output test CPPTRAJ: 3D data read/write test CPPTRAJ: Standard 3D data write test CPPTRAJ: Standard 3D data read test CPPTRAJ: Standard 3D data read/append test CPPTRAJ: Standard 3D data, sparse CPPTRAJ: Nonorthogonal grid standard write/read tests. CPPTRAJ: Read specific columns test. CPPTRAJ: Write non-square matrix CPPTRAJ: Read non-square matrix CPPTRAJ: Read square matrix All 15 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_GIST CPPTRAJ: GIST water-water interaction test CPPTRAJ: GIST test, orthogonal cell CPPTRAJ: GIST test, nonorthogonal cell All 11 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_GIST_Order CPPTRAJ: TIP3P water cluster test CPPTRAJ: TIP4P water cluster test CPPTRAJ: TIP5P water cluster test All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_systemVF CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_AtomicCorr CPPTRAJ: Atomic Correlation test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_AutoCorr CPPTRAJ: AutoCorr test. All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Box CPPTRAJ: Box Test (Add box info) CPPTRAJ: Box test (remove box info) CPPTRAJ: Box test (Modify box length) CPPTRAJ: Box test (auto orthogonal box, no radii) CPPTRAJ: Box test (auto orthogonal box, VDW radii) All 7 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_AtomTypeSelect CPPTRAJ: Selection by atom type test. All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_AvgRef CPPTRAJ: RMSD Test with averaged reference coordinates. All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Crank_Stat CPPTRAJ: Crankshaft test All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CreateCrd CPPTRAJ: COORDS data set creation and CRDFLUCT test. CPPTRAJ: COORDS data set creation with velocities test CPPTRAJ: TRAJ data set creation and CRDFLUCT test. CPPTRAJ: TRAJ data set creation with velocities test. CPPTRAJ: COORDS data set append test CPPTRAJ: COORDS test storing frame metadata CPPTRAJ: TRAJ test storing frame metadata All 8 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_AutoImage CPPTRAJ: AutoImage test (split DNA duplex) CPPTRAJ: AutoImage test, use anchor mask All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_LoadCrd CPPTRAJ: LoadCrd test. CPPTRAJ: LoadTraj test. CPPTRAJ: LoadTraj from trajin test. CPPTRAJ: LoadCrd append from multiple files test All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_MultiVector CPPTRAJ: Multivector test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Lifetime CPPTRAJ: Lifetime test. CPPTRAJ: Lifetime test with data set caching. CPPTRAJ: Lifetime average and cumulative average test. All 12 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_FFT CPPTRAJ: FFT test. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Timecorr CPPTRAJ: Timecorr test. All 7 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CrossCorr CPPTRAJ: CrossCorr test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_SymmRmsd CPPTRAJ: SymmRmsd CPPTRAJ: ASP symmetry-corrected RMSD test CPPTRAJ: GLU symmetry-corrected RMSD test CPPTRAJ: TYR symmetry-corrected RMSD test CPPTRAJ: Longer symmetry-corrected RMSD test. All 8 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Multidihedral CPPTRAJ: Multidihedral test CPPTRAJ: Multidihedral Nucleotide CHI test CPPTRAJ: Multidihedral protein dihedrals test CPPTRAJ: Multidihedral cyclic molecule test All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Ensemble_MREMD CPPTRAJ: M-REMD sort test. CPPTRAJ: M-REMD actions test. CPPTRAJ: M-REMD ensemble outtraj test. CPPTRAJ: M-REMD no sort, running average test CPPTRAJ: M-REMD, generate RMS data CPPTRAJ: M-REMD, meltcurve analysis All 17 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_MakeStructure CPPTRAJ: Basic makestructure test CPPTRAJ: Makestructure test with reference. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Rotate CPPTRAJ: Rotation (and inverse) of coords from matrices CPPTRAJ: Rotate with defined axis All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Integrate CPPTRAJ: Integration test. All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_NativeContacts CPPTRAJ: NativeContacts test. CPPTRAJ: NativeContacts test, save non-native contacts, residue time series CPPTRAJ: NativeContacts test, orthorhombic imaging. All 17 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CheckChiral CPPTRAJ: Check chirality test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Energy CPPTRAJ: Simple energy tests CPPTRAJ: Test kinetic energy calculation CPPTRAJ: Test total energy calculation CPPTRAJ: Test partial energy calculation All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_LESsplit CPPTRAJ: LES split/average test All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_PermuteDihedrals CPPTRAJ: PermuteDihedrals interval -120, phi psi CPPTRAJ: PermuteDihedrals, random rotations All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CCP4 CPPTRAJ: CCP4 read/write and DX conversion test. All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_DihCovar CPPTRAJ: Dihedral Covariance Matrix Test All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CurveFit CPPTRAJ: Curve fitting test. CPPTRAJ: Curve fitting multi-exponential tests. CPPTRAJ: Curve fitting, custom output range. All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Multicurve CPPTRAJ: Multicurve test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_DataSetAverage CPPTRAJ: Data set averaging and averaging over all sets test. All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_VectorMath CPPTRAJ: Vector dot/cross product test All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Esander SANDER energy tests (long) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. SKIP: SANDER energy tests (long) ******************************************************************************** TEST: /<>/test/Test_Esander_Short Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. SKIP: Energy via sander API short tests (GB/PME) ******************************************************************************** TEST: /<>/test/Test_Temperature CPPTRAJ: Temperature test. CPPTRAJ: Temperature with SHAKE on hydrogens. CPPTRAJ: Temperature with SHAKE on all atoms. CPPTRAJ: Temperature calc with extra points. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Spline CPPTRAJ: Spline test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_KDE CPPTRAJ: KDE test. CPPTRAJ: KDE with Kullback-Leibler divergence test All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Wavelet CPPTRAJ: Wavelet analysis test CPPTRAJ: Wavelet WAFEX test All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CIF CPPTRAJ: CIF read test CPPTRAJ: Generate offset traj from PDB CPPTRAJ: Generate offset traj from CIF All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_PDB CPPTRAJ: PDB format read/write test CPPTRAJ: PQR file write with various radii CPPTRAJ: PDB filter alternate atom location IDs test CPPTRAJ: Adding PDB info to topology All 10 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Align CPPTRAJ: Align Tests. CPPTRAJ: Align, unit cell rotation/imaging test. All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_VelocityAutoCorr CPPTRAJ: Velocity autocorrelation test All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_VelFrc CPPTRAJ: Test combining coordinates, velocities, and forces. CPPTRAJ: Test using velocities as coordinates. CPPTRAJ: Test writing velocities (MDVEL) CPPTRAJ: Test using forces as coordinates. CPPTRAJ: Test writing forces (MDFRC) CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_RotateDihedral CPPTRAJ: Rotate dihedral to target value. CPPTRAJ: Rotate dihedral by increment CPPTRAJ: Rotate dihedral in TRAJ data set All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_DataSetCmd CPPTRAJ: Data Set commands test All 10 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Remap CPPTRAJ: Remap Test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CompareTop CPPTRAJ: Compare topology test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Filter CPPTRAJ: Basic filter test CPPTRAJ: Data filter test. CPPTRAJ: Filter matrix test. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CombineCrd CPPTRAJ: Combine COORDS test. CPPTRAJ: Combine COORDS test with box info. CPPTRAJ: Split coords and recombine test. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_TopInfo CPPTRAJ: Topology info print test. CPPTRAJ: Topology info with reference coords test All 12 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_GromacsTrr CPPTRAJ: TRR force/velocity read -> NetCDF write test CPPTRAJ: TRR force/velocity read -> TRR write test CPPTRAJ: CRD => TRR CPPTRAJ: TRR => CRD CPPTRAJ: CRD(1-5) => TRR CPPTRAJ: CRD(6-10) => TRR CPPTRAJ: TRR (appended) => CRD CPPTRAJ: GMX: CRD with offset CPPTRAJ: GMX: TRR with offset All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_GromacsXtc CPPTRAJ: XTC read test CPPTRAJ: CRD => XTC CPPTRAJ: XTC => CRD CPPTRAJ: CRD(1-5) => XTC CPPTRAJ: CRD(6-10) => XTC CPPTRAJ: XTC (appended) => CRD CPPTRAJ: GMX: CRD with offset CPPTRAJ: GMX: XTC with offset All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_GromacsTNG CPPTRAJ: TNG read test CPPTRAJ: TNG read test (with offset) All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Ewald CPPTRAJ: Direct sum test CPPTRAJ: Ewald test (NaCl crystal) CPPTRAJ: Ewald test (trunc. oct) CPPTRAJ: Ewald test (partial system, trunc. oct) Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: Ewald test (trunc. oct), 10 frames Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: Ewald test (ortho), 10 frames All 4 comparisons passed. 2 comparisons skipped. ******************************************************************************** TEST: /<>/test/Test_LibPME CPPTRAJ: Particle mesh Ewald test (NaCl crystal) CPPTRAJ: Particle mesh Ewald test (trunc. oct) CPPTRAJ: Particle mesh Ewald test (ortho) CPPTRAJ: Particle mesh Ewald test (ortho, with mask) CPPTRAJ: PME test (partial system, trunc. oct) PME test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: PME test (trunc. oct), 10 frames All 5 comparisons passed. 1 comparisons skipped. ******************************************************************************** TEST: /<>/test/Test_LJ_PME CPPTRAJ: LJ PME test. CPPTRAJ: LJ PME kappa sweep test, 0.25 CPPTRAJ: LJ PME kappa sweep test, 0.35 CPPTRAJ: LJ PME kappa sweep test, 0.45 CPPTRAJ: LJ PME kappa sweep test, 0.5 CPPTRAJ: LJ with switch function test All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_TI CPPTRAJ: TI analysis test. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_FixImagedBonds CPPTRAJ: Fix imaged bonds test (Ortho.) CPPTRAJ: Fix imaged bonds test (Non-ortho.) All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Distance CPPTRAJ: Distance tests CPPTRAJ: Orthogonal imaged distance CPPTRAJ: Non-orthogonal imaged distance All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Volume CPPTRAJ: Volume tests All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_SetVelocity CPPTRAJ: Set Velocity test CPPTRAJ: Scale velocity test All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Remlog CPPTRAJ: Replica log read/analyze test. All 7 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_AreaPerMol CPPTRAJ: Area per molecule test All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_DistBasedMask CPPTRAJ: Distance-based atom mask tests (atom, residue) CPPTRAJ: Distance-based atom mask tests (molecule) All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Calc CPPTRAJ: Calc test CPPTRAJ: Calc test with data sets CPPTRAJ: Test math functions All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CalcState CPPTRAJ: Calcstate test All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Change CPPTRAJ: Change atom and residue name tests CPPTRAJ: Change chain ID test CPPTRAJ: Change chain ID of COORDS set test All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CreateReservoir CPPTRAJ: Create RREMD NetCDF reservoir test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_FixAtomOrder CPPTRAJ: Out of order molecules test All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_LowestCurve CPPTRAJ: LowestCurve test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_MinImage CPPTRAJ: Minimum Image test. All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Regress CPPTRAJ: Linear regression test. All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Rst CPPTRAJ: Generate restraints (rst) test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Pairwise CPPTRAJ: Pairwise tests CPPTRAJ: Pairwise test, partial system All 10 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_ParmBox CPPTRAJ: Parmbox test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Solvent CPPTRAJ: Test solvent command with closest All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Translate CPPTRAJ: Translate test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_ReplicateCell CPPTRAJ: Replicate cell test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_ScaleDihedralK CPPTRAJ: Scale dihedral force constant test CPPTRAJ: Scale dihedral force constant with 'useall' All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_PhiPsi CPPTRAJ: Phipsi test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Control CPPTRAJ: Loop tests CPPTRAJ: Test set command CPPTRAJ: Test reading comma-separated list of strings CPPTRAJ: Test nested loops and variables in loops CPPTRAJ: Test loop over data set blocks CPPTRAJ: Test for filename wildcards and oversets All 13 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_InfraredSpec CPPTRAJ: Infrared spectrum calculation test All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Cphstats CPPTRAJ: Explicit pH REMD ensemble data read / sort CPPTRAJ: Constant pH stats test CPPTRAJ: Sorted implicit constant pH stats test CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats CPPTRAJ: Unsorted pH read/write test All 16 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CmdLine CPPTRAJ: Command line trajectory args test, part 1 CPPTRAJ: Command line test trajectory args test, part 2 CPPTRAJ: Command line wildcard test, part 1 CPPTRAJ: Command line wildcard test, part 2 All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_XYZformat CPPTRAJ: XYZ format write CPPTRAJ: Atom XYZ format read, test 1 CPPTRAJ: Atom XYZ format read, test 2 CPPTRAJ: Atom XYZ format read, test 3 CPPTRAJ: Atom XYZ format read, test 4 CPPTRAJ: Atom XYZ format read, test 5 CPPTRAJ: Atom XYZ format read, test 6 All 6 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Hausdorff CPPTRAJ: Simple Hausdorff distance test. CPPTRAJ: Hausdorff distance of 2D rms output test. CPPTRAJ: Hausdorff distance of 2D rms output test. All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_CatCrd CPPTRAJ: Concatenate COORDS data set test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_XtalSymm CPPTRAJ: XtalSymm Reference CPPTRAJ: XtalSymm Reimaging by Atom CPPTRAJ: XtalSymm Reimaging by Molecule All 3 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Time CPPTRAJ: Add time to restart test CPPTRAJ: Remove time from restart test CPPTRAJ: Add time to trajectory test CPPTRAJ: Modify time info test. All 4 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_SplitCoords CPPTRAJ: SplitCoords test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_DihedralRMS CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) CPPTRAJ: Dihedral RMSD test (to previous) CPPTRAJ: Dihedral RMS fluctuation test. All 5 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Slope CPPTRAJ: Finite difference test. All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Diagmatrix CPPTRAJ: MW covariance matrix thermo analysis test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Emin CPPTRAJ: Basic energy minimization test. CPPTRAJ: Energy minimization with angle term test. CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. CPPTRAJ: Energy minimization with nonbond term test. CPPTRAJ: OpenMM basic energy minimization tests (bonds) CPPTRAJ: OpenMM basic energy minimization tests (angles) CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) All 9 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_EvalPlateau CPPTRAJ: Evalulate plateau test All 2 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Graft CPPTRAJ: Graft test All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Flatten CPPTRAJ: Flatten test. All 1 comparisons passed. ******************************************************************************** TEST: /<>/test/Test_Random CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs CPPTRAJ: PCG32 RNG test. CPPTRAJ: Test Stdlib RNG CPPTRAJ: Test Mersenne Twister RNG All 4 comparisons passed. make[4]: Leaving directory '/<>/test' make[3]: Leaving directory '/<>/test' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/cpptraj/ make -j4 install DESTDIR=/<>/cpptraj-5.1.0\+dfsg/debian/cpptraj AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>' cd src && make install make[2]: Entering directory '/<>/src' Skipping bundled READLINE build Skipping bundled ARPACK build g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o -L/usr/lib/x86_64-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/x86_64-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/x86_64-linux-gnu/lib -lfftw3 -L/usr/lib/x86_64-linux-gnu/lib -lOpenMM -lnetcdf -lbz2 tng/libtng_io.a -lz xdrfile/libxdrfile.a -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro mv cpptraj "/<>/bin" make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a 2e1f72f08d56511b046451798ca336ccfc7f0b90 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 153 INFO: pkgstriptranslations version 153 pkgstriptranslations: processing cpptraj (in debian/cpptraj); do_strip: , oemstrip: pkgstriptranslations: processing cpptraj-dbgsym (in debian/.debhelper/cpptraj/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/cpptraj/DEBIAN/control, package cpptraj, directory debian/cpptraj pkgstripfiles: Running PNG optimization (using 4 cpus) for package cpptraj ... pkgstripfiles: No PNG files. dpkg-deb: building package 'cpptraj' in '../cpptraj_5.1.0+dfsg-3build1_amd64.deb'. pkgstripfiles: processing control file: debian/.debhelper/cpptraj/dbgsym-root/DEBIAN/control, package cpptraj-dbgsym, directory debian/.debhelper/cpptraj/dbgsym-root dpkg-deb: building package 'cpptraj-dbgsym' in 'debian/.debhelper/scratch-space/build-cpptraj/cpptraj-dbgsym_5.1.0+dfsg-3build1_amd64.deb'. Renaming cpptraj-dbgsym_5.1.0+dfsg-3build1_amd64.deb to cpptraj-dbgsym_5.1.0+dfsg-3build1_amd64.ddeb dpkg-genbuildinfo --build=binary -O../cpptraj_5.1.0+dfsg-3build1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../cpptraj_5.1.0+dfsg-3build1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-06-27T18:12:57Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ cpptraj_5.1.0+dfsg-3build1_amd64.changes: ----------------------------------------- Format: 1.8 Date: Tue, 27 Jun 2023 14:04:24 -0400 Source: cpptraj Binary: cpptraj Built-For-Profiles: noudeb Architecture: amd64 Version: 5.1.0+dfsg-3build1 Distribution: mantic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Jeremy Bícha Description: cpptraj - fast, parallelized molecular dynamics trajectory data analysis Changes: cpptraj (5.1.0+dfsg-3build1) mantic; urgency=medium . * Rebuild against latest openmm Checksums-Sha1: 94779e67172989a77021e1b9d257bd45095881f5 33334506 cpptraj-dbgsym_5.1.0+dfsg-3build1_amd64.ddeb 5cdd38fb53575bc52d315c332ddd90e86affb8d2 7994 cpptraj_5.1.0+dfsg-3build1_amd64.buildinfo d5cd925129c959c15fc35c26eb7e5c812e2fce9c 1818086 cpptraj_5.1.0+dfsg-3build1_amd64.deb Checksums-Sha256: bd971283f3e14e906be4e6ab4933fb488c30ff049103ec9b50f829db6a471f30 33334506 cpptraj-dbgsym_5.1.0+dfsg-3build1_amd64.ddeb 239874ef3ced9c29e893c27eaa94bdc0ec0ffea08bbea55e6f81cba462066a96 7994 cpptraj_5.1.0+dfsg-3build1_amd64.buildinfo b12df08651ee50a73acdd881915ceb3a3963884fa4a4c5ba6b0a6711a7b817a8 1818086 cpptraj_5.1.0+dfsg-3build1_amd64.deb Files: 55d1267838e21a6247b32499249c0dcc 33334506 debug optional cpptraj-dbgsym_5.1.0+dfsg-3build1_amd64.ddeb 3306adccff6b2345dd2dee84951c0201 7994 science optional cpptraj_5.1.0+dfsg-3build1_amd64.buildinfo 4af34b2485d7c7de20c7b040f3a68965 1818086 science optional cpptraj_5.1.0+dfsg-3build1_amd64.deb /<>/cpptraj_5.1.0+dfsg-3build1_amd64.changes.new could not be renamed to /<>/cpptraj_5.1.0+dfsg-3build1_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: cpptraj Binary: cpptraj cpptraj-dbgsym Architecture: amd64 Version: 5.1.0+dfsg-3build1 Checksums-Md5: 55d1267838e21a6247b32499249c0dcc 33334506 cpptraj-dbgsym_5.1.0+dfsg-3build1_amd64.ddeb 4af34b2485d7c7de20c7b040f3a68965 1818086 cpptraj_5.1.0+dfsg-3build1_amd64.deb Checksums-Sha1: 94779e67172989a77021e1b9d257bd45095881f5 33334506 cpptraj-dbgsym_5.1.0+dfsg-3build1_amd64.ddeb d5cd925129c959c15fc35c26eb7e5c812e2fce9c 1818086 cpptraj_5.1.0+dfsg-3build1_amd64.deb Checksums-Sha256: bd971283f3e14e906be4e6ab4933fb488c30ff049103ec9b50f829db6a471f30 33334506 cpptraj-dbgsym_5.1.0+dfsg-3build1_amd64.ddeb b12df08651ee50a73acdd881915ceb3a3963884fa4a4c5ba6b0a6711a7b817a8 1818086 cpptraj_5.1.0+dfsg-3build1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Tue, 27 Jun 2023 18:12:56 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-12), autotools-dev (= 20220109.1), base-files (= 13ubuntu1), base-passwd (= 3.6.1), bash (= 5.2.15-2ubuntu1), binutils (= 2.40.50.20230622-1ubuntu1), binutils-common (= 2.40.50.20230622-1ubuntu1), binutils-x86-64-linux-gnu (= 2.40.50.20230622-1ubuntu1), bsdextrautils (= 2.38.1-5ubuntu2), bsdutils (= 1:2.38.1-5ubuntu2), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), coreutils (= 9.1-1ubuntu2), cpp (= 4:12.2.0-3ubuntu1), cpp-12 (= 12.3.0-3ubuntu1), dash (= 0.5.12-2ubuntu1), debconf (= 1.5.82), debhelper (= 13.11.4ubuntu3), debianutils (= 5.7-0.4), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.8-4), dpkg (= 1.21.22ubuntu1), dpkg-dev (= 1.21.22ubuntu1), dwz (= 0.15-1), file (= 1:5.44-3), findutils (= 4.9.0-4ubuntu1), g++ (= 4:12.2.0-3ubuntu1), g++-12 (= 12.3.0-3ubuntu1), gcc (= 4:12.2.0-3ubuntu1), gcc-12 (= 12.3.0-3ubuntu1), gcc-12-base (= 12.3.0-3ubuntu1), gcc-13-base (= 13.1.0-6ubuntu1), gettext (= 0.21-12), gettext-base (= 0.21-12), gfortran (= 4:12.2.0-3ubuntu1), gfortran-12 (= 12.3.0-3ubuntu1), grep (= 3.8-5), groff-base (= 1.22.4-10), gzip (= 1.12-1ubuntu1), hdf5-helpers (= 1.10.8+repack1-1ubuntu1), hostname (= 3.23+nmu1ubuntu1), icu-devtools (= 72.1-3ubuntu2), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libaec-dev (= 1.0.6-1), libaec0 (= 1.0.6-1), libarchive-zip-perl (= 1.68-1), libarpack2 (= 3.8.0-3), libarpack2-dev (= 3.8.0-3), libasan8 (= 13.1.0-6ubuntu1), libatomic1 (= 13.1.0-6ubuntu1), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.0.9-1), libaudit1 (= 1:3.0.9-1), libbinutils (= 2.40.50.20230622-1ubuntu1), libblas-dev (= 3.11.0-2), libblas3 (= 3.11.0-2), libblkid1 (= 2.38.1-5ubuntu2), libbrotli1 (= 1.0.9-2build8), libbz2-1.0 (= 1.0.8-5build1), libbz2-dev (= 1.0.8-5build1), libc-bin (= 2.37-0ubuntu2), libc-dev-bin (= 2.37-0ubuntu2), libc6 (= 2.37-0ubuntu2), libc6-dev (= 2.37-0ubuntu2), libcap-ng0 (= 0.8.3-1build2), libcap2 (= 1:2.66-4ubuntu1), libcc1-0 (= 13.1.0-6ubuntu1), libcom-err2 (= 1.47.0-1ubuntu1), libcrypt-dev (= 1:4.4.35-1), libcrypt1 (= 1:4.4.35-1), libctf-nobfd0 (= 2.40.50.20230622-1ubuntu1), libctf0 (= 2.40.50.20230622-1ubuntu1), libcurl3-gnutls (= 7.88.1-10ubuntu1), libcurl4 (= 7.88.1-10ubuntu1), libcurl4-gnutls-dev (= 7.88.1-10ubuntu1), libdb5.3 (= 5.3.28+dfsg2-1), libdebconfclient0 (= 0.267ubuntu1), libdebhelper-perl (= 13.11.4ubuntu3), libdpkg-perl (= 1.21.22ubuntu1), libdw1 (= 0.188-2.1), libelf1 (= 0.188-2.1), libffi8 (= 3.4.4-1), libfftw3-bin (= 3.3.10-1ubuntu1), libfftw3-dev (= 3.3.10-1ubuntu1), libfftw3-double3 (= 3.3.10-1ubuntu1), libfftw3-long3 (= 3.3.10-1ubuntu1), libfftw3-quad3 (= 3.3.10-1ubuntu1), libfftw3-single3 (= 3.3.10-1ubuntu1), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-12-dev (= 12.3.0-3ubuntu1), libgcc-s1 (= 13.1.0-6ubuntu1), libgcrypt20 (= 1.10.1-3ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgfortran-12-dev (= 12.3.0-3ubuntu1), libgfortran5 (= 13.1.0-6ubuntu1), libgmp10 (= 2:6.2.1+dfsg1-1.1ubuntu1), libgnutls30 (= 3.7.9-2ubuntu1), libgomp1 (= 13.1.0-6ubuntu1), libgpg-error0 (= 1.46-1), libgprofng0 (= 2.40.50.20230622-1ubuntu1), libgssapi-krb5-2 (= 1.20.1-2), libhdf5-103-1 (= 1.10.8+repack1-1ubuntu1), libhdf5-cpp-103-1 (= 1.10.8+repack1-1ubuntu1), libhdf5-dev (= 1.10.8+repack1-1ubuntu1), libhdf5-fortran-102 (= 1.10.8+repack1-1ubuntu1), libhdf5-hl-100 (= 1.10.8+repack1-1ubuntu1), libhdf5-hl-cpp-100 (= 1.10.8+repack1-1ubuntu1), libhdf5-hl-fortran-100 (= 1.10.8+repack1-1ubuntu1), libhogweed6 (= 3.8.1-2), libicu-dev (= 72.1-3ubuntu2), libicu72 (= 72.1-3ubuntu2), libidn2-0 (= 2.3.3-1build1), libisl23 (= 0.26-3), libitm1 (= 13.1.0-6ubuntu1), libjansson4 (= 2.14-2), libjpeg-dev (= 8c-2ubuntu11), libjpeg-turbo8 (= 2.1.5-2ubuntu1), libjpeg-turbo8-dev (= 2.1.5-2ubuntu1), libjpeg8 (= 8c-2ubuntu11), libjpeg8-dev (= 8c-2ubuntu11), libk5crypto3 (= 1.20.1-2), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-2), libkrb5support0 (= 1.20.1-2), liblapack-dev (= 3.11.0-2), liblapack3 (= 3.11.0-2), libldap2 (= 2.6.3+dfsg-1~exp1ubuntu2), liblsan0 (= 13.1.0-6ubuntu1), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.1-0.2), libmagic-mgc (= 1:5.44-3), libmagic1 (= 1:5.44-3), libmd0 (= 1.1.0-1), libmount1 (= 2.38.1-5ubuntu2), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.0-1), libncurses-dev (= 6.4-4), libncurses6 (= 6.4-4), libncursesw6 (= 6.4-4), libnetcdf-dev (= 1:4.9.2-1), libnetcdf19 (= 1:4.9.2-1), libnettle8 (= 3.8.1-2), libnghttp2-14 (= 1.54.0-1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libopenmm-dev (= 8.0.0+dfsg-2), libopenmm8.0 (= 8.0.0+dfsg-2), libp11-kit0 (= 0.24.1-2ubuntu1), libpam-modules (= 1.5.2-6ubuntu1), libpam-modules-bin (= 1.5.2-6ubuntu1), libpam-runtime (= 1.5.2-6ubuntu1), libpam0g (= 1.5.2-6ubuntu1), libpcre2-8-0 (= 10.42-1), libperl5.36 (= 5.36.0-7ubuntu1), libpipeline1 (= 1.5.7-1), libpsl5 (= 0.21.2-1), libquadmath0 (= 13.1.0-6ubuntu1), libreadline-dev (= 8.2-1.3), libreadline8 (= 8.2-1.3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg1-1), libsasl2-modules-db (= 2.1.28+dfsg1-1), libseccomp2 (= 2.5.4-1ubuntu3), libselinux1 (= 3.4-1build4), libsmartcols1 (= 2.38.1-5ubuntu2), libssh-4 (= 0.10.5-2), libssl-dev (= 3.0.9-1ubuntu1), libssl3 (= 3.0.9-1ubuntu1), libstdc++-12-dev (= 12.3.0-3ubuntu1), libstdc++6 (= 13.1.0-6ubuntu1), libsub-override-perl (= 0.09-4), libsystemd0 (= 252.5-2ubuntu3), libsz2 (= 1.0.6-1), libtasn1-6 (= 4.19.0-2), libtinfo6 (= 6.4-4), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-5), libtsan2 (= 13.1.0-6ubuntu1), libubsan1 (= 13.1.0-6ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 252.5-2ubuntu3), libunistring2 (= 1.0-2), libuuid1 (= 2.38.1-5ubuntu2), libxml2 (= 2.9.14+dfsg-1.2), libxml2-dev (= 2.9.14+dfsg-1.2), libzstd1 (= 1.5.4+dfsg2-5), linux-libc-dev (= 6.3.0-7.7), login (= 1:4.13+dfsg1-1ubuntu1), lto-disabled-list (= 41), m4 (= 1.4.19-3), make (= 4.3-4.1build1), man-db (= 2.11.2-2), mawk (= 1.3.4.20230525-1), ncurses-base (= 6.4-4), ncurses-bin (= 6.4-4), netcdf-bin (= 1:4.9.2-1), patch (= 2.7.6-7build2), perl (= 5.36.0-7ubuntu1), perl-base (= 5.36.0-7ubuntu1), perl-modules-5.36 (= 5.36.0-7ubuntu1), po-debconf (= 1.0.21+nmu1), readline-common (= 8.2-1.3), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-1), sensible-utils (= 0.0.20), sysvinit-utils (= 3.06-4ubuntu1), tar (= 1.34+dfsg-1.2ubuntu1), usrmerge (= 35ubuntu1), util-linux (= 2.38.1-5ubuntu2), util-linux-extra (= 2.38.1-5ubuntu2), xz-utils (= 5.4.1-0.2), zlib1g (= 1:1.2.13.dfsg-1ubuntu4), zlib1g-dev (= 1:1.2.13.dfsg-1ubuntu4) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1687889064" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ cpptraj_5.1.0+dfsg-3build1_amd64.deb ------------------------------------ new Debian package, version 2.0. size 1818086 bytes: control archive=853 bytes. 885 bytes, 15 lines control 328 bytes, 5 lines md5sums Package: cpptraj Version: 5.1.0+dfsg-3build1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debichem Team Installed-Size: 4942 Depends: libarpack2 (>= 2.1), libbz2-1.0, libc6 (>= 2.34), libfftw3-double3 (>= 3.3.10), libgcc-s1 (>= 3.3.1), liblapack3 | liblapack.so.3, libnetcdf19 (>= 3.6.1), libopenmm8.0 (>= 8.0.0+dfsg), libreadline8 (>= 6.0), libstdc++6 (>= 11), zlib1g (>= 1:1.2.3.4) Section: science Priority: optional Homepage: https://github.com/Amber-MD/cpptraj Description: fast, parallelized molecular dynamics trajectory data analysis CPPTRAJ is a program designed to process and analyze molecular dynamics trajectories and relevant data sets derived from their analysis. CPPTRAJ supports many popular MD software packages including Amber, CHARMM, Gromacs, and NAMD. drwxr-xr-x root/root 0 2023-06-27 18:04 ./ drwxr-xr-x root/root 0 2023-06-27 18:04 ./usr/ drwxr-xr-x root/root 0 2023-06-27 18:04 ./usr/bin/ -rwxr-xr-x root/root 5042280 2023-06-27 18:04 ./usr/bin/cpptraj drwxr-xr-x root/root 0 2023-06-27 18:04 ./usr/share/ drwxr-xr-x root/root 0 2023-06-27 18:04 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-06-27 18:04 ./usr/share/doc/cpptraj/ -rw-r--r-- root/root 343 2022-11-24 15:08 ./usr/share/doc/cpptraj/README.Debian -rw-r--r-- root/root 422 2023-06-27 18:04 ./usr/share/doc/cpptraj/changelog.Debian.gz -rw-r--r-- root/root 4005 2022-11-24 15:08 ./usr/share/doc/cpptraj/copyright drwxr-xr-x root/root 0 2023-06-27 18:04 ./usr/share/man/ drwxr-xr-x root/root 0 2023-06-27 18:04 ./usr/share/man/man1/ -rw-r--r-- root/root 1034 2023-06-27 18:04 ./usr/share/man/man1/cpptraj.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 1521068 Build-Time: 320 Distribution: mantic-proposed Host Architecture: amd64 Install-Time: 9 Job: cpptraj_5.1.0+dfsg-3build1.dsc Machine Architecture: amd64 Package: cpptraj Package-Time: 333 Source-Version: 5.1.0+dfsg-3build1 Space: 1521068 Status: successful Version: 5.1.0+dfsg-3build1 -------------------------------------------------------------------------------- Finished at 2023-06-27T18:12:57Z Build needed 00:05:33, 1521068k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26342895 Scanning for processes to kill in build PACKAGEBUILD-26342895