debspawn 0.6.5 on estragon at 2025-03-18 16:57:17 UTC-0400 dpkg-source: info: extracting cpptraj in cpptraj-5.1.0+dfsg dpkg-source: info: unpacking cpptraj_5.1.0+dfsg.orig.tar.xz dpkg-source: info: unpacking cpptraj_5.1.0+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-system-libraries.patch dpkg-source: info: applying skip-failing-test.patch ╔═══════════════════════╗ ║ Package build ║ ╚═══════════════════════╝ Package: cpptraj Version: 5.1.0+dfsg-4 Distribution: landing Architecture: arm64 Free space in workspace: 173.1GiB ┌───────────────────────────────────────┐ │ Preparing container for build │ └───────────────────────────────────────┘ Get:1 https://repo.pureos.net/pureos landing InRelease [9625 B] Get:2 https://repo.pureos.net/pureos landing/main all Packages [3954 kB] Get:3 https://repo.pureos.net/pureos landing/main arm64 Packages [4516 kB] Fetched 8480 kB in 5s (1816 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libapt-pkg6.0t64 libgnutls30t64 libperl5.38t64 libpython3.12-minimal perl-modules-5.38 python3.12-minimal Use 'apt autoremove' to remove them. The following NEW packages will be installed: libapt-pkg7.0 libperl5.40 libpython3.13-minimal perl-modules-5.40 python3.13-minimal sqv The following packages will be upgraded: adduser apt base-passwd bash binutils binutils-aarch64-linux-gnu binutils-common bsdutils build-essential ca-certificates coreutils cpp-12 cpp-14 cpp-14-aarch64-linux-gnu dash debconf debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot g++-12 g++-14 g++-14-aarch64-linux-gnu gcc-12 gcc-12-base gcc-14 gcc-14-aarch64-linux-gnu gcc-14-base gpgv grep gzip init-system-helpers libacl1 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 libctf-nobfd0 libctf0 libdb5.3t64 libdebconfclient0 libdpkg-perl libeatmydata1 libexpat1 libext2fs2t64 libfakeroot libffi8 libgcc-12-dev libgcc-14-dev libgcc-s1 libgcrypt20 libgmp10 libgnutls30t64 libgomp1 libgpg-error0 libgprofng0 libgssapi-krb5-2 libhogweed6t64 libhwasan0 libidn2-0 libitm1 libjansson4 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblsan0 liblz4-1 liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libnettle8t64 libnsl-dev libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpython3.12-minimal libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libss2 libssl3t64 libstdc++-12-dev libstdc++-14-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtirpc-dev libtirpc3t64 libtsan2 libubsan1 libudev1 libunistring5 libuuid1 libxxhash0 libzstd1 linux-libc-dev login login.defs logsave make mawk mount ncurses-base ncurses-bin openssl openssl-provider-legacy passwd patch perl perl-base python3-minimal python3.12-minimal rpcsvc-proto sed sysvinit-utils tar tzdata usrmerge util-linux util-linux-extra xz-utils zlib1g 149 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. 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Leaving 'diversion of /sbin/ctrlaltdel to /sbin/ctrlaltdel.usr-is-merged by util-linux-extra' Leaving 'diversion of /sbin/fsck.cramfs to /sbin/fsck.cramfs.usr-is-merged by util-linux-extra' Leaving 'diversion of /sbin/fsck.minix to /sbin/fsck.minix.usr-is-merged by util-linux-extra' Leaving 'diversion of /sbin/mkfs.bfs to /sbin/mkfs.bfs.usr-is-merged by util-linux-extra' Leaving 'diversion of /sbin/mkfs.cramfs to /sbin/mkfs.cramfs.usr-is-merged by util-linux-extra' Leaving 'diversion of /sbin/mkfs.minix to /sbin/mkfs.minix.usr-is-merged by util-linux-extra' Unpacking util-linux-extra (2.40.4-5) over (2.40.2-9) ... Preparing to unpack .../libnettle8t64_3.10.1-1_arm64.deb ... Unpacking libnettle8t64:arm64 (3.10.1-1) over (3.10-1) ... Setting up libnettle8t64:arm64 (3.10.1-1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19500 files and directories currently installed.) Preparing to unpack .../liblzma5_5.6.4-1_arm64.deb ... Unpacking liblzma5:arm64 (5.6.4-1) over (5.6.2-2) ... Setting up liblzma5:arm64 (5.6.4-1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19500 files and directories currently installed.) Preparing to unpack .../libapt-pkg7.0_2.9.33_arm64.deb ... Unpacking libapt-pkg7.0:arm64 (2.9.33) ... Setting up libapt-pkg7.0:arm64 (2.9.33) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19549 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.277_arm64.deb ... Unpacking libdebconfclient0:arm64 (0.277) over (0.272) ... Setting up libdebconfclient0:arm64 (0.277) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19550 files and directories currently installed.) Preparing to unpack .../libacl1_2.3.2-2+b1_arm64.deb ... Unpacking libacl1:arm64 (2.3.2-2+b1) over (2.3.2-2) ... Setting up libacl1:arm64 (2.3.2-2+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19551 files and directories currently installed.) Preparing to unpack .../libattr1_1%3a2.5.2-3_arm64.deb ... Unpacking libattr1:arm64 (1:2.5.2-3) over (1:2.5.2-1) ... Setting up libattr1:arm64 (1:2.5.2-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19551 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.8-1_all.deb ... Unpacking libsemanage-common (3.8-1) over (3.7-2) ... Setting up libsemanage-common (3.8-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19551 files and directories currently installed.) Preparing to unpack .../libsepol2_3.8-1_arm64.deb ... Unpacking libsepol2:arm64 (3.8-1) over (3.7-1) ... Setting up libsepol2:arm64 (3.8-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19551 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.8-1+b1_arm64.deb ... Unpacking libsemanage2:arm64 (3.8-1+b1) over (3.7-2) ... Setting up libsemanage2:arm64 (3.8-1+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19552 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.17.3-1_arm64.deb ... Unpacking passwd (1:4.17.3-1) over (1:4.16.0-4) ... Setting up passwd (1:4.17.3-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19549 files and directories currently installed.) Preparing to unpack .../archives/adduser_3.145_all.deb ... Unpacking adduser (3.145) over (3.137) ... Setting up adduser (3.145) ... Installing new version of config file /etc/adduser.conf ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19531 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-2+b1_arm64.deb ... Unpacking libseccomp2:arm64 (2.5.5-2+b1) over (2.5.5-1+b1) ... Setting up libseccomp2:arm64 (2.5.5-2+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19531 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.33_arm64.deb ... Unpacking apt (2.9.33) over (2.9.8) ... Setting up apt (2.9.33) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19526 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.68_all.deb ... Unpacking init-system-helpers (1.68) over (1.67) ... Setting up init-system-helpers (1.68) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19526 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.5+20250216-2_all.deb ... Unpacking ncurses-base (6.5+20250216-2) over (6.5-2) ... Setting up ncurses-base (6.5+20250216-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19526 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.14-4_arm64.deb ... Unpacking sysvinit-utils (3.14-4) over (3.10-2) ... Setting up sysvinit-utils (3.14-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19526 files and directories currently installed.) Preparing to unpack .../logsave_1.47.2-1_arm64.deb ... Unpacking logsave (1.47.2-1) over (1.47.1-1) ... Preparing to unpack .../libext2fs2t64_1.47.2-1_arm64.deb ... Leaving 'diversion of /lib/aarch64-linux-gnu/libe2p.so.2 to /lib/aarch64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' Leaving 'diversion of /lib/aarch64-linux-gnu/libe2p.so.2.3 to /lib/aarch64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' Leaving 'diversion of /lib/aarch64-linux-gnu/libext2fs.so.2 to /lib/aarch64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' Leaving 'diversion of /lib/aarch64-linux-gnu/libext2fs.so.2.4 to /lib/aarch64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' Unpacking libext2fs2t64:arm64 (1.47.2-1) over (1.47.1-1) ... Setting up libcom-err2:arm64 (1.47.2-1) ... Setting up libext2fs2t64:arm64 (1.47.2-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19526 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.47.2-1_arm64.deb ... Unpacking e2fsprogs (1.47.2-1) over (1.47.1-1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.2-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.2-1) ... Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) over (2.6.3-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_arm64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:arm64 (3.13.2-1) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19849 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.13.2-2_arm64.deb ... Unpacking python3-minimal (3.13.2-2) over (3.12.6-1) ... Preparing to unpack .../python3.12-minimal_3.12.9-1_arm64.deb ... Unpacking python3.12-minimal (3.12.9-1) over (3.12.6-1) ... Preparing to unpack .../libpython3.12-minimal_3.12.9-1_arm64.deb ... find: ‘/usr/lib/python3’: No such file or directory Unpacking libpython3.12-minimal:arm64 (3.12.9-1) over (3.12.6-1) ... Preparing to unpack .../libgpg-error0_1.51-3_arm64.deb ... Unpacking libgpg-error0:arm64 (1.51-3) over (1.50-4) ... Setting up libgpg-error0:arm64 (1.51-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19849 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.11.0-7_arm64.deb ... Unpacking libgcrypt20:arm64 (1.11.0-7) over (1.11.0-6) ... Setting up libgcrypt20:arm64 (1.11.0-7) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19849 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.46-1+b1_arm64.deb ... Unpacking gpgv (2.2.46-1+b1) over (2.2.43-8+b1) ... Setting up gpgv (2.2.46-1+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19849 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.7-1_arm64.deb ... Unpacking libffi8:arm64 (3.4.7-1) over (3.4.6-1) ... Setting up libffi8:arm64 (3.4.7-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19849 files and directories currently installed.) Preparing to unpack .../libunistring5_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) over (1.2-1) ... Setting up libunistring5:arm64 (1.3-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19849 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.8-1_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.8-1) over (2.3.7-2) ... Setting up libidn2-0:arm64 (2.3.8-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19849 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.25.5-3_arm64.deb ... Unpacking libp11-kit0:arm64 (0.25.5-3) over (0.25.5-2) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19849 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.20.0-2_arm64.deb ... Unpacking libtasn1-6:arm64 (4.20.0-2) over (4.19.0-3+b2) ... Setting up libtasn1-6:arm64 (4.20.0-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19848 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.9-2_arm64.deb ... Unpacking libgnutls30t64:arm64 (3.8.9-2) over (3.8.6-2) ... Setting up libgnutls30t64:arm64 (3.8.9-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19848 files and directories currently installed.) Preparing to unpack .../libmd0_1.1.0-2+b1_arm64.deb ... Unpacking libmd0:arm64 (1.1.0-2+b1) over (1.1.0-2) ... Setting up libmd0:arm64 (1.1.0-2+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19849 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.5+20250216-2_arm64.deb ... Unpacking libtinfo6:arm64 (6.5+20250216-2) over (6.5-2) ... Setting up libtinfo6:arm64 (6.5+20250216-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19849 files and directories currently installed.) Preparing to unpack .../usrmerge_39+nmu2_all.deb ... Unpacking usrmerge (39+nmu2) over (39) ... Setting up perl-modules-5.40 (5.40.1-2) ... Setting up libperl5.40:arm64 (5.40.1-2) ... Setting up perl (5.40.1-2) ... Setting up usrmerge (39+nmu2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19849 files and directories currently installed.) Preparing to unpack .../00-mawk_1.3.4.20250131-1_arm64.deb ... Unpacking mawk (1.3.4.20250131-1) over (1.3.4.20240905-1) ... Preparing to unpack .../01-tzdata_2025a-2_all.deb ... Unpacking tzdata (2025a-2) over (2024a-4) ... Preparing to unpack .../02-xz-utils_5.6.4-1_arm64.deb ... Unpacking xz-utils (5.6.4-1) over (5.6.2-2) ... Preparing to unpack .../03-make_4.4.1-1_arm64.deb ... 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Setting up rpcsvc-proto (1.4.3-1+b1) ... Setting up make (4.4.1-1) ... Setting up libmpfr6:arm64 (4.2.1-1+b2) ... Setting up xz-utils (5.6.4-1) ... Setting up libmpc3:arm64 (1.3.1-1+b3) ... Setting up libatomic1:arm64 (14.2.0-16) ... Setting up patch (2.7.6-7+b1) ... Setting up libss2:arm64 (1.47.2-1) ... Setting up libk5crypto3:arm64 (1.21.3-5) ... Setting up libdpkg-perl (1.22.18pureos1) ... Setting up logsave (1.47.2-1) ... Setting up libubsan1:arm64 (14.2.0-16) ... Setting up mount (2.40.4-5) ... Setting up cpp-14-aarch64-linux-gnu (14.2.0-16) ... Setting up libhwasan0:arm64 (14.2.0-16) ... Setting up libcrypt-dev:arm64 (1:4.4.38-1) ... Setting up libasan8:arm64 (14.2.0-16) ... Setting up libeatmydata1:arm64 (131-2+b1) ... Setting up python3-minimal (3.13.2-2) ... Setting up mawk (1.3.4.20250131-1) ... Setting up libkrb5-3:arm64 (1.21.3-5) ... Setting up libtsan2:arm64 (14.2.0-16) ... Setting up libbinutils:arm64 (2.44-3) ... Setting up libc-dev-bin (2.41-4) ... Setting up openssl (3.4.1-1) ... Setting up libcc1-0:arm64 (14.2.0-16) ... Setting up liblsan0:arm64 (14.2.0-16) ... Setting up libitm1:arm64 (14.2.0-16) ... Setting up util-linux-extra (2.40.4-5) ... Setting up libctf0:arm64 (2.44-3) ... Setting up python3.12-minimal (3.12.9-1) ... Setting up cpp-12 (12.4.0-4) ... Setting up binutils-aarch64-linux-gnu (2.44-3) ... Setting up e2fsprogs (1.47.2-1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt, it does not contain exactly one certificate or CRL 7 added, 1 removed; done. Setting up libgprofng0:arm64 (2.44-3) ... Setting up libgcc-12-dev:arm64 (12.4.0-4) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ... Setting up cpp-14 (14.2.0-16) ... Setting up libc6-dev:arm64 (2.41-4) ... Setting up libgcc-14-dev:arm64 (14.2.0-16) ... Setting up libstdc++-14-dev:arm64 (14.2.0-16) ... Setting up libstdc++-12-dev:arm64 (12.4.0-4) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Setting up binutils (2.44-3) ... Setting up dpkg-dev (1.22.18pureos1) ... Setting up libtirpc-dev:arm64 (1.3.4+ds-1.3+b1) ... Setting up gcc-12 (12.4.0-4) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up build-essential (12.12) ... Setting up gcc-14-aarch64-linux-gnu (14.2.0-16) ... Setting up g++-12 (12.4.0-4) ... Setting up g++-14-aarch64-linux-gnu (14.2.0-16) ... Setting up gcc-14 (14.2.0-16) ... Setting up libnsl-dev:arm64 (1.3.0-3+b3) ... Setting up g++-14 (14.2.0-16) ... Processing triggers for debianutils (5.21) ... Processing triggers for libc-bin (2.41-4) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... build-essential is already the newest version (12.12). dpkg-dev is already the newest version (1.22.18pureos1). fakeroot is already the newest version (1.37-1). The following packages were automatically installed and are no longer required: libapt-pkg6.0t64 libgnutls30t64 libperl5.38t64 libpython3.12-minimal perl-modules-5.38 python3.12-minimal Use 'apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. ┌───────────────────────────────────────────────┐ │ Installing package build-dependencies │ └───────────────────────────────────────────────┘ Note, using directory './' to get the build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libapt-pkg6.0t64 libperl5.38t64 libpython3.12-minimal perl-modules-5.38 python3.12-minimal Use 'apt autoremove' to remove them. The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils comerr-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gfortran gfortran-14 gfortran-14-aarch64-linux-gnu gfortran-aarch64-linux-gnu groff-base hdf5-helpers icu-devtools intltool-debian krb5-multidev libaec-dev libaec0 libarchive-zip-perl libarpack2-dev libarpack2t64 libblas-dev libblas3 libbrotli-dev libbrotli1 libbz2-dev libcurl3t64-gnutls libcurl4-gnutls-dev libcurl4t64 libdebhelper-perl libelf1t64 libevent-2.1-7t64 libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-single3 libfile-stripnondeterminism-perl libgfortran-14-dev libgfortran5 libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssrpc4t64 libhdf5-310 libhdf5-cpp-310 libhdf5-dev libhdf5-fortran-310 libhdf5-hl-310 libhdf5-hl-cpp-310 libhdf5-hl-fortran-310 libicu-dev libicu76 libidn2-dev libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkrb5-dev liblapack-dev liblapack3 libldap-dev libldap2 libmagic-mgc libmagic1t64 libncurses-dev libncurses6 libncursesw6 libnetcdf-dev libnetcdf22 libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libopenmm-dev libopenmm8.1 libp11-kit-dev libpipeline1 libpkgconf3 libpsl-dev libpsl5t64 libreadline-dev libreadline8t64 librtmp-dev librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1-dev libssh2-1t64 libssl-dev libsz2 libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2 libxml2-dev libzstd-dev m4 man-db netcdf-bin nettle-dev pkgconf pkgconf-bin po-debconf readline-common sensible-utils zlib1g-dev 0 upgraded, 122 newly installed, 0 to remove and 0 not upgraded. Need to get 25.4 MB/73.8 MB of archives. After this operation, 311 MB of additional disk space will be used. Get:1 https://repo.pureos.net/pureos landing/main arm64 libgfortran-14-dev arm64 14.2.0-16 [418 kB] Get:2 https://repo.pureos.net/pureos landing/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-16 [9795 kB] Get:3 https://repo.pureos.net/pureos landing/main arm64 gfortran-14 arm64 14.2.0-16 [13.6 kB] Get:4 https://repo.pureos.net/pureos landing/main arm64 hdf5-helpers arm64 1.14.5+repack-3 [26.6 kB] Get:5 https://repo.pureos.net/pureos landing/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB] Get:6 https://repo.pureos.net/pureos landing/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B] Get:7 https://repo.pureos.net/pureos landing/main arm64 libaec-dev arm64 1.1.3-1+b1 [20.2 kB] Get:8 https://repo.pureos.net/pureos landing/main arm64 libarpack2t64 arm64 3.9.1-4 [83.7 kB] Get:9 https://repo.pureos.net/pureos landing/main arm64 libblas-dev arm64 3.12.1-2 [111 kB] Get:10 https://repo.pureos.net/pureos landing/main arm64 liblapack-dev arm64 3.12.1-2 [3726 kB] Get:11 https://repo.pureos.net/pureos landing/main arm64 libarpack2-dev arm64 3.9.1-4 [102 kB] Get:12 https://repo.pureos.net/pureos landing/main arm64 libngtcp2-16 arm64 1.11.0-1 [121 kB] Get:13 https://repo.pureos.net/pureos landing/main arm64 libngtcp2-crypto-gnutls8 arm64 1.11.0-1 [28.2 kB] Get:14 https://repo.pureos.net/pureos landing/main arm64 libcurl3t64-gnutls arm64 8.12.1-3 [336 kB] Get:15 https://repo.pureos.net/pureos landing/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.11.0-1 [33.9 kB] Get:16 https://repo.pureos.net/pureos landing/main arm64 libngtcp2-dev arm64 1.11.0-1 [174 kB] Get:17 https://repo.pureos.net/pureos landing/main arm64 libcurl4-gnutls-dev arm64 8.12.1-3 [465 kB] Get:18 https://repo.pureos.net/pureos landing/main arm64 libfftw3-double3 arm64 3.3.10-2+b1 [337 kB] Get:19 https://repo.pureos.net/pureos landing/main arm64 libfftw3-long3 arm64 3.3.10-2+b1 [546 kB] Get:20 https://repo.pureos.net/pureos landing/main arm64 libfftw3-single3 arm64 3.3.10-2+b1 [517 kB] Get:21 https://repo.pureos.net/pureos landing/main arm64 libfftw3-bin arm64 3.3.10-2+b1 [44.3 kB] Get:22 https://repo.pureos.net/pureos landing/main arm64 libfftw3-dev arm64 3.3.10-2+b1 [1280 kB] Get:23 https://repo.pureos.net/pureos landing/main arm64 libhdf5-310 arm64 1.14.5+repack-3 [1155 kB] Get:24 https://repo.pureos.net/pureos landing/main arm64 libhdf5-cpp-310 arm64 1.14.5+repack-3 [121 kB] Get:25 https://repo.pureos.net/pureos landing/main arm64 libhdf5-fortran-310 arm64 1.14.5+repack-3 [110 kB] Get:26 https://repo.pureos.net/pureos landing/main arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [66.1 kB] Get:27 https://repo.pureos.net/pureos landing/main arm64 libhdf5-hl-fortran-310 arm64 1.14.5+repack-3 [42.1 kB] Get:28 https://repo.pureos.net/pureos landing/main arm64 libhdf5-hl-cpp-310 arm64 1.14.5+repack-3 [24.4 kB] Get:29 https://repo.pureos.net/pureos landing/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-3.1 [293 kB] Get:30 https://repo.pureos.net/pureos landing/main arm64 libjpeg-dev arm64 1:2.1.5-3.1 [72.0 kB] Get:31 https://repo.pureos.net/pureos landing/main arm64 libhdf5-dev arm64 1.14.5+repack-3 [3225 kB] Get:32 https://repo.pureos.net/pureos landing/main arm64 libnetcdf22 arm64 1:4.9.3-1 [481 kB] Get:33 https://repo.pureos.net/pureos landing/main arm64 libnetcdf-dev arm64 1:4.9.3-1 [116 kB] Get:34 https://repo.pureos.net/pureos landing/main arm64 libopenmm8.1 arm64 8.1.2+dfsg-4+b1 [922 kB] Get:35 https://repo.pureos.net/pureos landing/main arm64 libopenmm-dev arm64 8.1.2+dfsg-4+b1 [330 kB] Get:36 https://repo.pureos.net/pureos landing/main arm64 netcdf-bin arm64 1:4.9.3-1 [245 kB] Fetched 25.4 MB in 4s (6027 kB/s) Extracting templates from packages: 24% Extracting templates from packages: 49% Extracting templates from packages: 73% Extracting templates from packages: 98% Extracting templates from packages: 100% Preconfiguring packages ... Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19909 files and directories currently installed.) Preparing to unpack .../000-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. 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Preparing to unpack .../094-libcurl4t64_8.12.1-3_arm64.deb ... Unpacking libcurl4t64:arm64 (8.12.1-3) ... Selecting previously unselected package libfftw3-double3:arm64. Preparing to unpack .../095-libfftw3-double3_3.3.10-2+b1_arm64.deb ... Unpacking libfftw3-double3:arm64 (3.3.10-2+b1) ... Selecting previously unselected package libfftw3-long3:arm64. Preparing to unpack .../096-libfftw3-long3_3.3.10-2+b1_arm64.deb ... Unpacking libfftw3-long3:arm64 (3.3.10-2+b1) ... Selecting previously unselected package libfftw3-single3:arm64. Preparing to unpack .../097-libfftw3-single3_3.3.10-2+b1_arm64.deb ... Unpacking libfftw3-single3:arm64 (3.3.10-2+b1) ... Selecting previously unselected package libfftw3-bin. Preparing to unpack .../098-libfftw3-bin_3.3.10-2+b1_arm64.deb ... Unpacking libfftw3-bin (3.3.10-2+b1) ... Selecting previously unselected package libfftw3-dev:arm64. Preparing to unpack .../099-libfftw3-dev_3.3.10-2+b1_arm64.deb ... Unpacking libfftw3-dev:arm64 (3.3.10-2+b1) ... Selecting previously unselected package libhdf5-310:arm64. Preparing to unpack .../100-libhdf5-310_1.14.5+repack-3_arm64.deb ... Unpacking libhdf5-310:arm64 (1.14.5+repack-3) ... Selecting previously unselected package libhdf5-cpp-310:arm64. Preparing to unpack .../101-libhdf5-cpp-310_1.14.5+repack-3_arm64.deb ... Unpacking libhdf5-cpp-310:arm64 (1.14.5+repack-3) ... Selecting previously unselected package libhdf5-fortran-310:arm64. Preparing to unpack .../102-libhdf5-fortran-310_1.14.5+repack-3_arm64.deb ... Unpacking libhdf5-fortran-310:arm64 (1.14.5+repack-3) ... Selecting previously unselected package libhdf5-hl-310:arm64. Preparing to unpack .../103-libhdf5-hl-310_1.14.5+repack-3_arm64.deb ... Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3) ... Selecting previously unselected package libhdf5-hl-fortran-310:arm64. Preparing to unpack .../104-libhdf5-hl-fortran-310_1.14.5+repack-3_arm64.deb ... Unpacking libhdf5-hl-fortran-310:arm64 (1.14.5+repack-3) ... 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Unpacking libxml2-dev:arm64 (2.12.7+dfsg+really2.9.14-0.3+b1) ... Selecting previously unselected package libnetcdf-dev. Preparing to unpack .../116-libnetcdf-dev_1%3a4.9.3-1_arm64.deb ... Unpacking libnetcdf-dev (1:4.9.3-1) ... Selecting previously unselected package libopenmm8.1. Preparing to unpack .../117-libopenmm8.1_8.1.2+dfsg-4+b1_arm64.deb ... Unpacking libopenmm8.1 (8.1.2+dfsg-4+b1) ... Selecting previously unselected package libopenmm-dev. Preparing to unpack .../118-libopenmm-dev_8.1.2+dfsg-4+b1_arm64.deb ... Unpacking libopenmm-dev (8.1.2+dfsg-4+b1) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../119-libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libreadline-dev:arm64. Preparing to unpack .../120-libreadline-dev_8.2-6_arm64.deb ... Unpacking libreadline-dev:arm64 (8.2-6) ... Selecting previously unselected package netcdf-bin. Preparing to unpack .../121-netcdf-bin_1%3a4.9.3-1_arm64.deb ... Unpacking netcdf-bin (1:4.9.3-1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libgnutls-openssl27t64:arm64 (3.8.9-2) ... Setting up libfftw3-single3:arm64 (3.3.10-2+b1) ... Setting up libzstd-dev:arm64 (1.5.6+dfsg-2) ... Setting up bsdextrautils (2.40.4-5) ... Setting up hdf5-helpers (1.14.5+repack-3) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:arm64 (1.1.0-2+b7) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:arm64 (1.64.0-1) ... Setting up libfftw3-long3:arm64 (3.3.10-2+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-7) ... Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libaec0:arm64 (1.1.3-1+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libpsl-dev:arm64 (0.21.2-1.1+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-9) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libunbound8:arm64 (1.22.0-1+b1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-3) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3.1) ... Setting up libgnutls-dane0t64:arm64 (3.8.9-2) ... Setting up libjpeg62-turbo-dev:arm64 (1:2.1.5-3.1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:arm64 (1.21.3-5) ... Setting up libncurses6:arm64 (6.5+20250216-2) ... Setting up comerr-dev:arm64 (2.1-1.47.2-1) ... Setting up libssl-dev:arm64 (3.4.1-1) ... Setting up autopoint (0.23.1-1) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libncursesw6:arm64 (6.5+20250216-2) ... Setting up libidn2-dev:arm64 (2.3.8-1) ... Setting up libfftw3-double3:arm64 (3.3.10-2+b1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:arm64 (14.2.0-16) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.8.0-1) ... Setting up libnghttp3-dev:arm64 (1.8.0-1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libngtcp2-16:arm64 (1.11.0-1) ... Setting up libicu76:arm64 (76.1-3) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libtasn1-6-dev:arm64 (4.20.0-2) ... Setting up libopenmm8.1 (8.1.2+dfsg-4+b1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.3+b1) ... Setting up libldap2:arm64 (2.6.9+dfsg-2) ... Setting up libbrotli-dev:arm64 (1.1.0-2+b7) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.11.0-1) ... Setting up libp11-kit-dev:arm64 (0.25.5-3) ... Setting up libblas-dev:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up libsz2:arm64 (1.1.3-1+b1) ... Setting up libkadm5clnt-mit12:arm64 (1.21.3-5) ... Setting up libbz2-dev:arm64 (1.0.8-6) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:arm64 (14.2.0-16) ... Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libncurses-dev:arm64 (6.5+20250216-2) ... Setting up gettext (0.23.1-1) ... Setting up libarpack2t64:arm64 (3.9.1-4) ... Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:arm64 (3.10.1-1) ... Setting up libcurl4t64:arm64 (8.12.1-3) ... Setting up libkdb5-10t64:arm64 (1.21.3-5) ... Setting up libtool (2.5.4-4) ... Setting up libfftw3-bin (3.3.10-2+b1) ... Setting up libaec-dev:arm64 (1.1.3-1+b1) ... Setting up libjpeg-dev:arm64 (1:2.1.5-3.1) ... Setting up libcurl3t64-gnutls:arm64 (8.12.1-3) ... Setting up libngtcp2-crypto-gnutls-dev:arm64 (1.11.0-1) ... Setting up libngtcp2-dev:arm64 (1.11.0-1) ... Setting up libopenmm-dev (8.1.2+dfsg-4+b1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libldap-dev:arm64 (2.6.9+dfsg-2) ... Setting up liblapack-dev:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up icu-devtools (76.1-3) ... Setting up libssh2-1-dev:arm64 (1.11.1-1) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up libhdf5-310:arm64 (1.14.5+repack-3) ... Setting up groff-base (1.23.0-7) ... Setting up gfortran-14-aarch64-linux-gnu (14.2.0-16) ... Setting up libkadm5srv-mit12:arm64 (1.21.3-5) ... Setting up gfortran-aarch64-linux-gnu (4:14.2.0-1) ... Setting up gfortran-14 (14.2.0-16) ... Setting up libhdf5-fortran-310:arm64 (1.14.5+repack-3) ... Setting up libfftw3-dev:arm64 (3.3.10-2+b1) ... Setting up libicu-dev:arm64 (76.1-3) ... Setting up krb5-multidev:arm64 (1.21.3-5) ... Setting up libhdf5-cpp-310:arm64 (1.14.5+repack-3) ... Setting up libgnutls28-dev:arm64 (3.8.9-2) ... Setting up libnghttp2-dev:arm64 (1.64.0-1) ... Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ... Setting up libarpack2-dev:arm64 (3.9.1-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libnetcdf22:arm64 (1:4.9.3-1) ... Setting up libreadline-dev:arm64 (8.2-6) ... Setting up man-db (2.13.0-1) ... Building database of manual pages ... Setting up gfortran (4:14.2.0-1) ... 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 netcdf-bin (1:4.9.3-1) ... Setting up libkrb5-dev:arm64 (1.21.3-5) ... Setting up libxml2-dev:arm64 (2.12.7+dfsg+really2.9.14-0.3+b1) ... Setting up librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhdf5-hl-cpp-310:arm64 (1.14.5+repack-3) ... Setting up libhdf5-hl-fortran-310:arm64 (1.14.5+repack-3) ... Setting up debhelper (13.24.1) ... Setting up libcurl4-gnutls-dev:arm64 (8.12.1-3) ... Setting up libhdf5-dev (1.14.5+repack-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libnetcdf-dev (1:4.9.3-1) ... Processing triggers for libc-bin (2.41-4) ... ┌───────────────┐ │ Build │ └───────────────┘ dpkg-buildpackage: info: source package cpptraj dpkg-buildpackage: info: source version 5.1.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: host architecture arm64  dpkg-source --before-build .  debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg' touch config.h external.config.h dh_auto_clean make -j32 clean make[2]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg' cd src && make clean make[3]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg/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 '/srv/build/cpptraj-5.1.0+dfsg/src/xdrfile' /bin/rm -f *.o libxdrfile.a a.out test.trr test.xtc test.xdr make[4]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg/src/xdrfile' # cd arpack && make clean cd cuda_kernels && make clean make[4]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg/src/cuda_kernels' /bin/rm -f *.o libcpptraj_cuda.a make[4]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg/src/cuda_kernels' cd tng && make clean make[4]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg/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 '/srv/build/cpptraj-5.1.0+dfsg/src/tng' make[3]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg/src' cd test && make clean make[3]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg/test' Cleaning all test directories: make test.complete test.libcpptraj OPT=clean make[4]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg/test' make[5]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg/test' make[5]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg/test' make[4]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg/test' make[3]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg/test' cd unitTests && make clean make[3]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg/unitTests' Cleaning unit tests. make test.complete OPT=clean make[4]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ source directory: /srv/build/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /srv/build/cpptraj-5.1.0+dfsg/config.h make[5]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg/unitTests' make[5]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg/unitTests' make[4]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg/unitTests' make[3]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg/unitTests' make[2]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg' rm -rf bin make[1]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg' dh_clean  debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg' ./configure gnu --with-arpack=/usr/lib/aarch64-linux-gnu --with-fftw3=/usr/lib/aarch64-linux-gnu --with-readline=/usr/lib/aarch64-linux-gnu --with-openmm=/usr/lib/aarch64-linux-gnu arpack specified: /usr/lib/aarch64-linux-gnu fftw3 specified: /usr/lib/aarch64-linux-gnu readline specified: /usr/lib/aarch64-linux-gnu openmm specified: /usr/lib/aarch64-linux-gnu Testing C++ compiler: OK Testing C compiler: OK Testing basic C++11 support: OK Testing system headers for C++11 support: OK Warning: Compilation of sanderlib requires AMBERHOME to be set Warning: if --with-sanderlib not specified. Checking BZLIB: OK Checking ZLIB: OK Checking NetCDF: OK Checking LAPACK/BLAS: OK Checking ARPACK: OK Checking FFTW3: OK Checking Readline: OK Checking OpenMM: OK vmdplugin disabled due to nonfree source. Configuration summary: Build type: Serial Options: netcdf bzlib tng zlib arpack lapack blas fftw3 readline xdrfile openmm Target platform: Linux, 64-bit. gnu compilers in use. C++11 support enabled. PME support enabled. Compiler optimizations are on. Cleaning source directory. -------------------------------------------------------------------------------- An environment resource file for CPPTRAJ has been created: /srv/build/cpptraj-5.1.0+dfsg/cpptraj.sh You may 'source' this file to set up your environment for CPPTRAJ. -------------------------------------------------------------------------------- CPPTRAJ configuration complete. make[1]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg' dh_auto_build -a make -j32 make[1]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg' cd src && make install make[2]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg/src' CXX SpaceGroup.cpp CXX ActionFrameCounter.cpp CXX ActionList.cpp CXX ActionTopWriter.cpp CXX Action_Align.cpp CXX Action_Angle.cpp CXX Action_AreaPerMol.cpp CXX Action_AtomMap.cpp CXX Action_AtomicCorr.cpp CXX Action_AtomicFluct.cpp CXX Action_AutoImage.cpp CXX Action_Average.cpp CXX Action_Bounds.cpp CXX Action_Box.cpp CXX Action_Center.cpp CXX Action_Channel.cpp CXX Action_CheckChirality.cpp CXX Action_CheckStructure.cpp CXX Action_Closest.cpp CXX Action_ClusterDihedral.cpp CXX Action_Contacts.cpp CXX Action_CreateCrd.cpp CXX Action_CreateReservoir.cpp CXX Action_DNAionTracker.cpp CXX Action_DSSP.cpp CXX Action_Density.cpp CXX Action_Diffusion.cpp CXX Action_Dihedral.cpp CXX Action_DihedralRMS.cpp CXX Action_Dipole.cpp CXX Action_Distance.cpp CXX Action_DistRmsd.cpp CXX Action_Energy.cpp In file included from Ewald_ParticleMesh.h:5, from Action_Energy.cpp:4: helpme_standalone.h:2323: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 2323 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:2343: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 2343 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3014: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 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’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 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’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 3247 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3701: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 3701 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3739: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 3739 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3802: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 3802 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3840: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 3840 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4044: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4044 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4052: warning: ignoring ‘#pragma omp for’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4052 | #pragma omp for helpme_standalone.h:4097: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4097 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4145: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4145 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4172: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4172 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4224: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4224 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4228: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4228 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4275: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4275 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4388: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4388 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4419: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4503: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4503 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4510: warning: ignoring ‘#pragma omp for’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4510 | #pragma omp for CXX Action_FilterByData.cpp CXX Action_FixAtomOrder.cpp CXX Action_FixImagedBonds.cpp CXX Action_GIST.cpp CXX Action_Grid.cpp CXX Action_GridFreeEnergy.cpp CXX Action_HydrogenBond.cpp CXX Action_Image.cpp CXX Action_InfraredSpectrum.cpp CXX Action_Jcoupling.cpp CXX Action_LESsplit.cpp CXX Action_LIE.cpp CXX Action_LipidOrder.cpp CXX Action_MakeStructure.cpp CXX Action_Mask.cpp CXX Action_Matrix.cpp CXX Action_MinImage.cpp CXX Action_Molsurf.cpp CXX Action_MultiDihedral.cpp CXX Action_MultiVector.cpp CXX Action_NAstruct.cpp CXX Action_NativeContacts.cpp CXX Action_NMRrst.cpp CXX Action_OrderParameter.cpp CXX Action_Outtraj.cpp CXX Action_PairDist.cpp CXX Action_Pairwise.cpp CXX Action_Principal.cpp CXX Action_Projection.cpp CXX Action_Pucker.cpp CXX Action_Radgyr.cpp CXX Action_Radial.cpp CXX Action_RandomizeIons.cpp CXX Action_Remap.cpp CXX Action_ReplicateCell.cpp CXX Action_Rmsd.cpp CXX Action_Rotate.cpp CXX Action_RunningAvg.cpp CXX Action_STFC_Diffusion.cpp 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 Vec3::operator-(const Vec3&) const’, inlined from ‘void Action_GIST::Order(const Frame&)’ at Action_GIST.cpp:814:31: Vec3.h:76:23: warning: ‘WAT’ may be used uninitialized []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmaybe-uninitialized-Wmaybe-uninitialized]8;;] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function ‘void Action_GIST::Order(const Frame&)’: Action_GIST.cpp:783:10: note: ‘WAT’ declared here 783 | Vec3 WAT[4]; | ^~~ In member function ‘Vec3 Vec3::operator-(const Vec3&) const’, inlined from ‘void Action_GIST::Order(const Frame&)’ at Action_GIST.cpp:814:31: Vec3.h:76:40: warning: ‘WAT’ may be used uninitialized []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmaybe-uninitialized-Wmaybe-uninitialized]8;;] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function ‘void Action_GIST::Order(const Frame&)’: Action_GIST.cpp:783:10: note: ‘WAT’ declared here 783 | Vec3 WAT[4]; | ^~~ In member function ‘Vec3 Vec3::operator-(const Vec3&) const’, inlined from ‘void Action_GIST::Order(const Frame&)’ at Action_GIST.cpp:814:31: Vec3.h:76:57: warning: ‘WAT’ may be used uninitialized []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmaybe-uninitialized-Wmaybe-uninitialized]8;;] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function ‘void Action_GIST::Order(const Frame&)’: Action_GIST.cpp:783:10: note: ‘WAT’ declared here 783 | Vec3 WAT[4]; | ^~~ In member function ‘Vec3 Vec3::operator-(const Vec3&) const’, inlined from ‘void Action_GIST::Order(const Frame&)’ at Action_GIST.cpp:815:31: Vec3.h:76:23: warning: ‘WAT’ may be used uninitialized []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmaybe-uninitialized-Wmaybe-uninitialized]8;;] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function ‘void Action_GIST::Order(const Frame&)’: Action_GIST.cpp:783:10: note: ‘WAT’ declared here 783 | Vec3 WAT[4]; | ^~~ In member function ‘Vec3 Vec3::operator-(const Vec3&) const’, inlined from ‘void Action_GIST::Order(const Frame&)’ at Action_GIST.cpp:815:31: Vec3.h:76:40: warning: ‘WAT’ may be used uninitialized []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmaybe-uninitialized-Wmaybe-uninitialized]8;;] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function ‘void Action_GIST::Order(const Frame&)’: Action_GIST.cpp:783:10: note: ‘WAT’ declared here 783 | Vec3 WAT[4]; | ^~~ In member function ‘Vec3 Vec3::operator-(const Vec3&) const’, inlined from ‘void Action_GIST::Order(const Frame&)’ at Action_GIST.cpp:815:31: Vec3.h:76:57: warning: ‘WAT’ may be used uninitialized []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmaybe-uninitialized-Wmaybe-uninitialized]8;;] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function ‘void Action_GIST::Order(const Frame&)’: Action_GIST.cpp:783:10: note: ‘WAT’ declared here 783 | Vec3 WAT[4]; | ^~~ 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 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 In file included from /usr/include/c++/14/vector:66, from ArgList.h:3, from Action.h:4, from Action_XtalSymm.h:3, from Action_XtalSymm.cpp:1: In member function ‘void std::vector<_Tp, _Alloc>::assign(size_type, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]’, inlined from ‘virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)’ at Action_XtalSymm.cpp:57:12: /usr/include/c++/14/bits/stl_vector.h:809:23: warning: ‘’ may be used uninitialized []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmaybe-uninitialized-Wmaybe-uninitialized]8;;] 809 | { _M_fill_assign(__n, __val); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:72: /usr/include/c++/14/bits/vector.tcc: In member function ‘virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)’: /usr/include/c++/14/bits/vector.tcc:270:5: note: by argument 3 of type ‘const std::vector::value_type&’ {aka ‘const Vec3&’} to ‘void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]’ declared here 270 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ Action_XtalSymm.cpp:57:33: note: ‘’ declared here 57 | T_.assign( nCopyTotal, Vec3()); | ^ In member function ‘void std::vector<_Tp, _Alloc>::assign(size_type, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]’, inlined from ‘virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)’ at Action_XtalSymm.cpp:58:15: /usr/include/c++/14/bits/stl_vector.h:809:23: warning: ‘’ may be used uninitialized []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmaybe-uninitialized-Wmaybe-uninitialized]8;;] 809 | { _M_fill_assign(__n, __val); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/14/bits/vector.tcc: In member function ‘virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)’: /usr/include/c++/14/bits/vector.tcc:270:5: note: by argument 3 of type ‘const std::vector::value_type&’ {aka ‘const Vec3&’} to ‘void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]’ declared here 270 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ Action_XtalSymm.cpp:58:33: note: ‘’ declared here 58 | RefT_.assign(nCopyTotal, Vec3()); | ^ CXX CoordinateInfo.cpp CXX Corr.cpp CXX Cph.cpp CXX CpptrajFile.cpp CXX CpptrajState.cpp CXX CpptrajStdio.cpp CXX CurveFit.cpp CXX DataFile.cpp CXX DataFileList.cpp CXX DataFilter.cpp CXX DataIO.cpp CXX DataIO_CCP4.cpp CXX DataIO_CharmmFastRep.cpp CXX DataIO_CharmmOutput.cpp CXX DataIO_CharmmRepLog.cpp CXX DataIO_CharmmRtfPrm.cpp CXX DataIO_Cmatrix.cpp CXX DataIO_Cpout.cpp CXX DataIO_Evecs.cpp CXX DataIO_Gnuplot.cpp CXX DataIO_Grace.cpp CXX DataIO_OpenDx.cpp CXX DataIO_Peaks.cpp CXX DataIO_Mdout.cpp CXX DataIO_NC_Cmatrix.cpp CXX DataIO_RemLog.cpp CXX DataIO_Std.cpp CXX DataIO_VecTraj.cpp CXX DataIO_Xplor.cpp CXX DataIO_XVG.cpp CXX DataSet.cpp CXX DataSetList.cpp CXX DataSet_1D.cpp CXX DataSet_3D.cpp CXX DataSet_Cmatrix.cpp CXX DataSet_Cmatrix_DISK.cpp CXX DataSet_Cmatrix_MEM.cpp CXX DataSet_Cmatrix_NOMEM.cpp CXX DataSet_Coords.cpp CXX DataSet_Coords_CRD.cpp CXX DataSet_Coords_REF.cpp CXX DataSet_Coords_TRJ.cpp CXX DataSet_GridDbl.cpp CXX DataSet_GridFlt.cpp CXX DataSet_Mat3x3.cpp CXX DataSet_MatrixDbl.cpp CXX DataSet_MatrixFlt.cpp CXX DataSet_Mesh.cpp CXX DataSet_Modes.cpp CXX DataSet_Parameters.cpp CXX DataSet_pH.cpp CXX DataSet_PHREMD_Explicit.cpp CXX DataSet_PHREMD_Implicit.cpp CXX DataSet_RemLog.cpp CXX DataSet_Topology.cpp CXX DataSet_Vector.cpp CXX DataSet_Vector_Scalar.cpp CXX DataSet_double.cpp CXX DataSet_float.cpp CXX DataSet_integer_disk.cpp CXX DataSet_integer_mem.cpp CXX DataSet_string.cpp CXX DataSet_StringVar.cpp CXX DataSet_Tensor.cpp CXX DataSet_unsignedInt.cpp CXX Deprecated.cpp CXX DihedralSearch.cpp CXX DistRoutines.cpp CXX Energy.cpp CXX EnergyArray.cpp CXX EnsembleIn.cpp CXX EnsembleIn_Multi.cpp CXX EnsembleIn_Single.cpp CXX EnsembleNavigator.cpp CXX EnsembleOut.cpp CXX EnsembleOut_Multi.cpp CXX EnsembleOut_Single.cpp CXX EnsembleOutList.cpp CXX Ewald.cpp CXX Ewald_ParticleMesh.cpp CXX Ewald_Regular.cpp CXX ExclusionArray.cpp CXX Exec_AddMissingRes.cpp CXX Exec_Analyze.cpp CXX Exec_Calc.cpp CXX Exec_CatCrd.cpp In file included from Ewald_ParticleMesh.h:5, from Ewald_ParticleMesh.cpp:4: helpme_standalone.h:2323: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 2323 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:2343: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 2343 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3014: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 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’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 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’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 3247 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3701: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 3701 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3739: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 3739 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3802: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 3802 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3840: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 3840 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4044: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4044 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4052: warning: ignoring ‘#pragma omp for’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4052 | #pragma omp for helpme_standalone.h:4097: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4097 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4145: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4145 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4172: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4172 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4224: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4224 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4228: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4228 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4275: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4275 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4388: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4388 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4419: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4503: warning: ignoring ‘#pragma omp parallel’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4503 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4510: warning: ignoring ‘#pragma omp for’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unknown-pragmas-Wunknown-pragmas]8;;] 4510 | #pragma omp for CXX Exec_Change.cpp CXX Exec_ClusterMap.cpp CXX Exec_CombineCoords.cpp 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 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]’ 3898 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 |  boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 |  PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:1010:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-sign-compare-Wsign-compare]8;;] 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’} []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-sign-compare-Wsign-compare]8;;] 1013 | for (int val = 0; val < nRows_; ++val) { | ~~~~^~~~~~~~ CXX Exec_Emin.cpp 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]’ 5018 | sanityChecks(parameterAngMom, parameters, coordinates); | ^~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3198:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-sign-compare-Wsign-compare]8;;] 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]’ 5019 | filterAtomsAndBuildSplineCache(parameterAngMom, coordinates); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3746:45: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-sign-compare-Wsign-compare]8;;] 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’} []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-sign-compare-Wsign-compare]8;;] 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’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-sign-compare-Wsign-compare]8;;] 3761 | if (cGridIterator.size() && thisAtomsThread == threadID) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~ helpme_standalone.h:3750:25: warning: unused variable ‘gridIteratorC’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unused-variable-Wunused-variable]8;;] 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’} []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-sign-compare-Wsign-compare]8;;] 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’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-sign-compare-Wsign-compare]8;;] 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]’ 5020 | auto realGrid = spreadParameters(parameterAngMom, parameters); | ^~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3708:45: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-sign-compare-Wsign-compare]8;;] 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]’ 5023 | auto gridAddress = forwardTransform(realGrid); | ^~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:4004:28: warning: variable ‘realCBA’ set but not used []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unused-but-set-variable-Wunused-but-set-variable]8;;] 4004 | Real *__restrict__ realCBA; | ^~~~~~~ CXX Exec_Flatten.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]’ 1000 | assertSymmetric(); | ^~~~~~~~~~~~~~~ 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]’ 3898 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 |  boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 |  PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:796:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-sign-compare-Wsign-compare]8;;] 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]’ 1006 | JacobiCyclicDiagonalization(eigenValues[0], unsortedEigenVectors[0], cbegin(), nRows_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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]’ 3898 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 |  boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 |  PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:213:20: warning: variable ‘cos_2phi’ set but not used []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-unused-but-set-variable-Wunused-but-set-variable]8;;] 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]’ 785 | return this->applyOperation([](Real& element) { element = 1 / element; }); | ~~~~~~^~~~~~~~~~~~~~ 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]’ 3910 | recVecs_ = boxVecs_.inverse(); | ~~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 |  boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 |  PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:824:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-sign-compare-Wsign-compare]8;;] 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]’ 3829 | atomSplines.aSpline.update(aStartingGridPoint, gridDimensionA_ * aCoord - aStartingGridPoint, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3830 |  splineOrder_, splineDerivativeLevel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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]’ 5019 | filterAtomsAndBuildSplineCache(parameterAngMom, coordinates); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:2208:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-sign-compare-Wsign-compare]8;;] 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’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-sign-compare-Wsign-compare]8;;] 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]’ 877 | Matrix operator*(const Matrix& other) const { return this->multiply(other); } | ~~~~~~^~~~~~~~ helpme_standalone.h:829:22: required from ‘helpme::Matrix helpme::Matrix::applyOperation(const std::function&) const [with Real = double]’ 829 | return evecs * evecsT; | ~~~~~~^~~~~~~~ helpme_standalone.h:785:26: required from ‘helpme::Matrix helpme::Matrix::inverse() const [with Real = double]’ 785 | return this->applyOperation([](Real& element) { element = 1 / element; }); | ~~~~~~^~~~~~~~~~~~~~ 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]’ 3910 | recVecs_ = boxVecs_.inverse(); | ~~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 |  boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 |  PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:860:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-sign-compare-Wsign-compare]8;;] 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’} []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-sign-compare-Wsign-compare]8;;] 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’} []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-sign-compare-Wsign-compare]8;;] 863 | for (int link = 0; link < nCols_; ++link) { | ~~~~~^~~~~~~~ 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 ParmFile.cpp CXX ParallelNetcdf.cpp CXX Parm_Amber.cpp CXX Parm_CharmmPsf.cpp CXX Parm_CIF.cpp CXX Parm_Gromacs.cpp helpme_standalone.h: In function ‘void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]’: helpme_standalone.h:3470:17: warning: ‘*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))’ may be used uninitialized []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmaybe-uninitialized-Wmaybe-uninitialized]8;;] 3470 | fftHelperA_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3470:31: note: ‘’ declared here 3470 | fftHelperA_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3471:17: warning: ‘*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))’ may be used uninitialized []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmaybe-uninitialized-Wmaybe-uninitialized]8;;] 3471 | fftHelperB_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3471:31: note: ‘’ declared here 3471 | fftHelperB_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3472:17: warning: ‘*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))’ may be used uninitialized []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmaybe-uninitialized-Wmaybe-uninitialized]8;;] 3472 | fftHelperC_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3472:31: note: ‘’ declared here 3472 | fftHelperC_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ In member function ‘helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)’, inlined from ‘void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]’ at helpme_standalone.h:3503:43: helpme_standalone.h:519:7: warning: ‘.helpme::Matrix::data_’ may be used uninitialized []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmaybe-uninitialized-Wmaybe-uninitialized]8;;] 519 | class Matrix { | ^~~~~~ helpme_standalone.h: In function ‘void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]’: helpme_standalone.h:3503:45: note: ‘’ declared here 3503 | compressionCoefficientsA_ = RealMat(); | ^~~~~~~~~ In member function ‘helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)’, inlined from ‘void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]’ at helpme_standalone.h:3504:43: helpme_standalone.h:519:7: warning: ‘.helpme::Matrix::data_’ may be used uninitialized []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmaybe-uninitialized-Wmaybe-uninitialized]8;;] 519 | class Matrix { | ^~~~~~ helpme_standalone.h: In function ‘void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]’: helpme_standalone.h:3504:45: note: ‘’ declared here 3504 | compressionCoefficientsB_ = RealMat(); | ^~~~~~~~~ In member function ‘helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)’, inlined from ‘void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]’ at helpme_standalone.h:3505:43: helpme_standalone.h:519:7: warning: ‘.helpme::Matrix::data_’ may be used uninitialized []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmaybe-uninitialized-Wmaybe-uninitialized]8;;] 519 | class Matrix { | ^~~~~~ helpme_standalone.h: In function ‘void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]’: helpme_standalone.h:3505:45: note: ‘’ declared here 3505 | compressionCoefficientsC_ = RealMat(); | ^~~~~~~~~ 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 helpme_standalone.h: In member function ‘Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0]’: helpme_standalone.h:5031:16: warning: ‘energy’ may be used uninitialized []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wmaybe-uninitialized-Wmaybe-uninitialized]8;;] 5031 | return energy; | ^~~~~~ helpme_standalone.h:5021:14: note: ‘energy’ was declared here 5021 | Real energy; | ^~~~~~ 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’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-sign-compare-Wsign-compare]8;;] 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’ []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-sign-compare-Wsign-compare]8;;] 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 '/srv/build/cpptraj-5.1.0+dfsg/src/xdrfile' CC xdrfile.c Skipping bundled ARPACK build cd tng && make all make[3]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg/src/tng' CC md5.c CC tng_io.c CC tng_compress.c CC coder.c CC warnmalloc.c CC fixpoint.c CC xtc3.c 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 CC xdr_seek.c CC xdrfile_trr.c CC xdrfile_xtc.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 []8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wno-stringop-truncation-Wstringop-truncation]8;;] 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); | ^~~~~~~~~~~~~~~~~~ /bin/rm -f libxdrfile.a ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o make[3]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg/src/xdrfile' /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 '/srv/build/cpptraj-5.1.0+dfsg/src/tng' g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o -L/usr/lib/aarch64-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/aarch64-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/aarch64-linux-gnu/lib -lfftw3 -L/usr/lib/aarch64-linux-gnu/lib -lOpenMM -lnetcdf -lbz2 tng/libtng_io.a -lz xdrfile/libxdrfile.a -Wl,-z,relro mv cpptraj "/srv/build/cpptraj-5.1.0+dfsg/bin" make[2]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg/src' make[1]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg' dh_auto_test -- check unittest make -j32 test "TESTSUITEFLAGS=-j32 --verbose" VERBOSE=1 check unittest make[2]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg' make[2]: Nothing to be done for 'test'. cd test && make test.complete summary cd unitTests && make test.complete summary make[3]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg/unitTests' make[3]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg/test' CPPTRAJ source directory: /srv/build/cpptraj-5.1.0+dfsg/src CPPTRAJ source directory: /srv/build/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /srv/build/cpptraj-5.1.0+dfsg/config.h CPPTRAJ config.h file: /srv/build/cpptraj-5.1.0+dfsg/config.h make[4]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg/unitTests' ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/unitTests/NameType ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/unitTests/ArgList CPPTRAJ: NameType class unit test. CPPTRAJ: ArgList class unit test. make[5]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg/unitTests/NameType' g++ -Wall -O3 -g -O2 -ffile-prefix-map=/srv/build/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/srv/build/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp make[5]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg/unitTests/ArgList' g++ -Wall -O3 -g -O2 -ffile-prefix-map=/srv/build/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/srv/build/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp 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=/srv/build/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/srv/build/cpptraj-5.1.0+dfsg/src -c -o NameType.o /srv/build/cpptraj-5.1.0+dfsg/src/NameType.cpp 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=/srv/build/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/srv/build/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /srv/build/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp 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=/srv/build/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/srv/build/cpptraj-5.1.0+dfsg/src -c -o ArgList.o /srv/build/cpptraj-5.1.0+dfsg/src/ArgList.cpp 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=/srv/build/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/srv/build/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /srv/build/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp 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=/srv/build/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/srv/build/cpptraj-5.1.0+dfsg/src -c -o StringRoutines.o /srv/build/cpptraj-5.1.0+dfsg/src/StringRoutines.cpp -rwxr-xr-x 1 builder builder 183506880 Mar 18 17:06 ../bin/cpptraj -rwxr-xr-x 1 builder builder 183506880 Mar 18 17:06 ../bin/cpptraj make[4]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg/test' ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj ******************************************************************************** ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Strip TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_General ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_TrajinOffset ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_RemdTraj ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_DSSP ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Center ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_NCrestart ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Surf ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_trajout_framerange CPPTRAJ: Broken Traj: Running good trajectory. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Image CPPTRAJ: One frame strip command test CPPTRAJ: Normal trajectory read with offsets. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Radgyr ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Hbond ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Outtraj ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Jcoupling CPPTRAJ: Secstruct (DSSP) command test. CPPTRAJ: CRD Replica Trajectory Run with offset ******************************************************************************** CPPTRAJ: Per-Residue RMSD Test. TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Diffusion CPPTRAJ: Center command test. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Charmm ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj ******************************************************************************** ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Mask TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Rotdif CPPTRAJ: Surface calculation test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Runavg CPPTRAJ: Trajout Frame Range [Amber Restart] CPPTRAJ: NetCDF Restart Test - TXT->NetCDF CPPTRAJ: General tests CPPTRAJ: Orthorhombic imaged distance test. CPPTRAJ: Radius of gyration command test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_RMSD CPPTRAJ: RMSD Test with outtraj. CPPTRAJ: J-Coupling single frame test CPPTRAJ: Convert mdcrd -> NetCDF CPPTRAJ: Rotational diffusion calculation test CPPTRAJ: Solute Hbond test CPPTRAJ: Mask single frame test CPPTRAJ: CHARMM PSF/DCD test CPPTRAJ: Coordinate Running Average test. CPPTRAJ: Diffusion test, no imaging. ******************************************************************************** ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_2DRMS TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Mol2 CPPTRAJ: Basic RMSD tests CPPTRAJ: Mol2 Parm/Traj Read/Write Test. CPPTRAJ: 2D RMSD Test. CPPTRAJ: NetCDF Restart Test - NetCDF->TXT CPPTRAJ: Gzipped trajectory read with offsets J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. Skipped test: J-Coupling extended test CPPTRAJ: CRD Replica Trajectory Run All 1 comparisons passed. 1 comparisons skipped. CPPTRAJ: CHARMM DCD Write, step 1. CPPTRAJ: Coordinate Running Average Traj Write CPPTRAJ: 2D RMSD Test, mass-weighted. CPPTRAJ: Broken Traj: Running broken trajectory. CPPTRAJ: PDB => Mol2 CPPTRAJ: Center origin command test. CPPTRAJ: Non-orthorhombic imaged distance test. All 2 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_NAstruct CPPTRAJ: Per-Residue RMSD Test with averaging All 4 comparisons passed. CPPTRAJ: NAstruct command test. CPPTRAJ: Diffusion test, old syntax. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Average ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Pucker CPPTRAJ: Mask longer command test. CPPTRAJ: Trajout Frame Range [Amber Coordinates] CPPTRAJ: Average Test. CPPTRAJ: Pucker command test CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Datafile ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_AtomMap CPPTRAJ: Data file output precision test CPPTRAJ: AtomMap Test CPPTRAJ: Unstrip (Lig/Rec/Complex) command test CPPTRAJ: Solute Hbond test with disk caching CPPTRAJ: Convert NetCDF -> mdcrd CPPTRAJ: RMS coordinate rotation/rotation matrices test CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF CPPTRAJ: NetCDF Replica Trajectory Run test CPPTRAJ: CHARMM DCD Write, step 2. CPPTRAJ: Bzip2ed trajectory read with offsets All 2 comparisons passed. CPPTRAJ: 2D RMSD Test with reference trajectory CPPTRAJ: Amber Top/Rst => Mol2 ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Radial CPPTRAJ: Center origin mass command test. CPPTRAJ: Orthorhombic coordinate imaging test All 6 comparisons passed. CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test CPPTRAJ: Radial test, non-orthogonal imaging All 2 comparisons passed. CPPTRAJ: Secstruct (DSSP) command with changing number of residues. CPPTRAJ: Per-Residue RMSD Test with residue centering. All 5 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Hist ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Closest CPPTRAJ: 1D/2D Histogram Analysis test CPPTRAJ: Standard -> Grace Data CPPTRAJ: Closest command test using first solvent atom. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_DRMSD CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj CPPTRAJ: CHAMBER topology read/strip test. CPPTRAJ: Distance RMSD test CPPTRAJ: AtomMap with 'rmsfit' CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. CPPTRAJ: Diffusion test, new syntax. Skipped test: Amber Top/Rst => Mol2, SYBYL atom types All 4 comparisons passed. 1 comparisons skipped. CPPTRAJ: Start argument offset CPPTRAJ: 2D DME Test. CPPTRAJ: Solute-solvent hbond test CPPTRAJ: RMS fit with no coordinates modification test. CPPTRAJ: NAstruct command test, single strand CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Cluster CPPTRAJ: Cluster command test, in-memory pairwise distances. CPPTRAJ: Center reference command test. CPPTRAJ: Multi frame strip command test. CPPTRAJ: Grace -> Standard Data CPPTRAJ: Nonorthorhombic coordinate imaging test CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj All 3 comparisons passed. CPPTRAJ: Read CHARMM restart CPPTRAJ: Secstruct (DSSP): SS assign output test CPPTRAJ: Atom map charmm->amber atom order All 4 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_IRED CPPTRAJ: 2D RMSD with reference mask test. All 1 comparisons passed. CPPTRAJ: IRED vector/matrix test CPPTRAJ: Compressed broken trajectory test All 3 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons All 11 comparisons passed. All 2 comparisons passed. CPPTRAJ: randomizeions test (original algorithm) CPPTRAJ: Diffusion test, nonorthogonal box ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Molsurf CPPTRAJ: Molsurf test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Corr CPPTRAJ: 3D histogram test. CPPTRAJ: Correlation test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_NAstruct_8OG ******************************************************************************** CPPTRAJ: Strip topology with PDB info TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_CheckStructure CPPTRAJ: NA test (8OG) CPPTRAJ: Structure Check CPPTRAJ: Hbond, no intramolecular hydrogen bonds test CPPTRAJ: Center point test. CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj CPPTRAJ: CHARMM PSF write CPPTRAJ: FtuFabI Assignment test CPPTRAJ: X column format/precision test. CPPTRAJ: Cluster command test, read pairwise distances. CPPTRAJ: Outtraj Test with maxmin. CPPTRAJ: Atom map charmm->amber atom order, by residue CPPTRAJ: 2D RMSD test, no fitting. All 1 comparisons passed. CPPTRAJ: RMS fit to previous test CPPTRAJ: Closest command test using all solvent atoms. CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar All 2 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_RmsAvgCorr All 7 comparisons passed. All 11 comparisons passed. CPPTRAJ: RmsAvgCorr Reference CPPTRAJ: STFC Diffusion Test All 2 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Contacts CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj All 5 comparisons passed. CPPTRAJ: CHARMM COORdinates test CPPTRAJ: Contacts test. CPPTRAJ: Structure Check with Around and Skip ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_ClusterDihedral ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Principal CPPTRAJ: clusterdihedral test CPPTRAJ: Principal Test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Matrix ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Vector CPPTRAJ: Data file group by name test CPPTRAJ: Matrix Tests All 9 comparisons passed. CPPTRAJ: Basic vector tests All 6 comparisons passed. CPPTRAJ: RMS: imaging after unit cell rotation CPPTRAJ: Cluster command test, read NetCDF pairwise distances. All 3 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Grid ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Unwrap CPPTRAJ: Dipole test All 4 comparisons passed. CPPTRAJ: Unwrap non-orthogonal test CPPTRAJ: CRD Replica Trajectory Run with remdout All 6 comparisons passed. CPPTRAJ: STFC Diffusion Test with individual distances CPPTRAJ: RmsAvgCorr First ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Project CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM CPPTRAJ: Projection ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_CharmmParams CPPTRAJ: Test updating topology with Charmm parameters (single residue) All 4 comparisons passed. All 10 comparisons passed. CPPTRAJ: Hbond, specified solute masks All 3 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes CPPTRAJ: Data file group by aspect test CPPTRAJ: Partial Surface calculation test CPPTRAJ: Modes analysis, RMS fluctuations ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Watershell ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_AnalysisRunAvg CPPTRAJ: Watershell Test, non-orthorhombic imaging. CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. CPPTRAJ: Analysis Running Average All 12 comparisons passed. CPPTRAJ: Cluster command test, write ASCII pairwise distances. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Volmap CPPTRAJ: VMD VolMap Algorithm test CPPTRAJ: Grid test All 1 comparisons passed. All 8 comparisons passed. All 3 comparisons passed. All 2 comparisons passed. CPPTRAJ: STFC Diffusion Test with COM CPPTRAJ: Test vector center with magnitude CPPTRAJ: Unwrap orthogonal test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_SPAM ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_LIE ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Density CPPTRAJ: SPAM Test CPPTRAJ: LIE test CPPTRAJ: Density along axis tests ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_LipidOrder CPPTRAJ: Lipid Order Parameter Test. All 15 comparisons passed. All 6 comparisons passed. CPPTRAJ: Modes analysis, displacements All 6 comparisons passed. CPPTRAJ: Hbond, no angle cutoff test CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. All 2 comparisons passed. CPPTRAJ: Cluster command test, read ASCII pairwise distances. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Parallel ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_PairDist ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_ReadData CPPTRAJ: Parallel tests. CPPTRAJ: PairDist Test. CPPTRAJ: Read vector data test (no origins, origins) ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_GIST CPPTRAJ: GIST water-water interaction test CPPTRAJ: Momentum/velocity vector test. CPPTRAJ: STFC Diffusion Test with second mask CPPTRAJ: Structure Check with PBC CPPTRAJ: Modes analysis, dipole correlation VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. Skipped test: VMD VolMap Algorithm longer tests CPPTRAJ: Hbond, Bridge nointramol test All 2 comparisons passed. 1 comparisons skipped. All 2 comparisons passed. CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. CPPTRAJ: Read vector data set (origins, no origins) All 9 comparisons passed. CPPTRAJ: OpenDX Grid read test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_systemVF ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_AtomicCorr CPPTRAJ: Closest command test, using mask center CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test CPPTRAJ: Atomic Correlation test CPPTRAJ: Parallel test with trajectory offset ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve CPPTRAJ: Cluster, nosieve CPPTRAJ: Radial test, orthogonal and no imaging CPPTRAJ: Force vector test. All 1 comparisons passed. CPPTRAJ: Read Amber output test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_AutoCorr CPPTRAJ: Multi-frame density along axis test CPPTRAJ: Atomicfluct test with ADP output CPPTRAJ: Generate matrix with trajectory start/stop/offset CPPTRAJ: AutoCorr test. All 3 comparisons passed. CPPTRAJ: Pairdist test, orthogonal imaging. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Box CPPTRAJ: Box Test (Add box info) CPPTRAJ: Grid with specified center test. All 6 comparisons passed. CPPTRAJ: Closest command test, using mask center and solvent mask ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_LipidSCD All 14 comparisons passed. CPPTRAJ: Basic lipid order parameter test CPPTRAJ: Read CHARMM output test CPPTRAJ: Cluster, sieve5 CPPTRAJ: Generate matrix with action stop/start/offset All 9 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_AtomTypeSelect ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_AvgRef CPPTRAJ: Selection by atom type test. CPPTRAJ: RMSD Test with averaged reference coordinates. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Crank_Stat CPPTRAJ: Crankshaft test CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. CPPTRAJ: Box test (remove box info) CPPTRAJ: Total system density test CPPTRAJ: LCPO test with GAFF atom types ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_CreateCrd CPPTRAJ: COORDS data set creation and CRDFLUCT test. CPPTRAJ: 3D data read/write test All 15 comparisons passed. CPPTRAJ: Grid with box center offset test. CPPTRAJ: Closest command test, solvent mask, water oxygen only All 7 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_AutoImage CPPTRAJ: AutoImage test (split DNA duplex) All 1 comparisons passed. All 1 comparisons passed. CPPTRAJ: Randomize (around, overlap) ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_LoadCrd ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_MultiVector CPPTRAJ: LoadCrd test. CPPTRAJ: Box test (Modify box length) CPPTRAJ: Multivector test All 3 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Lifetime CPPTRAJ: Cluster, nosieve savepairdist CPPTRAJ: Lifetime test. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_FFT CPPTRAJ: Standard 3D data write test CPPTRAJ: Modes analysis, pseudo trajectory creation test All 13 comparisons passed. CPPTRAJ: FFT test. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Timecorr CPPTRAJ: COORDS data set creation with velocities test CPPTRAJ: Timecorr test. CPPTRAJ: New Lipid Order Parameter Test, DOPC. All 16 comparisons passed. All 7 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_CrossCorr CPPTRAJ: CrossCorr test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_SymmRmsd CPPTRAJ: Grid with mask center offset test. CPPTRAJ: SymmRmsd ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Multidihedral CPPTRAJ: Multidihedral test CPPTRAJ: LoadTraj test. All 1 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Ensemble_MREMD CPPTRAJ: Box test (auto orthogonal box, no radii) ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_MakeStructure CPPTRAJ: M-REMD sort test. CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test CPPTRAJ: Basic makestructure test CPPTRAJ: Standard 3D data read test All 1 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Rotate CPPTRAJ: Lifetime test with data set caching. CPPTRAJ: Rotation (and inverse) of coords from matrices All 5 comparisons passed. CPPTRAJ: ASP symmetry-corrected RMSD test CPPTRAJ: Cluster, nosieve loadpairdist ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Integrate All 7 comparisons passed. CPPTRAJ: Integration test. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_NativeContacts CPPTRAJ: NativeContacts test. CPPTRAJ: LoadTraj from trajin test. CPPTRAJ: Non-orthogonal grid test. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_CheckChiral CPPTRAJ: Multidihedral Nucleotide CHI test CPPTRAJ: Check chirality test CPPTRAJ: Box test (auto orthogonal box, VDW radii) All 4 comparisons passed. All 6 comparisons passed. All 1 comparisons passed. CPPTRAJ: Standard 3D data read/append test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Energy CPPTRAJ: Simple energy tests ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_LESsplit CPPTRAJ: LES split/average test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_PermuteDihedrals CPPTRAJ: Makestructure test with reference. CPPTRAJ: PermuteDihedrals interval -120, phi psi CPPTRAJ: GLU symmetry-corrected RMSD test All 2 comparisons passed. CPPTRAJ: TRAJ data set creation and CRDFLUCT test. CPPTRAJ: Rotate with defined axis CPPTRAJ: LoadCrd append from multiple files test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_CCP4 CPPTRAJ: CCP4 read/write and DX conversion test. CPPTRAJ: Multidihedral protein dihedrals test All 1 comparisons passed. CPPTRAJ: M-REMD actions test. CPPTRAJ: Cluster, sieve5 savepairdist All 7 comparisons passed. CPPTRAJ: Lifetime average and cumulative average test. ******************************************************************************** ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_DihCovar TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_CurveFit CPPTRAJ: Curve fitting test. CPPTRAJ: Dihedral Covariance Matrix Test All 5 comparisons passed. CPPTRAJ: TYR symmetry-corrected RMSD test CPPTRAJ: Standard 3D data, sparse ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_DataSetAverage CPPTRAJ: Data set averaging and averaging over all sets test. CPPTRAJ: TRAJ data set creation with velocities test. All 4 comparisons passed. CPPTRAJ: Multidihedral cyclic molecule test CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test CPPTRAJ: PermuteDihedrals, random rotations CPPTRAJ: AutoImage test, use anchor mask All 3 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_VectorMath CPPTRAJ: Vector dot/cross product test All 12 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/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) All 2 comparisons passed. CPPTRAJ: M-REMD ensemble outtraj test. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Temperature CPPTRAJ: Curve fitting multi-exponential tests. CPPTRAJ: Temperature test. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Spline CPPTRAJ: Longer symmetry-corrected RMSD test. CPPTRAJ: Spline test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/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) All 2 comparisons passed. CPPTRAJ: Nonorthogonal grid standard write/read tests. All 3 comparisons passed. All 6 comparisons passed. CPPTRAJ: Hbond with imaging ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_KDE ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Wavelet CPPTRAJ: KDE test. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_CIF CPPTRAJ: Wavelet analysis test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_PDB CPPTRAJ: CIF read test CPPTRAJ: PDB format read/write test All 4 comparisons passed. All 2 comparisons passed. CPPTRAJ: Grid generation from 'bounds' test. CPPTRAJ: COORDS data set append test All 2 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Align CPPTRAJ: NativeContacts test, save non-native contacts, residue time series CPPTRAJ: Align Tests. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_VelocityAutoCorr CPPTRAJ: Temperature with SHAKE on hydrogens. CPPTRAJ: Velocity autocorrelation test All 1 comparisons passed. All 8 comparisons passed. CPPTRAJ: M-REMD no sort, running average test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_VelFrc CPPTRAJ: Test combining coordinates, velocities, and forces. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_RotateDihedral ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_DataSetCmd CPPTRAJ: Rotate dihedral to target value. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Remap CPPTRAJ: Data Set commands test CPPTRAJ: Remap Test CPPTRAJ: Hbond, orthogonal imaging CPPTRAJ: COORDS test storing frame metadata CPPTRAJ: Temperature with SHAKE on all atoms. CPPTRAJ: Structure Check with Around All 2 comparisons passed. CPPTRAJ: Test using velocities as coordinates. CPPTRAJ: Curve fitting, custom output range. CPPTRAJ: M-REMD, generate RMS data ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_CompareTop CPPTRAJ: Compare topology test CPPTRAJ: Rotate dihedral by increment All 1 comparisons passed. CPPTRAJ: Randomize (around) CPPTRAJ: Align, unit cell rotation/imaging test. All 13 comparisons passed. CPPTRAJ: NativeContacts test, orthorhombic imaging. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Filter CPPTRAJ: Test kinetic energy calculation CPPTRAJ: Basic filter test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_CombineCrd All 23 comparisons passed. CPPTRAJ: Combine COORDS test. CPPTRAJ: Wavelet WAFEX test All 10 comparisons passed. CPPTRAJ: Temperature calc with extra points. CPPTRAJ: Generate offset traj from PDB CPPTRAJ: Cluster, sieve5 loadpairdist ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_TopInfo CPPTRAJ: Test writing velocities (MDVEL) CPPTRAJ: Topology info print test. CPPTRAJ: PQR file write with various radii All 6 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_GromacsTrr CPPTRAJ: M-REMD, meltcurve analysis CPPTRAJ: TRR force/velocity read -> NetCDF write test CPPTRAJ: Rotate dihedral in TRAJ data set CPPTRAJ: KDE with Kullback-Leibler divergence test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Multicurve ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Ewald CPPTRAJ: Multicurve test All 1 comparisons passed. CPPTRAJ: Direct sum test CPPTRAJ: Test total energy calculation ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_TI CPPTRAJ: TI analysis test. CPPTRAJ: Combine COORDS test with box info. CPPTRAJ: Generate offset traj from CIF CPPTRAJ: Test using forces as coordinates. All 17 comparisons passed. All 3 comparisons passed. CPPTRAJ: Data filter test. CPPTRAJ: TRAJ test storing frame metadata All 4 comparisons passed. ******************************************************************************** All 1 comparisons passed. TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Distance CPPTRAJ: Fix imaged bonds test (Ortho.) CPPTRAJ: PDB filter alternate atom location IDs test CPPTRAJ: Distance tests CPPTRAJ: Test partial energy calculation CPPTRAJ: Pairdist test, nonorthogonal imaging. All 5 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_SetVelocity ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Volume CPPTRAJ: Set Velocity test CPPTRAJ: Volume tests CPPTRAJ: Cluster, nosieve pairwisecache none All 5 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Remlog CPPTRAJ: Test writing forces (MDFRC) CPPTRAJ: Replica log read/analyze test. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_AreaPerMol CPPTRAJ: Area per molecule test All 8 comparisons passed. All 17 comparisons passed. CPPTRAJ: Orthogonal imaged distance All 3 comparisons passed. CPPTRAJ: Filter matrix test. CPPTRAJ: Split coords and recombine test. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_DistBasedMask CPPTRAJ: Distance-based atom mask tests (atom, residue) ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Calc ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_CalcState CPPTRAJ: Calc test CPPTRAJ: Calcstate test All 2 comparisons passed. CPPTRAJ: Scale velocity test CPPTRAJ: Fix imaged bonds test (Non-ortho.) CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. All 6 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Change CPPTRAJ: Change atom and residue name tests CPPTRAJ: Adding PDB info to topology ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_CreateReservoir CPPTRAJ: Create RREMD NetCDF reservoir test CPPTRAJ: Topology info with reference coords test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_FixAtomOrder All 7 comparisons passed. CPPTRAJ: Out of order molecules test All 5 comparisons passed. All 8 comparisons passed. CPPTRAJ: Calc test with data sets CPPTRAJ: Non-orthogonal imaged distance ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_LowestCurve CPPTRAJ: LowestCurve test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_MinImage 1 out of 3 comparisons failed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Regress CPPTRAJ: Minimum Image test. CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. All 8 comparisons passed. CPPTRAJ: Linear regression test. All 4 comparisons passed. CPPTRAJ: Distance-based atom mask tests (molecule) ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Rst All 10 comparisons passed. CPPTRAJ: Change chain ID test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Pairwise CPPTRAJ: Generate restraints (rst) test All 2 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_ParmBox CPPTRAJ: TRR force/velocity read -> TRR write test CPPTRAJ: Pairwise tests CPPTRAJ: Parmbox test All 12 comparisons passed. All 6 comparisons passed. ******************************************************************************** ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Translate TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Solvent CPPTRAJ: Translate test CPPTRAJ: Test solvent command with closest All 2 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_ReplicateCell ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_ScaleDihedralK CPPTRAJ: Replicate cell test CPPTRAJ: Scale dihedral force constant test CPPTRAJ: Test math functions ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_PhiPsi CPPTRAJ: Cluster, sieve5 pairwisecache none CPPTRAJ: Phipsi test All 3 comparisons passed. All 1 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Control CPPTRAJ: Change chain ID of COORDS set test CPPTRAJ: Loop tests CPPTRAJ: CRD => TRR All 3 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Cphstats ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_InfraredSpec All 1 comparisons passed. CPPTRAJ: Explicit pH REMD ensemble data read / sort CPPTRAJ: Infrared spectrum calculation test All 1 comparisons passed. All 4 comparisons passed. CPPTRAJ: Scale dihedral force constant with 'useall' All 1 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_CmdLine CPPTRAJ: Command line trajectory args test, part 1 ******************************************************************************** All 1 comparisons passed. TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_XYZformat CPPTRAJ: XYZ format write All 1 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_CatCrd ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Hausdorff All 1 comparisons passed. CPPTRAJ: Concatenate COORDS data set test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_XtalSymm CPPTRAJ: Simple Hausdorff distance test. CPPTRAJ: XtalSymm Reference CPPTRAJ: Pairwise test, partial system ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Time ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_SplitCoords ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_DihedralRMS CPPTRAJ: SplitCoords test CPPTRAJ: Add time to restart test All 3 comparisons passed. CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) All 5 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Diagmatrix All 2 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Slope CPPTRAJ: MW covariance matrix thermo analysis test CPPTRAJ: Randomize (overlap) CPPTRAJ: Finite difference test. All 6 comparisons passed. CPPTRAJ: Cluster, random CPPTRAJ: Command line test trajectory args test, part 2 CPPTRAJ: Test set command ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Emin All 2 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau CPPTRAJ: Basic energy minimization test. All 1 comparisons passed. CPPTRAJ: Constant pH stats test CPPTRAJ: Hausdorff distance of 2D rms output test. CPPTRAJ: Evalulate plateau test All 1 comparisons passed. CPPTRAJ: Atom XYZ format read, test 1 CPPTRAJ: Remove time from restart test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Graft CPPTRAJ: TRR => CRD CPPTRAJ: Graft test ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Flatten ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Random CPPTRAJ: Flatten test. All 1 comparisons passed. CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs CPPTRAJ: Dihedral RMSD test (to previous) All 1 comparisons passed. All 10 comparisons passed. All 1 comparisons passed. CPPTRAJ: Energy minimization with angle term test. CPPTRAJ: Command line wildcard test, part 1 CPPTRAJ: Sorted implicit constant pH stats test CPPTRAJ: Add time to trajectory test CPPTRAJ: Test reading comma-separated list of strings All 2 comparisons passed. CPPTRAJ: Atom XYZ format read, test 2 All 1 comparisons passed. CPPTRAJ: PCG32 RNG test. All 1 comparisons passed. CPPTRAJ: Dihedral RMS fluctuation test. All 28 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). CPPTRAJ: Command line wildcard test, part 2 CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. CPPTRAJ: Randomize (no restrictions) CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats CPPTRAJ: Hausdorff distance of 2D rms output test. CPPTRAJ: Test Stdlib RNG CPPTRAJ: Atom XYZ format read, test 3 CPPTRAJ: Test nested loops and variables in loops All 5 comparisons passed. g++ -o a.out main.o NameType.o CpptrajStdio.o CPPTRAJ: Read specific columns test. All 2 comparisons passed. CPPTRAJ: CRD(1-5) => TRR CPPTRAJ: Energy minimization with nonbond term test. CPPTRAJ: Test Mersenne Twister RNG All 4 comparisons passed. CPPTRAJ: Test loop over data set blocks CPPTRAJ: Atom XYZ format read, test 4 CPPTRAJ: Unsorted pH read/write test CPPTRAJ: Modify time info test. CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). CPPTRAJ: Write non-square matrix All 4 comparisons passed. All 5 comparisons passed. CPPTRAJ: Atom XYZ format read, test 5 All 16 comparisons passed. CPPTRAJ: CRD(6-10) => TRR All 4 comparisons passed. CPPTRAJ: Test for filename wildcards and oversets CPPTRAJ: Read non-square matrix make[5]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg/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. CPPTRAJ: Atom XYZ format read, test 6 All 4 comparisons passed. All 13 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet CPPTRAJ: Clustering, One DataSet CPPTRAJ: Read square matrix CPPTRAJ: TRR (appended) => CRD All 6 comparisons passed. All 15 comparisons passed. CPPTRAJ: Clustering, Two DataSets All 1 comparisons passed. CPPTRAJ: Ewald test (NaCl crystal) CPPTRAJ: XtalSymm Reimaging by Atom CPPTRAJ: OpenMM basic energy minimization tests (bonds) CPPTRAJ: Clustering, dihedral DataSet CPPTRAJ: Ewald test (trunc. oct) CPPTRAJ: OpenMM basic energy minimization tests (angles) CPPTRAJ: GMX: CRD with offset CPPTRAJ: Clustering, two dihedral DataSets CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) CPPTRAJ: Pairdist test, 2 masks. CPPTRAJ: Clustering, dihedral DataSet, K-means CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) All 4 comparisons passed. CPPTRAJ: GMX: TRR with offset CPPTRAJ: Watershell Test, orthorhombic imaging. CPPTRAJ: Clustering, two dihedral DataSets, K-means All 8 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN CPPTRAJ: DBSCAN test All 5 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc CPPTRAJ: XTC read test CPPTRAJ: DBSCAN automatic parameter determination test. CPPTRAJ: DBSCAN kdist map test CPPTRAJ: CRD => XTC CPPTRAJ: DBSCAN with sieve CPPTRAJ: Watershell Test, no imaging. All 4 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans CPPTRAJ: Cpptraj Kmeans CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) CPPTRAJ: XTC => CRD CPPTRAJ: Ewald test (partial system, trunc. oct) CPPTRAJ: Cpptraj Kmeans random CPPTRAJ: CRD(1-5) => XTC 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: /srv/build/cpptraj-5.1.0+dfsg/test/Test_LibPME CPPTRAJ: Particle mesh Ewald test (NaCl crystal) All 6 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Cluster_SymmRMSD CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) All 3 comparisons passed. CPPTRAJ: CRD(6-10) => XTC CPPTRAJ: Particle mesh Ewald test (trunc. oct) CPPTRAJ: XTC (appended) => CRD All 5 comparisons passed. CPPTRAJ: GMX: CRD with offset ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites CPPTRAJ: Cluster command test, coordinate writes. CPPTRAJ: Particle mesh Ewald test (ortho) CPPTRAJ: Cluster command test, coordinate writes using info file. CPPTRAJ: GMX: XTC with offset All 4 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_GromacsTNG CPPTRAJ: TNG read test All 8 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Cluster_Dpeaks CPPTRAJ: Density peaks clustering test CPPTRAJ: GIST test, orthogonal cell All 3 comparisons passed. CPPTRAJ: Particle mesh Ewald test (ortho, with mask) ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_Cluster_Nreps CPPTRAJ: Clustering with specified # reps CPPTRAJ: TNG read test (with offset) CPPTRAJ: PME test (partial system, trunc. oct) g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o All 2 comparisons passed. All 5 comparisons passed. 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. All 9 comparisons passed. make[5]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg/unitTests/ArgList' Unit test passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_LJ_PME make[4]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg/unitTests' make[3]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ: LJ PME test. All 6 comparisons passed. 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: XtalSymm Reimaging by Molecule CPPTRAJ: LJ with switch function test All 5 comparisons passed. All 3 comparisons passed. CPPTRAJ: GIST test, nonorthogonal cell All 11 comparisons passed. ******************************************************************************** TEST: /srv/build/cpptraj-5.1.0+dfsg/test/Test_GIST_Order CPPTRAJ: TIP3P water cluster test CPPTRAJ: TIP4P water cluster test CPPTRAJ: TIP5P water cluster test All 4 comparisons passed. ../MasterTest.sh: line 495: 4213 Segmentation fault $cpptraj_cmd >> $CPPTRAJ_OUTPUT Error: cpptraj exited with status 139 CPPTRAJ: SPAM Pure Solvent Test 1 out of 2 executions exited with an error. 2 out of 5 comparisons failed. make[4]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg/test' make[3]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg/test' make[2]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg' /usr/bin/make -C test summary make[2]: Entering directory '/srv/build/cpptraj-5.1.0+dfsg/test' -rwxr-xr-x 1 builder builder 183506880 Mar 18 17:06 ../bin/cpptraj ===================== TEST SUMMARY ====================== 850 out of 859 comparisons OK (3 failed, 0 warnings, 6 skipped). 479 out of 480 program executions completed. 168 out of 173 tests completed with no issues. 2 tests skipped. ========================================================= make[2]: *** [Makefile:662: summary] Error 4 make[2]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg/test' make[1]: *** [debian/rules:17: override_dh_auto_test] Error 2 make[1]: Leaving directory '/srv/build/cpptraj-5.1.0+dfsg' make: *** [debian/rules:10: binary-arch] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 Command `dpkg-buildpackage --changes-option=-DDistribution=landing -B -mDebichem Team -eDebichem Team ` failed. Command debspawn build --no-buildlog --arch=arm64 --results-dir=/var/lib/lkspark/workspaces/5feb3f3a-ed26-411b-a142-124ee7013bbb --only=arch --maintainer=Debichem Team landing cpptraj_5.1.0+dfsg-4.dsc failed with error code 2