Sun Feb 16 12:33:36 UTC 2025 I: starting to build cpptraj/trixie/arm64 on jenkins on '2025-02-16 12:33' Sun Feb 16 12:33:36 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_1/60412/console.log Sun Feb 16 12:33:36 UTC 2025 I: Downloading source for trixie/cpptraj=5.1.0+dfsg-4 --2025-02-16 12:33:36-- http://deb.debian.org/debian/pool/main/c/cpptraj/cpptraj_5.1.0%2bdfsg-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2184 (2.1K) [text/prs.lines.tag] Saving to: ‘cpptraj_5.1.0+dfsg-4.dsc’ 0K .. 100% 376M=0s 2025-02-16 12:33:36 (376 MB/s) - ‘cpptraj_5.1.0+dfsg-4.dsc’ saved [2184/2184] Sun Feb 16 12:33:36 UTC 2025 I: cpptraj_5.1.0+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: cpptraj Binary: cpptraj Architecture: any Version: 5.1.0+dfsg-4 Maintainer: Debichem Team Uploaders: Andrius Merkys , Homepage: https://github.com/Amber-MD/cpptraj Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/debichem-team/cpptraj Vcs-Git: https://salsa.debian.org/debichem-team/cpptraj.git Testsuite: autopkgtest Testsuite-Triggers: netcdf-bin Build-Depends: debhelper-compat (= 13), gfortran, libarpack2-dev, libbz2-dev, libfftw3-dev, libnetcdf-dev, libopenmm-dev [amd64 arm64 armhf mips64el ppc64el riscv64], libreadline-dev, netcdf-bin Package-List: cpptraj deb science optional arch=any Checksums-Sha1: b326e493769758a5e5e29173898e049c6a60e9a2 28363024 cpptraj_5.1.0+dfsg.orig.tar.xz 01a62f884bc2739ce8f799c62b3e260f8205b82c 6084 cpptraj_5.1.0+dfsg-4.debian.tar.xz Checksums-Sha256: 89e279bbb5d35db4d2599fa98322bb8c4b876ce6117f8896e75520a3da1182f3 28363024 cpptraj_5.1.0+dfsg.orig.tar.xz 0e96d529626c3f73247201aa16e7b8c8afba853694be1a331a3ae73a5fe4bf3c 6084 cpptraj_5.1.0+dfsg-4.debian.tar.xz Files: bf932a3aed87ad43645613135c712505 28363024 cpptraj_5.1.0+dfsg.orig.tar.xz 6e26922e03d8c1c199dfd28f36581cba 6084 cpptraj_5.1.0+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmZCJuQSHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKHhmEP/igOOwHV5yAXVBSlVNtYT+DL2jzFwcLP /LYplbd5pvvDm9Aw8+6fAj7aDwFLhCQJg9/MR+Xu90VQ7ymrdWRRnqX0RcwggbPs JGGG0RRU0NrZnbyxTKD1Z/H6w1NkenykJpnoOrkBlFMZJc9kCAdWnLwKFSxcg2Xl SX11O3s7QwLrjlqcCF2gXy3eWGjKJHLiW0WN+O+j3PNYd5QcnrfvtFvV4lUoTv6q 9UFvejofK1hkx1ysw/P/V2DlAawOzX0BVzRBU9xCwXAXFv0lu5JJWdD66NWaCb0N ja6vW2eZTvs5Ble8s1AoF0EevpTh6PICJ75e6T/PIS2AH/DbBmCo6ATEbpnALd3Z pj4D1HTrBlaRw60ZlyqKK4iqKd35KmSJRDT1Fa2YilCBInJDd1fZQHgEVPj2WF7S DsyS59VonzRUmCznTxKPFybDCmUdVveN6jpxWpcYjYg+cO/L5rPXERwU28jDpCuK QWZz+AK0tzQLm05TFV4Qg7QJFgn/mIOPYF1HQgsGtJ/V0RNSBd+/NeKWGF1qSX7y +eERIOK+8DrYjOebe24bRUs/lR1Vx+HTxpAQw47+VZBvogGbyDfp1AiElZvb0Ia4 pQ5omJd6jxqbHFP0HdxVwMZYDPFJlkYN5O1sHQTFq+3wYzEhmvIzE0tV9fqCOBKw gP/0H6lIFBch =XQSu -----END PGP SIGNATURE----- Sun Feb 16 12:33:36 UTC 2025 I: Checking whether the package is not for us Sun Feb 16 12:33:36 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Sun Feb 16 12:33:36 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Sun Feb 16 12:39:07 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. W: cgroups are not available on the host, not using them. I: pbuilder: network access will be disabled during build I: Current time: Sat Mar 21 06:56:38 -12 2026 I: pbuilder-time-stamp: 1774119398 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [cpptraj_5.1.0+dfsg-4.dsc] I: copying [./cpptraj_5.1.0+dfsg.orig.tar.xz] I: copying [./cpptraj_5.1.0+dfsg-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./cpptraj_5.1.0+dfsg-4.dsc: unsupported subcommand 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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/548104/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='548104' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Q3UHNyTY/pbuilderrc_8Liv --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Q3UHNyTY/b1 --logfile b1/build.log cpptraj_5.1.0+dfsg-4.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/sbin/chroot' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/548104/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), gfortran, libarpack2-dev, libbz2-dev, libfftw3-dev, libnetcdf-dev, libopenmm-dev, libreadline-dev, netcdf-bin dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19922 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on libarpack2-dev; however: Package libarpack2-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on libnetcdf-dev; however: Package libnetcdf-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmm-dev; however: Package libopenmm-dev is not installed. pbuilder-satisfydepends-dummy depends on libreadline-dev; however: Package libreadline-dev is not installed. pbuilder-satisfydepends-dummy depends on netcdf-bin; however: Package netcdf-bin is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran{a} gfortran-14{a} gfortran-14-aarch64-linux-gnu{a} gfortran-aarch64-linux-gnu{a} groff-base{a} hdf5-helpers{a} icu-devtools{a} intltool-debian{a} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarpack2-dev{a} libarpack2t64{a} libblas-dev{a} libblas3{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libffi8{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-single3{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-310{a} libhdf5-cpp-310{a} libhdf5-dev{a} libhdf5-fortran-310{a} libhdf5-hl-310{a} libhdf5-hl-cpp-310{a} libhdf5-hl-fortran-310{a} libicu-dev{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-dev{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnetcdf-dev{a} libnetcdf22{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libopenmm-dev{a} libopenmm8.1{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} libreadline-dev{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsz2{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2{a} libxml2-dev{a} libzstd-dev{a} m4{a} man-db{a} netcdf-bin{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 133 newly installed, 0 to remove and 0 not upgraded. Need to get 76.0 MB of archives. After unpacking 319 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-3 [92.0 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.17-3 [862 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 comerr-dev arm64 2.1-1.47.2-1 [55.9 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-3 [539 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 25 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.24.1 [920 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14.2.0-16 [361 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libgfortran-14-dev arm64 14.2.0-16 [418 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-16 [9795 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 gfortran-14 arm64 14.2.0-16 [13.6 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1 [1284 B] Get: 39 http://deb.debian.org/debian trixie/main arm64 gfortran arm64 4:14.2.0-1 [1424 B] Get: 40 http://deb.debian.org/debian trixie/main arm64 hdf5-helpers arm64 1.14.5+repack-3 [26.6 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 icu-devtools arm64 72.1-6 [196 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 45 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libgssrpc4t64 arm64 1.21.3-4 [56.9 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libkadm5clnt-mit12 arm64 1.21.3-4 [41.0 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libkdb5-10t64 arm64 1.21.3-4 [41.0 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libkadm5srv-mit12 arm64 1.21.3-4 [53.1 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 krb5-multidev arm64 1.21.3-4 [126 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B] Get: 54 http://deb.debian.org/debian trixie/main arm64 libaec-dev arm64 1.1.3-1+b1 [20.2 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libblas3 arm64 3.12.1-2 [104 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libarpack2t64 arm64 3.9.1-4 [83.7 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libblas-dev arm64 3.12.1-2 [111 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 liblapack-dev arm64 3.12.1-2 [3726 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libarpack2-dev arm64 3.9.1-4 [102 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.9.1-1 [109 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.9.1-1 [17.3 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.12.0+git20250209.89ed161+ds-1 [336 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libunbound8 arm64 1.22.0-1+b1 [553 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libgnutls-dane0t64 arm64 3.8.9-2 [452 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libgnutls-openssl27t64 arm64 3.8.9-2 [452 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libp11-kit-dev arm64 0.25.5-3 [208 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libgnutls28-dev arm64 3.8.9-2 [1419 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libkrb5-dev arm64 1.21.3-4 [15.9 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libldap-dev arm64 2.6.9+dfsg-1 [305 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libnghttp3-dev arm64 1.6.0-2 [86.5 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.9.1-1 [23.0 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libngtcp2-dev arm64 1.9.1-1 [162 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libssl-dev arm64 3.4.0-2 [3234 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libzstd-dev arm64 1.5.6+dfsg-2 [329 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libcurl4-gnutls-dev arm64 8.12.0+git20250209.89ed161+ds-1 [465 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libcurl4t64 arm64 8.12.0+git20250209.89ed161+ds-1 [326 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libfftw3-double3 arm64 3.3.10-2+b1 [337 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libfftw3-long3 arm64 3.3.10-2+b1 [546 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libfftw3-single3 arm64 3.3.10-2+b1 [517 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libfftw3-bin arm64 3.3.10-2+b1 [44.3 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libfftw3-dev arm64 3.3.10-2+b1 [1280 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libhdf5-310 arm64 1.14.5+repack-3 [1155 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libhdf5-cpp-310 arm64 1.14.5+repack-3 [121 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libhdf5-fortran-310 arm64 1.14.5+repack-3 [110 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [66.1 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libhdf5-hl-fortran-310 arm64 1.14.5+repack-3 [42.1 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libhdf5-hl-cpp-310 arm64 1.14.5+repack-3 [24.4 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-3+b1 [293 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 libjpeg-dev arm64 1:2.1.5-3+b1 [72.2 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libhdf5-dev arm64 1.14.5+repack-3 [3225 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libicu-dev arm64 72.1-6 [10.3 MB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.5+20250125-2 [96.2 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libncurses-dev arm64 6.5+20250125-2 [340 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libnetcdf22 arm64 1:4.9.3-1 [481 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libxml2-dev arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [751 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 libnetcdf-dev arm64 1:4.9.3-1 [116 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 libopenmm8.1 arm64 8.1.2+dfsg-3 [921 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libopenmm-dev arm64 8.1.2+dfsg-3 [330 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libreadline-dev arm64 8.2-6 [155 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 netcdf-bin arm64 1:4.9.3-1 [245 kB] Fetched 76.0 MB in 0s (227 MB/s) 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 ... 19922 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. Preparing to unpack .../002-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../003-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../006-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../007-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../008-bsdextrautils_2.40.4-3_arm64.deb ... Unpacking bsdextrautils (2.40.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../009-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../010-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../011-m4_1.4.19-5_arm64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../012-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../013-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../014-automake_1%3a1.17-3_all.deb ... Unpacking automake (1:1.17-3) ... Selecting previously unselected package autopoint. Preparing to unpack .../015-autopoint_0.23.1-1_all.deb ... Unpacking autopoint (0.23.1-1) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../016-libcom-err2_1.47.2-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2-1) ... Selecting previously unselected package comerr-dev:arm64. Preparing to unpack .../017-comerr-dev_2.1-1.47.2-1_arm64.deb ... Unpacking comerr-dev:arm64 (2.1-1.47.2-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../018-libdebhelper-perl_13.24.1_all.deb ... Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../019-libtool_2.5.4-3_all.deb ... Unpacking libtool (2.5.4-3) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../020-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../021-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../022-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../023-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../024-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../025-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../026-libunistring5_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../027-libicu72_72.1-6_arm64.deb ... Unpacking libicu72:arm64 (72.1-6) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../028-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../029-gettext_0.23.1-1_arm64.deb ... Unpacking gettext (0.23.1-1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../030-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../031-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../032-debhelper_13.24.1_all.deb ... Unpacking debhelper (13.24.1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../033-libgfortran5_14.2.0-16_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-16) ... Selecting previously unselected package libgfortran-14-dev:arm64. Preparing to unpack .../034-libgfortran-14-dev_14.2.0-16_arm64.deb ... Unpacking libgfortran-14-dev:arm64 (14.2.0-16) ... Selecting previously unselected package gfortran-14-aarch64-linux-gnu. Preparing to unpack .../035-gfortran-14-aarch64-linux-gnu_14.2.0-16_arm64.deb ... Unpacking gfortran-14-aarch64-linux-gnu (14.2.0-16) ... Selecting previously unselected package gfortran-14. Preparing to unpack .../036-gfortran-14_14.2.0-16_arm64.deb ... Unpacking gfortran-14 (14.2.0-16) ... Selecting previously unselected package gfortran-aarch64-linux-gnu. Preparing to unpack .../037-gfortran-aarch64-linux-gnu_4%3a14.2.0-1_arm64.deb ... Unpacking gfortran-aarch64-linux-gnu (4:14.2.0-1) ... Selecting previously unselected package gfortran. Preparing to unpack .../038-gfortran_4%3a14.2.0-1_arm64.deb ... Unpacking gfortran (4:14.2.0-1) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../039-hdf5-helpers_1.14.5+repack-3_arm64.deb ... Unpacking hdf5-helpers (1.14.5+repack-3) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../040-icu-devtools_72.1-6_arm64.deb ... Unpacking icu-devtools (72.1-6) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../041-libkrb5support0_1.21.3-4_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-4) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../042-libk5crypto3_1.21.3-4_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-4) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../043-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../044-libkrb5-3_1.21.3-4_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-4) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../045-libgssapi-krb5-2_1.21.3-4_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-4) ... Selecting previously unselected package libgssrpc4t64:arm64. Preparing to unpack .../046-libgssrpc4t64_1.21.3-4_arm64.deb ... Unpacking libgssrpc4t64:arm64 (1.21.3-4) ... Selecting previously unselected package libkadm5clnt-mit12:arm64. Preparing to unpack .../047-libkadm5clnt-mit12_1.21.3-4_arm64.deb ... Unpacking libkadm5clnt-mit12:arm64 (1.21.3-4) ... Selecting previously unselected package libkdb5-10t64:arm64. Preparing to unpack .../048-libkdb5-10t64_1.21.3-4_arm64.deb ... Unpacking libkdb5-10t64:arm64 (1.21.3-4) ... Selecting previously unselected package libkadm5srv-mit12:arm64. Preparing to unpack .../049-libkadm5srv-mit12_1.21.3-4_arm64.deb ... Unpacking libkadm5srv-mit12:arm64 (1.21.3-4) ... Selecting previously unselected package krb5-multidev:arm64. Preparing to unpack .../050-krb5-multidev_1.21.3-4_arm64.deb ... Unpacking krb5-multidev:arm64 (1.21.3-4) ... Selecting previously unselected package libaec0:arm64. Preparing to unpack .../051-libaec0_1.1.3-1+b1_arm64.deb ... Unpacking libaec0:arm64 (1.1.3-1+b1) ... Selecting previously unselected package libsz2:arm64. Preparing to unpack .../052-libsz2_1.1.3-1+b1_arm64.deb ... Unpacking libsz2:arm64 (1.1.3-1+b1) ... Selecting previously unselected package libaec-dev:arm64. Preparing to unpack .../053-libaec-dev_1.1.3-1+b1_arm64.deb ... Unpacking libaec-dev:arm64 (1.1.3-1+b1) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../054-libblas3_3.12.1-2_arm64.deb ... Unpacking libblas3:arm64 (3.12.1-2) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../055-liblapack3_3.12.1-2_arm64.deb ... Unpacking liblapack3:arm64 (3.12.1-2) ... Selecting previously unselected package libarpack2t64:arm64. Preparing to unpack .../056-libarpack2t64_3.9.1-4_arm64.deb ... Unpacking libarpack2t64:arm64 (3.9.1-4) ... Selecting previously unselected package libblas-dev:arm64. Preparing to unpack .../057-libblas-dev_3.12.1-2_arm64.deb ... Unpacking libblas-dev:arm64 (3.12.1-2) ... Selecting previously unselected package liblapack-dev:arm64. Preparing to unpack .../058-liblapack-dev_3.12.1-2_arm64.deb ... Unpacking liblapack-dev:arm64 (3.12.1-2) ... Selecting previously unselected package libarpack2-dev:arm64. Preparing to unpack .../059-libarpack2-dev_3.9.1-4_arm64.deb ... Unpacking libarpack2-dev:arm64 (3.9.1-4) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../060-libbrotli1_1.1.0-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b6) ... Selecting previously unselected package libbrotli-dev:arm64. Preparing to unpack .../061-libbrotli-dev_1.1.0-2+b6_arm64.deb ... Unpacking libbrotli-dev:arm64 (1.1.0-2+b6) ... Selecting previously unselected package libbz2-dev:arm64. Preparing to unpack .../062-libbz2-dev_1.0.8-6_arm64.deb ... Unpacking libbz2-dev:arm64 (1.0.8-6) ... Selecting previously unselected package libidn2-0:arm64. Preparing to unpack .../063-libidn2-0_2.3.7-2+b1_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.7-2+b1) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../064-libffi8_3.4.6-1_arm64.deb ... Unpacking libffi8:arm64 (3.4.6-1) ... Selecting previously unselected package libp11-kit0:arm64. Preparing to unpack .../065-libp11-kit0_0.25.5-3_arm64.deb ... Unpacking libp11-kit0:arm64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:arm64. Preparing to unpack .../066-libtasn1-6_4.19.0-3+b3_arm64.deb ... Unpacking libtasn1-6:arm64 (4.19.0-3+b3) ... Selecting previously unselected package libgnutls30t64:arm64. Preparing to unpack .../067-libgnutls30t64_3.8.9-2_arm64.deb ... 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Selecting previously unselected package libgnutls28-dev:arm64. Preparing to unpack .../089-libgnutls28-dev_3.8.9-2_arm64.deb ... Unpacking libgnutls28-dev:arm64 (3.8.9-2) ... Selecting previously unselected package libkrb5-dev:arm64. Preparing to unpack .../090-libkrb5-dev_1.21.3-4_arm64.deb ... Unpacking libkrb5-dev:arm64 (1.21.3-4) ... Selecting previously unselected package libldap-dev:arm64. Preparing to unpack .../091-libldap-dev_2.6.9+dfsg-1_arm64.deb ... Unpacking libldap-dev:arm64 (2.6.9+dfsg-1) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../092-libpkgconf3_1.8.1-4_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../093-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../094-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Selecting previously unselected package libnghttp2-dev:arm64. Preparing to unpack .../095-libnghttp2-dev_1.64.0-1_arm64.deb ... Unpacking libnghttp2-dev:arm64 (1.64.0-1) ... Selecting previously unselected package libnghttp3-dev:arm64. Preparing to unpack .../096-libnghttp3-dev_1.6.0-2_arm64.deb ... Unpacking libnghttp3-dev:arm64 (1.6.0-2) ... Selecting previously unselected package libngtcp2-crypto-gnutls-dev:arm64. Preparing to unpack .../097-libngtcp2-crypto-gnutls-dev_1.9.1-1_arm64.deb ... Unpacking libngtcp2-crypto-gnutls-dev:arm64 (1.9.1-1) ... Selecting previously unselected package libngtcp2-dev:arm64. Preparing to unpack .../098-libngtcp2-dev_1.9.1-1_arm64.deb ... Unpacking libngtcp2-dev:arm64 (1.9.1-1) ... Selecting previously unselected package libpsl-dev:arm64. Preparing to unpack .../099-libpsl-dev_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl-dev:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package zlib1g-dev:arm64. 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Preparing to unpack .../105-libcurl4-gnutls-dev_8.12.0+git20250209.89ed161+ds-1_arm64.deb ... Unpacking libcurl4-gnutls-dev:arm64 (8.12.0+git20250209.89ed161+ds-1) ... Selecting previously unselected package libcurl4t64:arm64. Preparing to unpack .../106-libcurl4t64_8.12.0+git20250209.89ed161+ds-1_arm64.deb ... Unpacking libcurl4t64:arm64 (8.12.0+git20250209.89ed161+ds-1) ... Selecting previously unselected package libfftw3-double3:arm64. Preparing to unpack .../107-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 .../108-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 .../109-libfftw3-single3_3.3.10-2+b1_arm64.deb ... Unpacking libfftw3-single3:arm64 (3.3.10-2+b1) ... Selecting previously unselected package libfftw3-bin. 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Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3) ... Selecting previously unselected package libhdf5-hl-fortran-310:arm64. Preparing to unpack .../116-libhdf5-hl-fortran-310_1.14.5+repack-3_arm64.deb ... Unpacking libhdf5-hl-fortran-310:arm64 (1.14.5+repack-3) ... Selecting previously unselected package libhdf5-hl-cpp-310:arm64. Preparing to unpack .../117-libhdf5-hl-cpp-310_1.14.5+repack-3_arm64.deb ... Unpacking libhdf5-hl-cpp-310:arm64 (1.14.5+repack-3) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../118-libjpeg62-turbo_1%3a2.1.5-3+b1_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Selecting previously unselected package libjpeg62-turbo-dev:arm64. Preparing to unpack .../119-libjpeg62-turbo-dev_1%3a2.1.5-3+b1_arm64.deb ... Unpacking libjpeg62-turbo-dev:arm64 (1:2.1.5-3+b1) ... Selecting previously unselected package libjpeg-dev:arm64. Preparing to unpack .../120-libjpeg-dev_1%3a2.1.5-3+b1_arm64.deb ... Unpacking libjpeg-dev:arm64 (1:2.1.5-3+b1) ... Selecting previously unselected package libhdf5-dev. Preparing to unpack .../121-libhdf5-dev_1.14.5+repack-3_arm64.deb ... Unpacking libhdf5-dev (1.14.5+repack-3) ... Selecting previously unselected package libicu-dev:arm64. Preparing to unpack .../122-libicu-dev_72.1-6_arm64.deb ... Unpacking libicu-dev:arm64 (72.1-6) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../123-libncurses6_6.5+20250125-2_arm64.deb ... Unpacking libncurses6:arm64 (6.5+20250125-2) ... Selecting previously unselected package libncurses-dev:arm64. Preparing to unpack .../124-libncurses-dev_6.5+20250125-2_arm64.deb ... Unpacking libncurses-dev:arm64 (6.5+20250125-2) ... Selecting previously unselected package libnetcdf22:arm64. Preparing to unpack .../125-libnetcdf22_1%3a4.9.3-1_arm64.deb ... Unpacking libnetcdf22:arm64 (1:4.9.3-1) ... Selecting previously unselected package libxml2-dev:arm64. Preparing to unpack .../126-libxml2-dev_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2-dev:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package libnetcdf-dev. Preparing to unpack .../127-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 .../128-libopenmm8.1_8.1.2+dfsg-3_arm64.deb ... Unpacking libopenmm8.1 (8.1.2+dfsg-3) ... Selecting previously unselected package libopenmm-dev. Preparing to unpack .../129-libopenmm-dev_8.1.2+dfsg-3_arm64.deb ... Unpacking libopenmm-dev (8.1.2+dfsg-3) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../130-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 .../131-libreadline-dev_8.2-6_arm64.deb ... Unpacking libreadline-dev:arm64 (8.2-6) ... Selecting previously unselected package netcdf-bin. Preparing to unpack .../132-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 libkeyutils1:arm64 (1.6.3-4) ... Setting up libfftw3-single3:arm64 (3.3.10-2+b1) ... Setting up libicu72:arm64 (72.1-6) ... Setting up libzstd-dev:arm64 (1.5.6+dfsg-2) ... Setting up bsdextrautils (2.40.4-3) ... 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+b6) ... Setting up libmagic1t64:arm64 (1:5.45-3+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 (1.4.19-5) ... Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libcom-err2:arm64 (1.47.2-1) ... 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 libkrb5support0:arm64 (1.21.3-4) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8+b1) ... 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+b1) ... Setting up libjpeg62-turbo-dev:arm64 (1:2.1.5-3+b1) ... Setting up libncurses6:arm64 (6.5+20250125-2) ... Setting up comerr-dev:arm64 (2.1-1.47.2-1) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up libssl-dev:arm64 (3.4.0-2) ... Setting up autopoint (0.23.1-1) ... Setting up icu-devtools (72.1-6) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:arm64 (1.21.3-4) ... Setting up libfftw3-double3:arm64 (3.3.10-2+b1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-8+b1) ... Setting up libgfortran5:arm64 (14.2.0-16) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.6.0-2) ... Setting up libnghttp3-dev:arm64 (1.6.0-2) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.6-1) ... 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 libtasn1-6:arm64 (4.19.0-3+b3) ... Setting up libngtcp2-16:arm64 (1.9.1-1) ... Setting up libkrb5-3:arm64 (1.21.3-4) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libtasn1-6-dev:arm64 (4.19.0-3+b3) ... Setting up libopenmm8.1 (8.1.2+dfsg-3) ... Setting up readline-common (8.2-6) ... Setting up libicu-dev:arm64 (72.1-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libldap2:arm64 (2.6.9+dfsg-1) ... Setting up libbrotli-dev:arm64 (1.1.0-2+b6) ... 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 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+20250125-2) ... 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+b1) ... Setting up libtool (2.5.4-3) ... 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+b1) ... Setting up libidn2-0:arm64 (2.3.7-2+b1) ... Setting up libngtcp2-dev:arm64 (1.9.1-1) ... Setting up libopenmm-dev (8.1.2+dfsg-3) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libxml2-dev:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libldap-dev:arm64 (2.6.9+dfsg-1) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... 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 libgssapi-krb5-2:arm64 (1.21.3-4) ... Setting up libssh2-1-dev:arm64 (1.11.1-1) ... Setting up libidn2-dev:arm64 (2.3.7-2+b1) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up gfortran-14-aarch64-linux-gnu (14.2.0-16) ... Setting up gfortran-aarch64-linux-gnu (4:14.2.0-1) ... Setting up gfortran-14 (14.2.0-16) ... Setting up libfftw3-dev:arm64 (3.3.10-2+b1) ... Setting up libp11-kit-dev:arm64 (0.25.5-3) ... Setting up libgnutls30t64:arm64 (3.8.9-2) ... Setting up libgnutls-openssl27t64:arm64 (3.8.9-2) ... Setting up libnghttp2-dev:arm64 (1.64.0-1) ... Setting up libarpack2-dev:arm64 (3.9.1-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up libreadline-dev:arm64 (8.2-6) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. 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 libpsl-dev:arm64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:arm64 (3.8.9-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:arm64 (1.21.3-4) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.9.1-1) ... Setting up libkadm5clnt-mit12:arm64 (1.21.3-4) ... Setting up libgnutls28-dev:arm64 (3.8.9-2) ... Setting up libcurl4t64:arm64 (8.12.0+git20250209.89ed161+ds-1) ... Setting up libkdb5-10t64:arm64 (1.21.3-4) ... Setting up libcurl3t64-gnutls:arm64 (8.12.0+git20250209.89ed161+ds-1) ... Setting up debhelper (13.24.1) ... Setting up libngtcp2-crypto-gnutls-dev:arm64 (1.9.1-1) ... Setting up librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhdf5-310:arm64 (1.14.5+repack-3) ... Setting up libkadm5srv-mit12:arm64 (1.21.3-4) ... Setting up libhdf5-fortran-310:arm64 (1.14.5+repack-3) ... Setting up krb5-multidev:arm64 (1.21.3-4) ... Setting up libhdf5-cpp-310:arm64 (1.14.5+repack-3) ... Setting up libhdf5-hl-310:arm64 (1.14.5+repack-3) ... Setting up libnetcdf22:arm64 (1:4.9.3-1) ... Setting up netcdf-bin (1:4.9.3-1) ... Setting up libkrb5-dev:arm64 (1.21.3-4) ... 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 libcurl4-gnutls-dev:arm64 (8.12.0+git20250209.89ed161+ds-1) ... 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 (2.40-6) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/cpptraj-5.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../cpptraj_5.1.0+dfsg-4_source.changes 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: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' touch config.h external.config.h dh_auto_clean make -j12 clean make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make clean make[3]: Entering directory '/build/reproducible-path/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 '/build/reproducible-path/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 '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' # cd arpack && make clean cd cuda_kernels && make clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/cuda_kernels' /bin/rm -f *.o libcpptraj_cuda.a make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/cuda_kernels' cd tng && make clean make[4]: Entering directory '/build/reproducible-path/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 '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' cd test && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' Cleaning all test directories: make test.complete test.libcpptraj OPT=clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' cd unitTests && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' Cleaning unit tests. make test.complete OPT=clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' rm -rf bin make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/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: /build/reproducible-path/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 '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make install make[2]: Entering directory '/build/reproducible-path/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 CXX Action_FilterByData.cpp In file included from Ewald_ParticleMesh.h:5, from Action_Energy.cpp:4: helpme_standalone.h:2323: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2323 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:2343: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2343 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3014: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3014 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3120: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3120 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3247: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3247 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3701: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3701 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3739: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3739 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3802: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3802 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3840: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3840 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4044: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4044 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4052: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4052 | #pragma omp for helpme_standalone.h:4097: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4097 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4145: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4145 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4172: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4172 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4224: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4224 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4228: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4228 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4275: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4275 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4388: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4388 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4419: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4503: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4503 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4510: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4510 | #pragma omp for CXX Action_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 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 [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function '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 [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function '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 [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function '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 [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function '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 [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function '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 [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ CXX Action_Matrix.cpp CXX Action_MinImage.cpp CXX Action_Molsurf.cpp CXX Action_MultiDihedral.cpp CXX Action_MultiVector.cpp CXX Action_NAstruct.cpp CXX Action_NativeContacts.cpp CXX Action_NMRrst.cpp CXX Action_OrderParameter.cpp CXX Action_Outtraj.cpp CXX Action_PairDist.cpp CXX Action_Pairwise.cpp CXX Action_Principal.cpp CXX Action_Projection.cpp CXX Action_Pucker.cpp CXX Action_Radgyr.cpp CXX Action_Radial.cpp CXX Action_RandomizeIons.cpp CXX Action_Remap.cpp CXX Action_ReplicateCell.cpp CXX Action_Rmsd.cpp CXX Action_Rotate.cpp CXX Action_RunningAvg.cpp CXX Action_STFC_Diffusion.cpp CXX Action_Scale.cpp CXX Action_SetVelocity.cpp CXX Action_Spam.cpp CXX Action_Strip.cpp CXX Action_Surf.cpp CXX Action_SymmetricRmsd.cpp CXX Action_Temperature.cpp CXX Action_Time.cpp CXX Action_Translate.cpp CXX Action_Unstrip.cpp CXX Action_Unwrap.cpp CXX Action_Vector.cpp CXX Action_VelocityAutoCorr.cpp CXX Action_Volmap.cpp CXX Action_Volume.cpp CXX Action_Watershell.cpp CXX Action_XtalSymm.cpp CXX AnalysisList.cpp CXX Analysis_AmdBias.cpp CXX Analysis_AutoCorr.cpp CXX Analysis_Average.cpp CXX Analysis_Clustering.cpp CXX Analysis_Corr.cpp 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 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 [-Wmaybe-uninitialized] 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 [-Wmaybe-uninitialized] 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 Analysis_Matrix.cpp CXX Analysis_MeltCurve.cpp CXX Analysis_Modes.cpp CXX Analysis_Multicurve.cpp CXX Analysis_MultiHist.cpp CXX Analysis_Overlap.cpp CXX Analysis_PhiPsi.cpp CXX Analysis_Regression.cpp CXX Analysis_RemLog.cpp CXX Analysis_Rms2d.cpp CXX Analysis_RmsAvgCorr.cpp CXX Analysis_Rotdif.cpp CXX Analysis_RunningAvg.cpp CXX Analysis_Slope.cpp CXX Analysis_Spline.cpp CXX Analysis_State.cpp CXX Analysis_Statistics.cpp CXX Analysis_TI.cpp CXX Analysis_Timecorr.cpp CXX Analysis_VectorMath.cpp CXX Analysis_Wavelet.cpp CXX ArgList.cpp CXX Array1D.cpp CXX AssociatedData.cpp CXX Atom.cpp CXX AtomMap.cpp CXX AtomMask.cpp CXX AxisType.cpp CXX BondSearch.cpp CXX Box.cpp CXX BoxArgs.cpp CXX BufferedFrame.cpp CXX BufferedLine.cpp CXX ByteRoutines.cpp CXX CharMask.cpp CXX CharmmParamFile.cpp CXX CIFfile.cpp CXX ClusterDist.cpp CXX ClusterList.cpp CXX ClusterMap.cpp CXX ClusterMatrix.cpp CXX ClusterNode.cpp CXX ClusterSieve.cpp CXX Cluster_DBSCAN.cpp CXX Cluster_DPeaks.cpp CXX Cluster_HierAgglo.cpp CXX Cluster_Kmeans.cpp CXX Cluster_ReadInfo.cpp CXX Cmd.cpp CXX CmdInput.cpp CXX CmdList.cpp CXX CompactFrameArray.cpp CXX ComplexArray.cpp CXX Constraints.cpp CXX ControlBlock_For.cpp CXX CoordinateInfo.cpp CXX Corr.cpp CXX Cph.cpp CXX CpptrajFile.cpp CXX CpptrajState.cpp CXX CpptrajStdio.cpp CXX CurveFit.cpp CXX DataFile.cpp CXX DataFileList.cpp CXX DataFilter.cpp CXX DataIO.cpp CXX DataIO_CCP4.cpp CXX DataIO_CharmmFastRep.cpp CXX DataIO_CharmmOutput.cpp CXX DataIO_CharmmRepLog.cpp CXX DataIO_CharmmRtfPrm.cpp CXX DataIO_Cmatrix.cpp CXX DataIO_Cpout.cpp CXX DataIO_Evecs.cpp CXX DataIO_Gnuplot.cpp CXX DataIO_Grace.cpp CXX DataIO_OpenDx.cpp CXX DataIO_Peaks.cpp CXX DataIO_Mdout.cpp CXX DataIO_NC_Cmatrix.cpp CXX DataIO_RemLog.cpp CXX DataIO_Std.cpp CXX DataIO_VecTraj.cpp CXX DataIO_Xplor.cpp CXX DataIO_XVG.cpp CXX DataSet.cpp CXX DataSetList.cpp CXX DataSet_1D.cpp CXX DataSet_3D.cpp CXX DataSet_Cmatrix.cpp CXX DataSet_Cmatrix_DISK.cpp CXX DataSet_Cmatrix_MEM.cpp CXX DataSet_Cmatrix_NOMEM.cpp CXX DataSet_Coords.cpp CXX DataSet_Coords_CRD.cpp CXX DataSet_Coords_REF.cpp CXX DataSet_Coords_TRJ.cpp CXX DataSet_GridDbl.cpp CXX DataSet_GridFlt.cpp CXX DataSet_Mat3x3.cpp CXX DataSet_MatrixDbl.cpp CXX DataSet_MatrixFlt.cpp CXX DataSet_Mesh.cpp CXX DataSet_Modes.cpp CXX DataSet_Parameters.cpp CXX DataSet_pH.cpp CXX DataSet_PHREMD_Explicit.cpp CXX DataSet_PHREMD_Implicit.cpp CXX DataSet_RemLog.cpp CXX DataSet_Topology.cpp CXX DataSet_Vector.cpp CXX DataSet_Vector_Scalar.cpp CXX DataSet_double.cpp CXX DataSet_float.cpp CXX DataSet_integer_disk.cpp CXX DataSet_integer_mem.cpp CXX DataSet_string.cpp CXX DataSet_StringVar.cpp CXX DataSet_Tensor.cpp CXX DataSet_unsignedInt.cpp CXX Deprecated.cpp CXX DihedralSearch.cpp CXX DistRoutines.cpp CXX Energy.cpp CXX EnergyArray.cpp CXX EnsembleIn.cpp CXX EnsembleIn_Multi.cpp CXX EnsembleIn_Single.cpp CXX EnsembleNavigator.cpp CXX EnsembleOut.cpp CXX EnsembleOut_Multi.cpp CXX EnsembleOut_Single.cpp CXX EnsembleOutList.cpp CXX Ewald.cpp CXX Ewald_ParticleMesh.cpp CXX Ewald_Regular.cpp In file included from Ewald_ParticleMesh.h:5, from Ewald_ParticleMesh.cpp:4: helpme_standalone.h:2323: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2323 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:2343: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2343 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3014: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3014 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3120: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3120 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3247: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3247 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3701: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3701 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3739: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3739 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3802: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3802 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3840: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3840 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4044: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4044 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4052: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4052 | #pragma omp for helpme_standalone.h:4097: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4097 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4145: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4145 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4172: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4172 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4224: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4224 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4228: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4228 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4275: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4275 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4388: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4388 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4419: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4503: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4503 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4510: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4510 | #pragma omp for CXX ExclusionArray.cpp CXX Exec_AddMissingRes.cpp CXX Exec_Analyze.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'} [-Wsign-compare] 1010 | for (int val = 0; val < nRows_; ++val) eigenPairs.push_back({eigenValues[val][0], unsortedEigenVectors[val]}); | ~~~~^~~~~~~~ helpme_standalone.h:1013:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 1013 | for (int val = 0; val < nRows_; ++val) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::PMEInstance >::sanityChecks(int, const RealMat&, const RealMat&, int) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5018:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 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' [-Wsign-compare] 3198 | if (parameters.nCols() != (nCartesian(parameterAngMom) - cartesianOffset)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::PMEInstance >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5019:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 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' [-Wsign-compare] 3746 | for (size_t row = threadID; row < gridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~ helpme_standalone.h:3753:37: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3753 | for (int atom = 0; atom < nAtoms; ++atom) { | ~~~~~^~~~~~~~ helpme_standalone.h:3761:61: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3761 | if (cGridIterator.size() && thisAtomsThread == threadID) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~ helpme_standalone.h:3750:25: warning: unused variable 'gridIteratorC' [-Wunused-variable] 3750 | const auto &gridIteratorC = threadedGridIteratorC_[threadID]; | ^~~~~~~~~~~~~ helpme_standalone.h:3794:55: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3794 | for (int atom = splineCache_.size(); atom < newSize; ++atom) | ~~~~~^~~~~~~~~ helpme_standalone.h:3810:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3810 | for (size_t cRow = threadID; cRow < gridDimensionC_; cRow += nThreads_) { | ~~~~~^~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'Real* helpme::PMEInstance >::spreadParameters(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5020:25: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 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' [-Wsign-compare] 3708 | for (size_t row = threadID; row < myGridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'helpme::PMEInstance >::Complex* helpme::PMEInstance >::forwardTransform(Real*) [with Real = double; typename std::enable_if::value, int>::type = 0; Complex = std::complex]': helpme_standalone.h:5023:32: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 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 [-Wunused-but-set-variable] 4004 | Real *__restrict__ realCBA; | ^~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::Matrix::assertSymmetric(const Real&) const [with Real = double]': helpme_standalone.h:1000:9: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 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'} [-Wsign-compare] 796 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::JacobiCyclicDiagonalization(Real*, Real*, const Real*, int) [with Real = double]': helpme_standalone.h:1006:42: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 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 [-Wunused-but-set-variable] 213 | Real sin_2phi, cos_2phi, cot_2phi; | ^~~~~~~~ helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::applyOperation(const std::function&) const [with Real = double]': helpme_standalone.h:785:26: required from 'helpme::Matrix helpme::Matrix::inverse() const [with Real = double]' 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'} [-Wsign-compare] 824 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::BSpline::update(short int, Real, short int, short int) [with Real = double]': helpme_standalone.h:3829:47: required from 'void helpme::PMEInstance >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 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' [-Wsign-compare] 2208 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:2208:72: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2208 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~ CXX Exec_Calc.cpp helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::multiply(const helpme::Matrix&) const [with Real = double]': helpme_standalone.h:877:64: required from 'helpme::Matrix helpme::Matrix::operator*(const helpme::Matrix&) const [with Real = double]' 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'} [-Wsign-compare] 860 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h:862:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 862 | for (int col = 0; col < other.nCols_; ++col) { | ~~~~^~~~~~~~~~~~~~ helpme_standalone.h:863:41: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 863 | for (int link = 0; link < nCols_; ++link) { | ~~~~~^~~~~~~~ CXX Exec_CatCrd.cpp CXX Exec_Change.cpp CXX Exec_ClusterMap.cpp 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 CXX Exec_Emin.cpp CXX Exec_Flatten.cpp CXX Exec_GenerateAmberRst.cpp CXX Exec_Graft.cpp CXX Exec_Help.cpp CXX Exec_LoadCrd.cpp CXX Exec_LoadTraj.cpp CXX Exec_ParallelAnalysis.cpp CXX Exec_ParmBox.cpp 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 [-Wmaybe-uninitialized] 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 [-Wmaybe-uninitialized] 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 [-Wmaybe-uninitialized] 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 [-Wmaybe-uninitialized] 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 [-Wmaybe-uninitialized] 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 [-Wmaybe-uninitialized] 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 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 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 [-Wmaybe-uninitialized] 5031 | return energy; | ^~~~~~ helpme_standalone.h:5021:14: note: 'energy' was declared here 5021 | Real energy; | ^~~~~~ CXX Exec_ReadData.cpp CXX Exec_ReadEnsembleData.cpp CXX Exec_ReadInput.cpp CXX Exec_RotateDihedral.cpp CXX Exec_RunAnalysis.cpp CXX Exec_ScaleDihedralK.cpp CXX Exec_Set.cpp CXX Exec_SequenceAlign.cpp CXX Exec_Show.cpp CXX Exec_SortEnsembleData.cpp CXX Exec_SplitCoords.cpp CXX Exec_System.cpp CXX Exec_Top.cpp CXX Exec_Traj.cpp CXX Exec_UpdateParameters.cpp CXX Exec_ViewRst.cpp CXX File_TempName.cpp CXX FileIO_Bzip2.cpp CXX FileIO_Gzip.cpp CXX FileIO_Mpi.cpp CXX FileIO_MpiShared.cpp CXX FileIO_Std.cpp CXX FileName.cpp CXX FileType.cpp CXX FileTypes.cpp CXX ForLoop.cpp CXX ForLoop_dataSetBlocks.cpp CXX ForLoop_integer.cpp CXX ForLoop_list.cpp CXX ForLoop_mask.cpp CXX ForLoop_overSets.cpp CXX Frame.cpp CXX GridAction.cpp CXX HistBin.cpp CXX Hungarian.cpp CXX ImageRoutines.cpp CXX Image_List_Mask.cpp CXX Image_List_Pair.cpp CXX Image_List_Unit.cpp CXX InputTrajCommon.cpp CXX KDE.cpp CXX MapAtom.cpp CXX MaskArray.cpp CXX MaskToken.cpp CXX Matrix_3x3.cpp CXX MdOpts.cpp CXX MetaData.cpp CXX Minimize_SteepestDescent.cpp CXX Mol.cpp CXX Mol2File.cpp CXX NameType.cpp CXX NC_Cmatrix.cpp CXX NC_Routines.cpp CXX NetcdfFile.cpp CXX OMM_helpers.cpp CXX OutputTrajCommon.cpp CXX ParameterSet.cpp CXX PDBfile.cpp CXX PairList.cpp CXX Parallel.cpp CXX ParallelNetcdf.cpp CXX ParmFile.cpp CXX Parm_Amber.cpp CXX Parm_CharmmPsf.cpp CXX Parm_CIF.cpp CXX Parm_Gromacs.cpp CXX Parm_Mol2.cpp CXX Parm_PDB.cpp CXX Parm_SDF.cpp CXX Parm_Tinker.cpp CXX PotentialFunction.cpp CXX PotentialTerm.cpp CXX PotentialTerm_Angle.cpp CXX PotentialTerm_Bond.cpp CXX PotentialTerm_Dihedral.cpp CXX PotentialTerm_LJ_Coulomb.cpp CXX PotentialTerm_OpenMM.cpp CXX ProgressBar.cpp CXX ProgressTimer.cpp CXX PubFFT.cpp CXX ExternalFxn.cpp CXX Random.cpp CXX Range.cpp CXX RNG.cpp CXX RNG_Marsaglia.cpp CXX RNG_MersenneTwister.cpp CXX RNG_PCG32.cpp CXX RNG_Stdlib.cpp CXX RNG_Xoshiro128pp.cpp CXX RPNcalc.cpp CXX ReferenceAction.cpp CXX RemdReservoirNC.cpp CXX Residue.cpp CXX SDFfile.cpp CXX SimplexMin.cpp CXX Spline.cpp CXX SplineFxnTable.cpp CXX StringRoutines.cpp CXX StructureCheck.cpp CXX StructureMapper.cpp CXX SymmetricRmsdCalc.cpp CXX TextFormat.cpp CXX Timer.cpp CXX TinkerFile.cpp CXX TopInfo.cpp CXX Topology.cpp CXX TorsionRoutines.cpp CXX Traj_AmberCoord.cpp CXX Traj_AmberNetcdf.cpp CXX Traj_AmberRestart.cpp CXX Traj_AmberRestartNC.cpp CXX Traj_Binpos.cpp CXX Traj_CharmmCor.cpp CXX Traj_CharmmDcd.cpp CXX Traj_CharmmRestart.cpp CXX Traj_CIF.cpp CXX Traj_Conflib.cpp CXX Traj_DTR.cpp CXX Traj_GmxDump.cpp CXX Traj_GmxTng.cpp CXX Traj_GmxTrX.cpp CXX Traj_GmxXtc.cpp CXX Traj_Gro.cpp CXX Traj_Mol2File.cpp CXX Traj_NcEnsemble.cpp CXX Traj_PDBfile.cpp CXX Traj_SDF.cpp CXX Traj_SQM.cpp CXX Traj_Tinker.cpp CXX Traj_XYZ.cpp CXX TrajectoryFile.cpp CXX TrajectoryIO.cpp CXX TrajFrameCounter.cpp CXX TrajinList.cpp CXX Trajin_Multi.cpp CXX Trajin_Single.cpp CXX TrajIOarray.cpp CXX Trajout_Single.cpp CXX TrajoutList.cpp CXX Vec3.cpp CXX ViewRst.cpp CXX xoshiro128plusplus.cpp xoshiro128plusplus.cpp: In function 'void jump()': xoshiro128plusplus.cpp:60:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 60 | for(int i = 0; i < sizeof JUMP / sizeof *JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ xoshiro128plusplus.cpp: In function 'void long_jump()': xoshiro128plusplus.cpp:90:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 90 | for(int i = 0; i < sizeof LONG_JUMP / sizeof *LONG_JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CXX Action_Esander.cpp CXX Command.cpp CXX Cpptraj.cpp CXX Energy_Sander.cpp CXX ReadLine.cpp CXX main.cpp CC molsurf.c Skipping bundled READLINE build cd xdrfile && make all make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' CC xdrfile.c Skipping bundled ARPACK build cd tng && make all make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' CC md5.c CC xdr_seek.c CC xdrfile_trr.c CC tng_io.c CC xdrfile_xtc.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 /bin/rm -f libxdrfile.a CC bwt.c ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' CC mtf.c CC rle.c CC lz77.c CC dict.c CC huffman.c CC merge_sort.c tng_io.c: In function 'tng_gen_data_block_add': tng_io.c:12600:9: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tng_io.c:12600:47: note: length computed here 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ /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 '/build/reproducible-path/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 "/build/reproducible-path/cpptraj-5.1.0+dfsg/bin" make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_auto_test -- check unittest make -j12 test "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 check unittest make[2]: Entering directory '/build/reproducible-path/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 '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList CPPTRAJ: ArgList class unit test. CPPTRAJ: NameType class unit test. make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' g++ -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' g++ -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/build/reproducible-path/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=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o ArgList.o /build/reproducible-path/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=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o NameType.o /build/reproducible-path/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=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/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=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/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=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o StringRoutines.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/StringRoutines.cpp -rwxr-xr-x 1 pbuilder1 pbuilder1 183492256 Mar 21 19:01 ../bin/cpptraj make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' -rwxr-xr-x 1 pbuilder1 pbuilder1 183492256 Mar 21 19:01 ../bin/cpptraj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RemdTraj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj CPPTRAJ: Broken Traj: Running good trajectory. CPPTRAJ: CRD Replica Trajectory Run with offset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_General ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TrajinOffset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Strip CPPTRAJ: One frame strip command test CPPTRAJ: Normal trajectory read with offsets. CPPTRAJ: General tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_trajout_framerange CPPTRAJ: Broken Traj: Running broken trajectory. CPPTRAJ: CRD Replica Trajectory Run CPPTRAJ: Trajout Frame Range [Amber Restart] ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD CPPTRAJ: Gzipped trajectory read with offsets CPPTRAJ: Per-Residue RMSD Test. CPPTRAJ: Unstrip (Lig/Rec/Complex) command test CPPTRAJ: NetCDF Replica Trajectory Run test CPPTRAJ: Per-Residue RMSD Test with averaging CPPTRAJ: Bzip2ed trajectory read with offsets CPPTRAJ: Trajout Frame Range [Amber Coordinates] CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj CPPTRAJ: Compressed broken trajectory test All 6 comparisons passed. CPPTRAJ: Start argument offset CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj All 4 comparisons passed. CPPTRAJ: Per-Residue RMSD Test with residue centering. CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DSSP CPPTRAJ: Multi frame strip command test. CPPTRAJ: Secstruct (DSSP) command test. CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Center All 2 comparisons passed. All 3 comparisons passed. CPPTRAJ: Center command test. CPPTRAJ: Strip topology with PDB info ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hbond CPPTRAJ: CRD Replica Trajectory Run with remdout CPPTRAJ: Solute Hbond test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NCrestart CPPTRAJ: NetCDF Restart Test - TXT->NetCDF All 11 comparisons passed. CPPTRAJ: NetCDF Restart Test - NetCDF->TXT CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Image CPPTRAJ: Orthorhombic imaged distance test. All 8 comparisons passed. CPPTRAJ: Center origin command test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf CPPTRAJ: Surface calculation test CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radgyr CPPTRAJ: Non-orthorhombic imaged distance test. CPPTRAJ: Radius of gyration command test CPPTRAJ: Solute Hbond test with disk caching CPPTRAJ: Center origin mass command test. CPPTRAJ: Secstruct (DSSP) command with changing number of residues. CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt CPPTRAJ: Orthorhombic coordinate imaging test All 15 comparisons passed. CPPTRAJ: Solute-solvent hbond test CPPTRAJ: Center reference command test. All 2 comparisons passed. CPPTRAJ: Secstruct (DSSP): SS assign output test All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Parallel CPPTRAJ: Parallel tests. CPPTRAJ: Center point test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Jcoupling CPPTRAJ: FtuFabI Assignment test CPPTRAJ: J-Coupling single frame test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mask CPPTRAJ: Mask single frame test CPPTRAJ: Nonorthorhombic coordinate imaging test CPPTRAJ: Hbond, no intramolecular hydrogen bonds test J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. Skipped test: J-Coupling extended test All 1 comparisons passed. 1 comparisons skipped. All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diffusion CPPTRAJ: Diffusion test, no imaging. All 10 comparisons passed. CPPTRAJ: Mask longer command test. CPPTRAJ: Parallel test with trajectory offset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj CPPTRAJ: Hbond, specified solute masks CPPTRAJ: RMSD Test with outtraj. CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm CPPTRAJ: CHARMM PSF/DCD test All 5 comparisons passed. CPPTRAJ: Diffusion test, old syntax. CPPTRAJ: Partial Surface calculation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotdif CPPTRAJ: Rotational diffusion calculation test CPPTRAJ: Hbond, no angle cutoff test CPPTRAJ: CHARMM DCD Write, step 1. CPPTRAJ: Hbond, Bridge nointramol test CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM CPPTRAJ: CHARMM DCD Write, step 2. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj CPPTRAJ: Diffusion test, new syntax. CPPTRAJ: Convert mdcrd -> NetCDF g++ -o a.out main.o NameType.o CpptrajStdio.o CPPTRAJ: CHAMBER topology read/strip test. All 7 comparisons passed. All 6 comparisons passed. All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RMSD CPPTRAJ: Read CHARMM restart CPPTRAJ: Basic RMSD tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Runavg CPPTRAJ: Coordinate Running Average test. CPPTRAJ: Diffusion test, nonorthogonal box CPPTRAJ: Convert NetCDF -> mdcrd ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_2DRMS CPPTRAJ: 2D RMSD Test. CPPTRAJ: CHARMM PSF write CPPTRAJ: Outtraj Test with maxmin. CPPTRAJ: Coordinate Running Average Traj Write make[5]: Leaving directory '/build/reproducible-path/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: LCPO test with GAFF atom types CPPTRAJ: CHARMM COORdinates test CPPTRAJ: STFC Diffusion Test All 4 comparisons passed. All 2 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mol2 CPPTRAJ: 2D RMSD Test, mass-weighted. CPPTRAJ: Mol2 Parm/Traj Read/Write Test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct CPPTRAJ: RMS coordinate rotation/rotation matrices test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Average All 6 comparisons passed. CPPTRAJ: Average Test. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pucker CPPTRAJ: STFC Diffusion Test with individual distances CPPTRAJ: NAstruct command test. CPPTRAJ: Pucker command test CPPTRAJ: Hbond with imaging CPPTRAJ: 2D RMSD Test with reference trajectory CPPTRAJ: PDB => Mol2 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CharmmParams CPPTRAJ: Test updating topology with Charmm parameters (single residue) CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomMap CPPTRAJ: Hbond, orthogonal imaging CPPTRAJ: STFC Diffusion Test with COM CPPTRAJ: AtomMap Test CPPTRAJ: Amber Top/Rst => Mol2 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Datafile CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. CPPTRAJ: Data file output precision test CPPTRAJ: RMS fit with no coordinates modification test. Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. Skipped test: Amber Top/Rst => Mol2, SYBYL atom types All 4 comparisons passed. 1 comparisons skipped. All 2 comparisons passed. CPPTRAJ: 2D DME Test. CPPTRAJ: STFC Diffusion Test with second mask CPPTRAJ: Standard -> Grace Data All 23 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial CPPTRAJ: Radial test, non-orthogonal imaging ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest CPPTRAJ: Closest command test using first solvent atom. CPPTRAJ: AtomMap with 'rmsfit' CPPTRAJ: NAstruct command test, single strand ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DRMSD CPPTRAJ: 1D/2D Histogram Analysis test CPPTRAJ: Grace -> Standard Data CPPTRAJ: Distance RMSD test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster CPPTRAJ: Cluster command test, in-memory pairwise distances. CPPTRAJ: 2D RMSD with reference mask test. CPPTRAJ: Atom map charmm->amber atom order CPPTRAJ: RMS fit to previous test CPPTRAJ: X column format/precision test. All 11 comparisons passed. CPPTRAJ: Atom map charmm->amber atom order, by residue All 1 comparisons passed. CPPTRAJ: 2D RMSD test, no fitting. CPPTRAJ: Data file group by name test CPPTRAJ: Closest command test using all solvent atoms. All 9 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct_8OG CPPTRAJ: NA test (8OG) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_IRED CPPTRAJ: IRED vector/matrix test CPPTRAJ: Data file group by aspect test CPPTRAJ: RMS: imaging after unit cell rotation CPPTRAJ: randomizeions test (original algorithm) CPPTRAJ: 3D histogram test. All 6 comparisons passed. All 3 comparisons passed. CPPTRAJ: Cluster command test, read pairwise distances. All 12 comparisons passed. All 6 comparisons passed. CPPTRAJ: Closest command test, using mask center ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Molsurf CPPTRAJ: Molsurf test All 7 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Corr CPPTRAJ: Correlation test All 16 comparisons passed. CPPTRAJ: Cluster command test, read NetCDF pairwise distances. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Contacts CPPTRAJ: Contacts test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckStructure CPPTRAJ: Closest command test, using mask center and solvent mask CPPTRAJ: Structure Check ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RmsAvgCorr CPPTRAJ: RmsAvgCorr Reference ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Principal CPPTRAJ: Principal Test CPPTRAJ: Closest command test, solvent mask, water oxygen only All 2 comparisons passed. CPPTRAJ: Structure Check with Around and Skip CPPTRAJ: Cluster command test, write ASCII pairwise distances. All 3 comparisons passed. CPPTRAJ: Radial test, orthogonal and no imaging ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ClusterDihedral CPPTRAJ: clusterdihedral test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Vector CPPTRAJ: RmsAvgCorr First CPPTRAJ: Basic vector tests CPPTRAJ: Cluster command test, read ASCII pairwise distances. All 1 comparisons passed. All 9 comparisons passed. g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o All 4 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Matrix CPPTRAJ: Matrix Tests All 9 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve CPPTRAJ: Cluster, nosieve ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Unwrap ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Grid CPPTRAJ: Unwrap non-orthogonal test CPPTRAJ: Dipole test CPPTRAJ: Structure Check with PBC ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Project CPPTRAJ: Projection CPPTRAJ: Cluster, sieve5 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes CPPTRAJ: Modes analysis, RMS fluctuations CPPTRAJ: Test vector center with magnitude CPPTRAJ: Grid test CPPTRAJ: Unwrap orthogonal test All 1 comparisons passed. CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. All 8 comparisons passed. make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Watershell CPPTRAJ: Watershell Test, non-orthorhombic imaging. CPPTRAJ: Modes analysis, displacements Unit test passed. make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' All 2 comparisons passed. CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. CPPTRAJ: Cluster, nosieve savepairdist CPPTRAJ: OpenDX Grid read test CPPTRAJ: Momentum/velocity vector test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AnalysisRunAvg CPPTRAJ: Generate matrix with trajectory start/stop/offset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volmap ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SPAM CPPTRAJ: VMD VolMap Algorithm test CPPTRAJ: Analysis Running Average CPPTRAJ: SPAM Test CPPTRAJ: Modes analysis, dipole correlation CPPTRAJ: Generate matrix with action stop/start/offset CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. CPPTRAJ: Cluster, nosieve loadpairdist CPPTRAJ: Grid with specified center test. CPPTRAJ: Force vector test. All 2 comparisons passed. All 15 comparisons passed. All 14 comparisons passed. CPPTRAJ: Cluster, sieve5 savepairdist CPPTRAJ: Atomicfluct test with ADP output VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. Skipped test: VMD VolMap Algorithm longer tests All 2 comparisons passed. 1 comparisons skipped. CPPTRAJ: Randomize (around, overlap) CPPTRAJ: Grid with box center offset test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LIE CPPTRAJ: LIE test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Density CPPTRAJ: Modes analysis, pseudo trajectory creation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidOrder CPPTRAJ: Lipid Order Parameter Test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PairDist CPPTRAJ: Density along axis tests CPPTRAJ: Grid with mask center offset test. CPPTRAJ: PairDist Test. CPPTRAJ: Structure Check with Around CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. CPPTRAJ: Non-orthogonal grid test. CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test CPPTRAJ: Cluster, sieve5 loadpairdist CPPTRAJ: Multi-frame density along axis test CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test All 13 comparisons passed. All 6 comparisons passed. CPPTRAJ: Pairdist test, orthogonal imaging. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReadData All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST CPPTRAJ: Grid generation from 'bounds' test. CPPTRAJ: Cluster, nosieve pairwisecache none CPPTRAJ: GIST water-water interaction test CPPTRAJ: Read vector data test (no origins, origins) CPPTRAJ: Total system density test CPPTRAJ: Randomize (around) All 6 comparisons passed. All 13 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_systemVF CPPTRAJ: Read vector data set (origins, no origins) CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test All 7 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidSCD CPPTRAJ: Read Amber output test CPPTRAJ: Basic lipid order parameter test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicCorr CPPTRAJ: Atomic Correlation test All 1 comparisons passed. CPPTRAJ: Read CHARMM output test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr CPPTRAJ: AutoCorr test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Box CPPTRAJ: Box Test (Add box info) CPPTRAJ: Cluster, sieve5 pairwisecache none All 1 comparisons passed. CPPTRAJ: 3D data read/write test CPPTRAJ: New Lipid Order Parameter Test, DOPC. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomTypeSelect All 1 comparisons passed. CPPTRAJ: Selection by atom type test. CPPTRAJ: Standard 3D data write test CPPTRAJ: Box test (remove box info) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AvgRef CPPTRAJ: RMSD Test with averaged reference coordinates. CPPTRAJ: Standard 3D data read test CPPTRAJ: Box test (Modify box length) All 1 comparisons passed. CPPTRAJ: Randomize (overlap) All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Crank_Stat All 4 comparisons passed. CPPTRAJ: Crankshaft test CPPTRAJ: Cluster, random CPPTRAJ: Pairdist test, nonorthogonal imaging. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateCrd CPPTRAJ: COORDS data set creation and CRDFLUCT test. CPPTRAJ: Standard 3D data read/append test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoImage CPPTRAJ: AutoImage test (split DNA duplex) All 3 comparisons passed. CPPTRAJ: Box test (auto orthogonal box, no radii) CPPTRAJ: COORDS data set creation with velocities test CPPTRAJ: Randomize (no restrictions) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LoadCrd CPPTRAJ: LoadCrd test. CPPTRAJ: Standard 3D data, sparse CPPTRAJ: Box test (auto orthogonal box, VDW radii) CPPTRAJ: LoadTraj test. All 5 comparisons passed. All 28 comparisons passed. All 1 comparisons passed. All 7 comparisons passed. CPPTRAJ: Nonorthogonal grid standard write/read tests. CPPTRAJ: Watershell Test, orthorhombic imaging. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Lifetime ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MultiVector CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). CPPTRAJ: Multivector test CPPTRAJ: Lifetime test. CPPTRAJ: AutoImage test, use anchor mask ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FFT CPPTRAJ: LoadTraj from trajin test. CPPTRAJ: FFT test. CPPTRAJ: TRAJ data set creation and CRDFLUCT test. All 1 comparisons passed. All 2 comparisons passed. CPPTRAJ: LoadCrd append from multiple files test CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). CPPTRAJ: TRAJ data set creation with velocities test. CPPTRAJ: Lifetime test with data set caching. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CrossCorr CPPTRAJ: CrossCorr test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Timecorr All 4 comparisons passed. CPPTRAJ: Timecorr test. All 5 comparisons passed. CPPTRAJ: Lifetime average and cumulative average test. CPPTRAJ: COORDS data set append test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multidihedral CPPTRAJ: Multidihedral test All 1 comparisons passed. All 12 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SymmRmsd CPPTRAJ: SymmRmsd CPPTRAJ: COORDS test storing frame metadata All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MakeStructure All 7 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ensemble_MREMD CPPTRAJ: M-REMD sort test. CPPTRAJ: Basic makestructure test CPPTRAJ: Multidihedral Nucleotide CHI test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet CPPTRAJ: ASP symmetry-corrected RMSD test CPPTRAJ: Clustering, One DataSet CPPTRAJ: Makestructure test with reference. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotate CPPTRAJ: Rotation (and inverse) of coords from matrices CPPTRAJ: Pairdist test, 2 masks. CPPTRAJ: Watershell Test, no imaging. CPPTRAJ: Multidihedral protein dihedrals test CPPTRAJ: TRAJ test storing frame metadata All 5 comparisons passed. CPPTRAJ: M-REMD actions test. CPPTRAJ: Multidihedral cyclic molecule test CPPTRAJ: GLU symmetry-corrected RMSD test All 4 comparisons passed. CPPTRAJ: Clustering, Two DataSets CPPTRAJ: Rotate with defined axis ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Integrate CPPTRAJ: Integration test. All 6 comparisons passed. CPPTRAJ: TYR symmetry-corrected RMSD test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts All 3 comparisons passed. CPPTRAJ: NativeContacts test. CPPTRAJ: Clustering, dihedral DataSet All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckChiral CPPTRAJ: Check chirality test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LESsplit CPPTRAJ: LES split/average test CPPTRAJ: Clustering, two dihedral DataSets CPPTRAJ: M-REMD ensemble outtraj test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Energy CPPTRAJ: Simple energy tests CPPTRAJ: Longer symmetry-corrected RMSD test. All 2 comparisons passed. All 1 comparisons passed. All 3 comparisons passed. All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CCP4 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihCovar CPPTRAJ: Dihedral Covariance Matrix Test CPPTRAJ: Clustering, dihedral DataSet, K-means CPPTRAJ: CCP4 read/write and DX conversion test. CPPTRAJ: M-REMD no sort, running average test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PermuteDihedrals CPPTRAJ: PermuteDihedrals interval -120, phi psi ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CurveFit CPPTRAJ: M-REMD, generate RMS data CPPTRAJ: PermuteDihedrals, random rotations CPPTRAJ: Curve fitting test. CPPTRAJ: Read specific columns test. All 2 comparisons passed. All 2 comparisons passed. CPPTRAJ: Clustering, two dihedral DataSets, K-means ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetAverage CPPTRAJ: Data set averaging and averaging over all sets test. CPPTRAJ: M-REMD, meltcurve analysis CPPTRAJ: Test kinetic energy calculation All 3 comparisons passed. CPPTRAJ: Curve fitting multi-exponential tests. CPPTRAJ: Write non-square matrix All 17 comparisons passed. All 2 comparisons passed. All 4 comparisons passed. All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Spline ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VectorMath CPPTRAJ: Vector dot/cross product test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Temperature ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN CPPTRAJ: Spline test CPPTRAJ: DBSCAN test CPPTRAJ: Temperature test. ******************************************************************************** TEST: /build/reproducible-path/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) CPPTRAJ: Read non-square matrix ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_KDE CPPTRAJ: KDE test. CPPTRAJ: Test total energy calculation ******************************************************************************** TEST: /build/reproducible-path/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) CPPTRAJ: Curve fitting, custom output range. All 1 comparisons passed. CPPTRAJ: Read square matrix CPPTRAJ: Test partial energy calculation All 2 comparisons passed. CPPTRAJ: DBSCAN automatic parameter determination test. All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Wavelet ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CIF CPPTRAJ: CIF read test All 15 comparisons passed. CPPTRAJ: Wavelet analysis test CPPTRAJ: NativeContacts test, save non-native contacts, residue time series CPPTRAJ: Temperature with SHAKE on hydrogens. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multicurve CPPTRAJ: Multicurve test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PDB ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Align CPPTRAJ: PDB format read/write test CPPTRAJ: KDE with Kullback-Leibler divergence test CPPTRAJ: Temperature with SHAKE on all atoms. CPPTRAJ: DBSCAN kdist map test CPPTRAJ: Align Tests. All 1 comparisons passed. CPPTRAJ: Generate offset traj from PDB All 6 comparisons passed. CPPTRAJ: Wavelet WAFEX test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelocityAutoCorr CPPTRAJ: Velocity autocorrelation test CPPTRAJ: Generate offset traj from CIF CPPTRAJ: DBSCAN with sieve CPPTRAJ: Temperature calc with extra points. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelFrc All 4 comparisons passed. CPPTRAJ: Test combining coordinates, velocities, and forces. All 2 comparisons passed. CPPTRAJ: Test using velocities as coordinates. All 4 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RotateDihedral CPPTRAJ: Rotate dihedral to target value. CPPTRAJ: NativeContacts test, orthorhombic imaging. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remap CPPTRAJ: Remap Test CPPTRAJ: Test writing velocities (MDVEL) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans All 3 comparisons passed. All 5 comparisons passed. CPPTRAJ: PQR file write with various radii CPPTRAJ: Cpptraj Kmeans ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetCmd CPPTRAJ: Rotate dihedral by increment CPPTRAJ: Data Set commands test CPPTRAJ: Align, unit cell rotation/imaging test. All 1 comparisons passed. CPPTRAJ: Test using forces as coordinates. CPPTRAJ: Rotate dihedral in TRAJ data set ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CompareTop CPPTRAJ: Compare topology test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Filter CPPTRAJ: Basic filter test All 17 comparisons passed. CPPTRAJ: Cpptraj Kmeans random All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CombineCrd CPPTRAJ: Combine COORDS test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TopInfo CPPTRAJ: Test writing forces (MDFRC) CPPTRAJ: Topology info print test. All 1 comparisons passed. CPPTRAJ: PDB filter alternate atom location IDs test CPPTRAJ: Combine COORDS test with box info. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTrr All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ewald CPPTRAJ: Data filter test. CPPTRAJ: TRR force/velocity read -> NetCDF write test CPPTRAJ: Direct sum test All 10 comparisons passed. CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. CPPTRAJ: Adding PDB info to topology ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_SymmRMSD CPPTRAJ: Filter matrix test. CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TI CPPTRAJ: Split coords and recombine test. All 10 comparisons passed. CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. CPPTRAJ: TI analysis test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds CPPTRAJ: Fix imaged bonds test (Ortho.) CPPTRAJ: GIST test, orthogonal cell All 5 comparisons passed. All 5 comparisons passed. CPPTRAJ: Fix imaged bonds test (Non-ortho.) CPPTRAJ: TRR force/velocity read -> TRR write test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Distance CPPTRAJ: Distance tests All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volume CPPTRAJ: CRD => TRR CPPTRAJ: Volume tests All 5 comparisons passed. All 2 comparisons passed. CPPTRAJ: Topology info with reference coords test CPPTRAJ: Orthogonal imaged distance ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SetVelocity CPPTRAJ: TRR => CRD CPPTRAJ: Set Velocity test All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remlog ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AreaPerMol CPPTRAJ: Area per molecule test All 12 comparisons passed. All 5 comparisons passed. CPPTRAJ: Replica log read/analyze test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DistBasedMask CPPTRAJ: Distance-based atom mask tests (atom, residue) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Calc CPPTRAJ: Calc test CPPTRAJ: Ewald test (NaCl crystal) CPPTRAJ: Non-orthogonal imaged distance ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites CPPTRAJ: Cluster command test, coordinate writes. CPPTRAJ: Calc test with data sets CPPTRAJ: Scale velocity test CPPTRAJ: CRD(1-5) => TRR CPPTRAJ: Ewald test (trunc. oct) 1 out of 3 comparisons failed. All 3 comparisons passed. CPPTRAJ: Cluster command test, coordinate writes using info file. All 6 comparisons passed. All 7 comparisons passed. CPPTRAJ: Distance-based atom mask tests (molecule) CPPTRAJ: Test math functions ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CalcState ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateReservoir ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Change CPPTRAJ: Create RREMD NetCDF reservoir test CPPTRAJ: Calcstate test CPPTRAJ: Change atom and residue name tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixAtomOrder CPPTRAJ: CRD(6-10) => TRR CPPTRAJ: Out of order molecules test All 4 comparisons passed. All 8 comparisons passed. All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Dpeaks CPPTRAJ: Change chain ID test CPPTRAJ: Density peaks clustering test CPPTRAJ: TRR (appended) => CRD All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MinImage CPPTRAJ: Minimum Image test. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LowestCurve ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rst CPPTRAJ: LowestCurve test CPPTRAJ: Change chain ID of COORDS set test CPPTRAJ: Generate restraints (rst) test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Regress All 3 comparisons passed. CPPTRAJ: Linear regression test. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pairwise CPPTRAJ: Pairwise tests All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Nreps CPPTRAJ: Clustering with specified # reps All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ParmBox CPPTRAJ: Parmbox test All 6 comparisons passed. All 3 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Solvent CPPTRAJ: Test solvent command with closest All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Translate CPPTRAJ: Translate test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ScaleDihedralK CPPTRAJ: Pairwise test, partial system CPPTRAJ: Scale dihedral force constant test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PhiPsi CPPTRAJ: Phipsi test All 1 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReplicateCell CPPTRAJ: Replicate cell test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_InfraredSpec CPPTRAJ: Scale dihedral force constant with 'useall' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Control CPPTRAJ: Infrared spectrum calculation test CPPTRAJ: Loop tests All 1 comparisons passed. All 2 comparisons passed. All 1 comparisons passed. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cphstats All 10 comparisons passed. CPPTRAJ: Explicit pH REMD ensemble data read / sort CPPTRAJ: GMX: CRD with offset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CmdLine CPPTRAJ: Command line trajectory args test, part 1 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hausdorff All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CatCrd CPPTRAJ: Concatenate COORDS data set test CPPTRAJ: Simple Hausdorff distance test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XYZformat ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XtalSymm CPPTRAJ: XtalSymm Reference CPPTRAJ: XYZ format write All 1 comparisons passed. CPPTRAJ: Command line test trajectory args test, part 2 CPPTRAJ: Constant pH stats test CPPTRAJ: Hausdorff distance of 2D rms output test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Time CPPTRAJ: Add time to restart test CPPTRAJ: Ewald test (partial system, trunc. oct) CPPTRAJ: Test set command CPPTRAJ: GMX: TRR with offset CPPTRAJ: Atom XYZ format read, test 1 CPPTRAJ: Command line wildcard test, part 1 CPPTRAJ: Sorted implicit constant pH stats test CPPTRAJ: Remove time from restart test CPPTRAJ: Hausdorff distance of 2D rms output test. CPPTRAJ: Add time to trajectory test CPPTRAJ: Test reading comma-separated list of strings CPPTRAJ: Atom XYZ format read, test 2 CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats CPPTRAJ: Command line wildcard test, part 2 All 5 comparisons passed. 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. CPPTRAJ: Atom XYZ format read, test 3 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LibPME CPPTRAJ: Particle mesh Ewald test (NaCl crystal) All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc CPPTRAJ: Test nested loops and variables in loops CPPTRAJ: Atom XYZ format read, test 4 CPPTRAJ: XTC read test All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SplitCoords CPPTRAJ: Modify time info test. All 3 comparisons passed. CPPTRAJ: SplitCoords test CPPTRAJ: Unsorted pH read/write test CPPTRAJ: Atom XYZ format read, test 5 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihedralRMS CPPTRAJ: Particle mesh Ewald test (trunc. oct) CPPTRAJ: Test loop over data set blocks CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) CPPTRAJ: XtalSymm Reimaging by Atom ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Slope CPPTRAJ: Finite difference test. CPPTRAJ: Atom XYZ format read, test 6 All 16 comparisons passed. All 4 comparisons passed. CPPTRAJ: Test for filename wildcards and oversets All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diagmatrix CPPTRAJ: CRD => XTC CPPTRAJ: MW covariance matrix thermo analysis test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Emin CPPTRAJ: Basic energy minimization test. All 6 comparisons passed. All 1 comparisons passed. CPPTRAJ: Dihedral RMSD test (to previous) All 1 comparisons passed. CPPTRAJ: Energy minimization with angle term test. All 13 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Flatten ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau CPPTRAJ: Flatten test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Random ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Graft CPPTRAJ: Evalulate plateau test CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs CPPTRAJ: Graft test CPPTRAJ: Dihedral RMS fluctuation test. All 1 comparisons passed. All 5 comparisons passed. CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. All 1 comparisons passed. All 2 comparisons passed. CPPTRAJ: Particle mesh Ewald test (ortho) CPPTRAJ: PCG32 RNG test. CPPTRAJ: Energy minimization with nonbond term test. CPPTRAJ: XTC => CRD CPPTRAJ: Test Stdlib RNG CPPTRAJ: Test Mersenne Twister RNG All 4 comparisons passed. CPPTRAJ: CRD(1-5) => XTC CPPTRAJ: OpenMM basic energy minimization tests (bonds) CPPTRAJ: Particle mesh Ewald test (ortho, with mask) CPPTRAJ: OpenMM basic energy minimization tests (angles) CPPTRAJ: CRD(6-10) => XTC CPPTRAJ: PME test (partial system, trunc. oct) CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) CPPTRAJ: XTC (appended) => CRD 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. CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LJ_PME CPPTRAJ: LJ PME test. CPPTRAJ: GMX: CRD with offset CPPTRAJ: LJ PME kappa sweep test, 0.25 CPPTRAJ: GMX: XTC with offset CPPTRAJ: LJ PME kappa sweep test, 0.35 CPPTRAJ: LJ PME kappa sweep test, 0.45 All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTNG CPPTRAJ: TNG read test CPPTRAJ: LJ PME kappa sweep test, 0.5 CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) CPPTRAJ: GIST test, nonorthogonal cell CPPTRAJ: LJ with switch function test All 5 comparisons passed. CPPTRAJ: TNG read test (with offset) All 6 comparisons passed. CPPTRAJ: XtalSymm Reimaging by Molecule All 3 comparisons passed. All 9 comparisons passed. All 11 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/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: 614566 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 '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' /usr/bin/make -C test summary make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' -rwxr-xr-x 1 pbuilder1 pbuilder1 183492256 Mar 21 19:01 ../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 '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[1]: *** [debian/rules:17: override_dh_auto_test] Error 2 make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' make: *** [debian/rules:10: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/548104 and its subdirectories Sun Feb 16 12:39:09 UTC 2025 W: No second build log, what happened?