I: pbuilder: network access will be disabled during build I: Current time: Sat Apr 4 00:46:34 -12 2026 I: pbuilder-time-stamp: 1775306794 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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/210217/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='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='50c7ec62cbb74d848ecfaac478d1549c' 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='210217' 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.iuv2TXNs/pbuilderrc_VVEr --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.iuv2TXNs/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/bin/systemd-run' 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/210217/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 ... 19892 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 unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-3 [862 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.2-1 [55.9 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-3 [539 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 25 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [630 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-17 [361 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libgfortran-14-dev arm64 14.2.0-17 [418 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 gfortran-14-aarch64-linux-gnu arm64 14.2.0-17 [9794 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 gfortran-14 arm64 14.2.0-17 [14.0 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 gfortran-aarch64-linux-gnu arm64 4:14.2.0-1 [1284 B] Get: 39 http://deb.debian.org/debian unstable/main arm64 gfortran arm64 4:14.2.0-1 [1424 B] Get: 40 http://deb.debian.org/debian unstable/main arm64 hdf5-helpers arm64 1.14.5+repack-3 [26.6 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 icu-devtools arm64 72.1-6 [196 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 45 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-4 [56.9 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-4 [41.0 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-4 [41.0 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-4 [53.1 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-4 [126 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B] Get: 54 http://deb.debian.org/debian unstable/main arm64 libaec-dev arm64 1.1.3-1+b1 [20.2 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.1-2 [104 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libarpack2t64 arm64 3.9.1-4 [83.7 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libblas-dev arm64 3.12.1-2 [111 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 liblapack-dev arm64 3.12.1-2 [3726 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libarpack2-dev arm64 3.9.1-4 [102 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b7 [308 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.7-1 [21.2 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.8.0-1 [63.2 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.11.0-1 [121 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.11.0-1 [28.2 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.12.1-3 [336 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.22.0-1+b1 [553 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.9-2 [452 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.9-2 [452 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.5-3 [208 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.20.0-2 [96.7 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10.1-1 [1325 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.9-2 [1419 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-4 [15.9 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.6.9+dfsg-1 [305 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libnghttp3-dev arm64 1.8.0-1 [89.4 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.11.0-1 [33.9 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libngtcp2-dev arm64 1.11.0-1 [174 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.4.1-1 [3232 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.6+dfsg-2 [329 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libcurl4-gnutls-dev arm64 8.12.1-3 [465 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.12.1-3 [339 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libfftw3-double3 arm64 3.3.10-2+b1 [337 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libfftw3-long3 arm64 3.3.10-2+b1 [546 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libfftw3-single3 arm64 3.3.10-2+b1 [517 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libfftw3-bin arm64 3.3.10-2+b1 [44.3 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libfftw3-dev arm64 3.3.10-2+b1 [1280 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libhdf5-310 arm64 1.14.5+repack-3 [1155 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libhdf5-cpp-310 arm64 1.14.5+repack-3 [121 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libhdf5-fortran-310 arm64 1.14.5+repack-3 [110 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [66.1 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-fortran-310 arm64 1.14.5+repack-3 [42.1 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-cpp-310 arm64 1.14.5+repack-3 [24.4 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3.1 [173 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-3.1 [293 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libjpeg-dev arm64 1:2.1.5-3.1 [72.0 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libhdf5-dev arm64 1.14.5+repack-3 [3225 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libicu-dev arm64 72.1-6 [10.3 MB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libncurses6 arm64 6.5+20250216-1 [96.1 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libncurses-dev arm64 6.5+20250216-1 [341 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libnetcdf22 arm64 1:4.9.3-1 [481 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libxml2-dev arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [751 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libnetcdf-dev arm64 1:4.9.3-1 [116 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libopenmm8.1 arm64 8.1.2+dfsg-4+b1 [922 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libopenmm-dev arm64 8.1.2+dfsg-4+b1 [330 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libreadline-dev arm64 8.2-6 [155 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 netcdf-bin arm64 1:4.9.3-1 [245 kB] Fetched 76.0 MB in 1s (111 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 ... 19892 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_2.40.4-5_arm64.deb ... Unpacking bsdextrautils (2.40.4-5) ... 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+b2_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... 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_14.2.0-17_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-17) ... Selecting previously unselected package libgfortran-14-dev:arm64. Preparing to unpack .../034-libgfortran-14-dev_14.2.0-17_arm64.deb ... Unpacking libgfortran-14-dev:arm64 (14.2.0-17) ... Selecting previously unselected package gfortran-14-aarch64-linux-gnu. Preparing to unpack .../035-gfortran-14-aarch64-linux-gnu_14.2.0-17_arm64.deb ... Unpacking gfortran-14-aarch64-linux-gnu (14.2.0-17) ... Selecting previously unselected package gfortran-14. Preparing to unpack .../036-gfortran-14_14.2.0-17_arm64.deb ... Unpacking gfortran-14 (14.2.0-17) ... 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+b7_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b7) ... Selecting previously unselected package libbrotli-dev:arm64. Preparing to unpack .../061-libbrotli-dev_1.1.0-2+b7_arm64.deb ... Unpacking libbrotli-dev:arm64 (1.1.0-2+b7) ... 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_3.4.7-1_arm64.deb ... Unpacking libffi8:arm64 (3.4.7-1) ... 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_4.20.0-2_arm64.deb ... Unpacking libtasn1-6:arm64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:arm64. Preparing to unpack .../067-libgnutls30t64_3.8.9-2_arm64.deb ... Unpacking libgnutls30t64:arm64 (3.8.9-2) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../068-libsasl2-modules-db_2.1.28+dfsg1-9_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../069-libsasl2-2_2.1.28+dfsg1-9_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:arm64. Preparing to unpack .../070-libldap2_2.6.9+dfsg-1_arm64.deb ... Unpacking libldap2:arm64 (2.6.9+dfsg-1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../071-libnghttp2-14_1.64.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1) ... Selecting previously unselected package libnghttp3-9:arm64. Preparing to unpack .../072-libnghttp3-9_1.8.0-1_arm64.deb ... Unpacking libnghttp3-9:arm64 (1.8.0-1) ... Selecting previously unselected package libngtcp2-16:arm64. Preparing to unpack .../073-libngtcp2-16_1.11.0-1_arm64.deb ... Unpacking libngtcp2-16:arm64 (1.11.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:arm64. Preparing to unpack .../074-libngtcp2-crypto-gnutls8_1.11.0-1_arm64.deb ... Unpacking libngtcp2-crypto-gnutls8:arm64 (1.11.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../075-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../076-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../077-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:arm64. Preparing to unpack .../078-libcurl3t64-gnutls_8.12.1-3_arm64.deb ... Unpacking libcurl3t64-gnutls:arm64 (8.12.1-3) ... Selecting previously unselected package libevent-2.1-7t64:arm64. Preparing to unpack .../079-libevent-2.1-7t64_2.1.12-stable-10+b1_arm64.deb ... Unpacking libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:arm64. Preparing to unpack .../080-libunbound8_1.22.0-1+b1_arm64.deb ... Unpacking libunbound8:arm64 (1.22.0-1+b1) ... Selecting previously unselected package libgnutls-dane0t64:arm64. Preparing to unpack .../081-libgnutls-dane0t64_3.8.9-2_arm64.deb ... Unpacking libgnutls-dane0t64:arm64 (3.8.9-2) ... Selecting previously unselected package libgnutls-openssl27t64:arm64. Preparing to unpack .../082-libgnutls-openssl27t64_3.8.9-2_arm64.deb ... Unpacking libgnutls-openssl27t64:arm64 (3.8.9-2) ... Selecting previously unselected package libidn2-dev:arm64. Preparing to unpack .../083-libidn2-dev_2.3.7-2+b1_arm64.deb ... Unpacking libidn2-dev:arm64 (2.3.7-2+b1) ... Selecting previously unselected package libp11-kit-dev:arm64. Preparing to unpack .../084-libp11-kit-dev_0.25.5-3_arm64.deb ... Unpacking libp11-kit-dev:arm64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6-dev:arm64. Preparing to unpack .../085-libtasn1-6-dev_4.20.0-2_arm64.deb ... Unpacking libtasn1-6-dev:arm64 (4.20.0-2) ... Selecting previously unselected package libgmpxx4ldbl:arm64. Preparing to unpack .../086-libgmpxx4ldbl_2%3a6.3.0+dfsg-3_arm64.deb ... Unpacking libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-3) ... Selecting previously unselected package libgmp-dev:arm64. Preparing to unpack .../087-libgmp-dev_2%3a6.3.0+dfsg-3_arm64.deb ... Unpacking libgmp-dev:arm64 (2:6.3.0+dfsg-3) ... Selecting previously unselected package nettle-dev:arm64. Preparing to unpack .../088-nettle-dev_3.10.1-1_arm64.deb ... Unpacking nettle-dev:arm64 (3.10.1-1) ... 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_1.8.0-1_arm64.deb ... Unpacking libnghttp3-dev:arm64 (1.8.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls-dev:arm64. Preparing to unpack .../097-libngtcp2-crypto-gnutls-dev_1.11.0-1_arm64.deb ... Unpacking libngtcp2-crypto-gnutls-dev:arm64 (1.11.0-1) ... Selecting previously unselected package libngtcp2-dev:arm64. Preparing to unpack .../098-libngtcp2-dev_1.11.0-1_arm64.deb ... Unpacking libngtcp2-dev:arm64 (1.11.0-1) ... 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. Preparing to unpack .../100-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package librtmp-dev:arm64. Preparing to unpack .../101-librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssl-dev:arm64. Preparing to unpack .../102-libssl-dev_3.4.1-1_arm64.deb ... Unpacking libssl-dev:arm64 (3.4.1-1) ... Selecting previously unselected package libssh2-1-dev:arm64. Preparing to unpack .../103-libssh2-1-dev_1.11.1-1_arm64.deb ... Unpacking libssh2-1-dev:arm64 (1.11.1-1) ... Selecting previously unselected package libzstd-dev:arm64. Preparing to unpack .../104-libzstd-dev_1.5.6+dfsg-2_arm64.deb ... Unpacking libzstd-dev:arm64 (1.5.6+dfsg-2) ... Selecting previously unselected package libcurl4-gnutls-dev:arm64. Preparing to unpack .../105-libcurl4-gnutls-dev_8.12.1-3_arm64.deb ... Unpacking libcurl4-gnutls-dev:arm64 (8.12.1-3) ... Selecting previously unselected package libcurl4t64:arm64. Preparing to unpack .../106-libcurl4t64_8.12.1-3_arm64.deb ... Unpacking libcurl4t64:arm64 (8.12.1-3) ... 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. Preparing to unpack .../110-libfftw3-bin_3.3.10-2+b1_arm64.deb ... Unpacking libfftw3-bin (3.3.10-2+b1) ... Selecting previously unselected package libfftw3-dev:arm64. Preparing to unpack .../111-libfftw3-dev_3.3.10-2+b1_arm64.deb ... Unpacking libfftw3-dev:arm64 (3.3.10-2+b1) ... Selecting previously unselected package libhdf5-310:arm64. Preparing to unpack .../112-libhdf5-310_1.14.5+repack-3_arm64.deb ... Unpacking libhdf5-310:arm64 (1.14.5+repack-3) ... Selecting previously unselected package libhdf5-cpp-310:arm64. Preparing to unpack .../113-libhdf5-cpp-310_1.14.5+repack-3_arm64.deb ... Unpacking libhdf5-cpp-310:arm64 (1.14.5+repack-3) ... Selecting previously unselected package libhdf5-fortran-310:arm64. Preparing to unpack .../114-libhdf5-fortran-310_1.14.5+repack-3_arm64.deb ... Unpacking libhdf5-fortran-310:arm64 (1.14.5+repack-3) ... Selecting previously unselected package libhdf5-hl-310:arm64. Preparing to unpack .../115-libhdf5-hl-310_1.14.5+repack-3_arm64.deb ... Unpacking libhdf5-hl-310:arm64 (1.14.5+repack-3) ... Selecting previously unselected package libhdf5-hl-fortran-310:arm64. Preparing to unpack .../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%3a2.1.5-3.1_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-3.1) ... Selecting previously unselected package libjpeg62-turbo-dev:arm64. Preparing to unpack .../119-libjpeg62-turbo-dev_1%3a2.1.5-3.1_arm64.deb ... Unpacking libjpeg62-turbo-dev:arm64 (1:2.1.5-3.1) ... Selecting previously unselected package libjpeg-dev:arm64. Preparing to unpack .../120-libjpeg-dev_1%3a2.1.5-3.1_arm64.deb ... Unpacking libjpeg-dev:arm64 (1:2.1.5-3.1) ... 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+20250216-1_arm64.deb ... Unpacking libncurses6:arm64 (6.5+20250216-1) ... Selecting previously unselected package libncurses-dev:arm64. Preparing to unpack .../124-libncurses-dev_6.5+20250216-1_arm64.deb ... Unpacking libncurses-dev:arm64 (6.5+20250216-1) ... 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+b2_arm64.deb ... Unpacking libxml2-dev:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... 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-4+b1_arm64.deb ... Unpacking libopenmm8.1 (8.1.2+dfsg-4+b1) ... Selecting previously unselected package libopenmm-dev. Preparing to unpack .../129-libopenmm-dev_8.1.2+dfsg-4+b1_arm64.deb ... Unpacking libopenmm-dev (8.1.2+dfsg-4+b1) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../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 (2.40.4-5) ... Setting up hdf5-helpers (1.14.5+repack-3) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:arm64 (1.1.0-2+b7) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up 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+dfsg1-9) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libunbound8:arm64 (1.22.0-1+b1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-3) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-3.1) ... Setting up libjpeg62-turbo-dev:arm64 (1:2.1.5-3.1) ... Setting up libncurses6:arm64 (6.5+20250216-1) ... Setting up comerr-dev:arm64 (2.1-1.47.2-1) ... Setting up libunistring5:arm64 (1.3-1) ... Setting up libssl-dev:arm64 (3.4.1-1) ... 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+dfsg1-9) ... Setting up libgfortran5:arm64 (14.2.0-17) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:arm64 (1.8.0-1) ... Setting up libnghttp3-dev:arm64 (1.8.0-1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.7-1) ... 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 (4.20.0-2) ... Setting up libngtcp2-16:arm64 (1.11.0-1) ... Setting up libkrb5-3:arm64 (1.21.3-4) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libtasn1-6-dev:arm64 (4.20.0-2) ... Setting up libopenmm8.1 (8.1.2+dfsg-4+b1) ... 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+b2) ... Setting up libldap2:arm64 (2.6.9+dfsg-1) ... Setting up libbrotli-dev:arm64 (1.1.0-2+b7) ... 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 (14.2.0-17) ... Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:arm64 (3.12.1-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libncurses-dev:arm64 (6.5+20250216-1) ... Setting up gettext (0.23.1-1) ... Setting up libarpack2t64:arm64 (3.9.1-4) ... Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:arm64 (3.10.1-1) ... Setting up 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 (1:2.1.5-3.1) ... Setting up libidn2-0:arm64 (2.3.7-2+b1) ... Setting up libngtcp2-dev:arm64 (1.11.0-1) ... Setting up libopenmm-dev (8.1.2+dfsg-4+b1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libxml2-dev:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... 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 (14.2.0-17) ... Setting up gfortran-aarch64-linux-gnu (4:14.2.0-1) ... Setting up gfortran-14 (14.2.0-17) ... 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 (1.11.0-1) ... Setting up libkadm5clnt-mit12:arm64 (1.21.3-4) ... Setting up libgnutls28-dev:arm64 (3.8.9-2) ... Setting up libcurl4t64:arm64 (8.12.1-3) ... Setting up libkdb5-10t64:arm64 (1.21.3-4) ... Setting up libcurl3t64-gnutls:arm64 (8.12.1-3) ... Setting up debhelper (13.24.1) ... Setting up libngtcp2-crypto-gnutls-dev:arm64 (1.11.0-1) ... 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 (8.12.1-3) ... Setting up libhdf5-dev (1.14.5+repack-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libnetcdf-dev (1:4.9.3-1) ... Processing triggers for libc-bin (2.41-3) ... 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 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_Mask.cpp CXX Action_Matrix.cpp CXX Action_MinImage.cpp CXX Action_Molsurf.cpp CXX Action_MultiDihedral.cpp CXX Action_MultiVector.cpp CXX Action_NAstruct.cpp CXX Action_NativeContacts.cpp CXX Action_NMRrst.cpp CXX Action_OrderParameter.cpp CXX Action_Outtraj.cpp CXX Action_PairDist.cpp CXX Action_Pairwise.cpp CXX Action_Principal.cpp CXX Action_Projection.cpp CXX Action_Pucker.cpp CXX Action_Radgyr.cpp CXX Action_Radial.cpp CXX Action_RandomizeIons.cpp CXX Action_Remap.cpp CXX Action_ReplicateCell.cpp CXX Action_Rmsd.cpp CXX Action_Rotate.cpp CXX Action_RunningAvg.cpp CXX Action_STFC_Diffusion.cpp CXX Action_Scale.cpp CXX Action_SetVelocity.cpp CXX Action_Spam.cpp CXX Action_Strip.cpp CXX Action_Surf.cpp CXX Action_SymmetricRmsd.cpp CXX Action_Temperature.cpp CXX Action_Time.cpp CXX Action_Translate.cpp CXX Action_Unstrip.cpp CXX Action_Unwrap.cpp CXX Action_Vector.cpp CXX Action_VelocityAutoCorr.cpp CXX Action_Volmap.cpp CXX Action_Volume.cpp CXX Action_Watershell.cpp CXX Action_XtalSymm.cpp CXX AnalysisList.cpp CXX Analysis_AmdBias.cpp CXX Analysis_AutoCorr.cpp CXX Analysis_Average.cpp CXX Analysis_Clustering.cpp CXX Analysis_Corr.cpp 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); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ CXX Analysis_Matrix.cpp 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_MeltCurve.cpp CXX Analysis_Modes.cpp CXX Analysis_Multicurve.cpp CXX Analysis_MultiHist.cpp CXX Analysis_Overlap.cpp CXX Analysis_PhiPsi.cpp CXX Analysis_Regression.cpp CXX Analysis_RemLog.cpp CXX Analysis_Rms2d.cpp CXX Analysis_RmsAvgCorr.cpp CXX Analysis_Rotdif.cpp CXX Analysis_RunningAvg.cpp CXX Analysis_Slope.cpp CXX Analysis_Spline.cpp CXX Analysis_State.cpp CXX Analysis_Statistics.cpp CXX Analysis_TI.cpp CXX Analysis_Timecorr.cpp CXX Analysis_VectorMath.cpp CXX Analysis_Wavelet.cpp CXX ArgList.cpp CXX Array1D.cpp CXX AssociatedData.cpp CXX Atom.cpp CXX AtomMap.cpp CXX AtomMask.cpp CXX AxisType.cpp CXX BondSearch.cpp CXX Box.cpp CXX BoxArgs.cpp CXX BufferedFrame.cpp CXX BufferedLine.cpp CXX ByteRoutines.cpp CXX CharMask.cpp CXX CharmmParamFile.cpp CXX CIFfile.cpp CXX ClusterDist.cpp CXX ClusterList.cpp CXX ClusterMap.cpp CXX ClusterMatrix.cpp CXX ClusterNode.cpp CXX ClusterSieve.cpp CXX Cluster_DBSCAN.cpp CXX Cluster_DPeaks.cpp CXX Cluster_HierAgglo.cpp CXX Cluster_Kmeans.cpp CXX Cluster_ReadInfo.cpp CXX Cmd.cpp CXX CmdInput.cpp CXX CmdList.cpp CXX CompactFrameArray.cpp CXX ComplexArray.cpp CXX Constraints.cpp CXX ControlBlock_For.cpp CXX CoordinateInfo.cpp CXX Corr.cpp CXX Cph.cpp CXX CpptrajFile.cpp CXX CpptrajState.cpp CXX CpptrajStdio.cpp CXX CurveFit.cpp CXX DataFile.cpp CXX DataFileList.cpp CXX DataFilter.cpp CXX DataIO.cpp CXX DataIO_CCP4.cpp CXX DataIO_CharmmFastRep.cpp CXX DataIO_CharmmOutput.cpp CXX DataIO_CharmmRepLog.cpp CXX DataIO_CharmmRtfPrm.cpp CXX DataIO_Cmatrix.cpp CXX DataIO_Cpout.cpp CXX DataIO_Evecs.cpp CXX DataIO_Gnuplot.cpp CXX DataIO_Grace.cpp CXX DataIO_OpenDx.cpp CXX DataIO_Peaks.cpp CXX DataIO_Mdout.cpp CXX DataIO_NC_Cmatrix.cpp CXX DataIO_RemLog.cpp CXX DataIO_Std.cpp CXX DataIO_VecTraj.cpp CXX DataIO_Xplor.cpp CXX DataIO_XVG.cpp CXX DataSet.cpp CXX DataSetList.cpp CXX DataSet_1D.cpp CXX DataSet_3D.cpp CXX DataSet_Cmatrix.cpp CXX DataSet_Cmatrix_DISK.cpp CXX DataSet_Cmatrix_MEM.cpp CXX DataSet_Cmatrix_NOMEM.cpp CXX DataSet_Coords.cpp CXX DataSet_Coords_CRD.cpp CXX DataSet_Coords_REF.cpp CXX DataSet_Coords_TRJ.cpp CXX DataSet_GridDbl.cpp CXX DataSet_GridFlt.cpp CXX DataSet_Mat3x3.cpp CXX DataSet_MatrixDbl.cpp CXX DataSet_MatrixFlt.cpp CXX DataSet_Mesh.cpp CXX DataSet_Modes.cpp CXX DataSet_Parameters.cpp CXX DataSet_pH.cpp CXX DataSet_PHREMD_Explicit.cpp CXX DataSet_PHREMD_Implicit.cpp CXX DataSet_RemLog.cpp CXX DataSet_Topology.cpp CXX DataSet_Vector.cpp CXX DataSet_Vector_Scalar.cpp CXX DataSet_double.cpp CXX DataSet_float.cpp CXX DataSet_integer_disk.cpp CXX DataSet_integer_mem.cpp CXX DataSet_string.cpp CXX DataSet_StringVar.cpp CXX DataSet_Tensor.cpp CXX DataSet_unsignedInt.cpp CXX Deprecated.cpp CXX DihedralSearch.cpp CXX DistRoutines.cpp CXX Energy.cpp CXX EnergyArray.cpp CXX EnsembleIn.cpp CXX EnsembleIn_Multi.cpp CXX EnsembleIn_Single.cpp CXX EnsembleNavigator.cpp CXX EnsembleOut.cpp CXX EnsembleOut_Multi.cpp CXX EnsembleOut_Single.cpp CXX EnsembleOutList.cpp CXX Ewald.cpp CXX Ewald_ParticleMesh.cpp In file included from Ewald_ParticleMesh.h:5, from Ewald_ParticleMesh.cpp:4: helpme_standalone.h:2323: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2323 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:2343: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2343 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3014: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3014 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3120: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3120 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3247: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3247 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3701: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3701 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3739: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3739 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3802: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3802 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3840: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3840 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4044: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4044 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4052: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4052 | #pragma omp for helpme_standalone.h:4097: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4097 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4145: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4145 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4172: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4172 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4224: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4224 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4228: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4228 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4275: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4275 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4388: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4388 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4419: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) 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 Ewald_Regular.cpp 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) { | ~~~~^~~~~~~~ CXX Exec_Calc.cpp helpme_standalone.h: In instantiation of 'void helpme::PMEInstance >::sanityChecks(int, const RealMat&, const RealMat&, int) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5018:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5018 | sanityChecks(parameterAngMom, parameters, coordinates); | ^~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3198:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-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_CatCrd.cpp CXX Exec_Change.cpp CXX Exec_ClusterMap.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_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 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_ParmBox.cpp CXX Exec_ParmSolvent.cpp CXX Exec_ParmStrip.cpp CXX Exec_ParmWrite.cpp CXX Exec_PermuteDihedrals.cpp CXX Exec_Precision.cpp CXX Exec_PrepareForLeap.cpp 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_PrintData.cpp CXX Exec_Random.cpp CXX Exec_ReadData.cpp CXX Exec_ReadEnsembleData.cpp CXX Exec_ReadInput.cpp CXX Exec_RotateDihedral.cpp CXX Exec_RunAnalysis.cpp CXX Exec_ScaleDihedralK.cpp CXX Exec_Set.cpp CXX Exec_SequenceAlign.cpp CXX Exec_Show.cpp CXX Exec_SortEnsembleData.cpp CXX Exec_SplitCoords.cpp CXX Exec_System.cpp CXX Exec_Top.cpp CXX Exec_Traj.cpp CXX Exec_UpdateParameters.cpp CXX Exec_ViewRst.cpp CXX File_TempName.cpp CXX FileIO_Bzip2.cpp CXX FileIO_Gzip.cpp CXX FileIO_Mpi.cpp CXX FileIO_MpiShared.cpp CXX FileIO_Std.cpp CXX FileName.cpp CXX FileType.cpp CXX FileTypes.cpp CXX ForLoop.cpp CXX ForLoop_dataSetBlocks.cpp CXX ForLoop_integer.cpp CXX ForLoop_list.cpp CXX ForLoop_mask.cpp CXX ForLoop_overSets.cpp CXX Frame.cpp CXX GridAction.cpp CXX HistBin.cpp CXX Hungarian.cpp CXX ImageRoutines.cpp CXX Image_List_Mask.cpp CXX Image_List_Pair.cpp CXX Image_List_Unit.cpp CXX InputTrajCommon.cpp CXX KDE.cpp CXX MapAtom.cpp CXX MaskArray.cpp CXX MaskToken.cpp CXX Matrix_3x3.cpp CXX MdOpts.cpp CXX MetaData.cpp CXX Minimize_SteepestDescent.cpp CXX Mol.cpp CXX Mol2File.cpp CXX NameType.cpp CXX NC_Cmatrix.cpp CXX NC_Routines.cpp CXX NetcdfFile.cpp CXX OMM_helpers.cpp CXX OutputTrajCommon.cpp CXX ParameterSet.cpp CXX PDBfile.cpp CXX PairList.cpp CXX Parallel.cpp CXX ParallelNetcdf.cpp CXX ParmFile.cpp CXX Parm_Amber.cpp CXX Parm_CharmmPsf.cpp CXX Parm_CIF.cpp CXX Parm_Gromacs.cpp CXX Parm_Mol2.cpp CXX Parm_PDB.cpp CXX Parm_SDF.cpp CXX Parm_Tinker.cpp CXX PotentialFunction.cpp CXX PotentialTerm.cpp CXX PotentialTerm_Angle.cpp CXX PotentialTerm_Bond.cpp CXX PotentialTerm_Dihedral.cpp CXX PotentialTerm_LJ_Coulomb.cpp CXX PotentialTerm_OpenMM.cpp CXX ProgressBar.cpp CXX ProgressTimer.cpp CXX PubFFT.cpp CXX ExternalFxn.cpp CXX Random.cpp CXX Range.cpp CXX RNG.cpp CXX RNG_Marsaglia.cpp CXX RNG_MersenneTwister.cpp CXX RNG_PCG32.cpp CXX RNG_Stdlib.cpp CXX RNG_Xoshiro128pp.cpp CXX RPNcalc.cpp CXX ReferenceAction.cpp CXX RemdReservoirNC.cpp CXX Residue.cpp CXX SDFfile.cpp CXX SimplexMin.cpp CXX Spline.cpp CXX SplineFxnTable.cpp CXX StringRoutines.cpp CXX StructureCheck.cpp CXX StructureMapper.cpp CXX SymmetricRmsdCalc.cpp CXX TextFormat.cpp CXX Timer.cpp CXX TinkerFile.cpp CXX TopInfo.cpp CXX Topology.cpp CXX TorsionRoutines.cpp CXX Traj_AmberCoord.cpp CXX Traj_AmberNetcdf.cpp CXX Traj_AmberRestart.cpp CXX Traj_AmberRestartNC.cpp CXX Traj_Binpos.cpp CXX Traj_CharmmCor.cpp CXX Traj_CharmmDcd.cpp CXX Traj_CharmmRestart.cpp CXX Traj_CIF.cpp CXX Traj_Conflib.cpp CXX Traj_DTR.cpp CXX Traj_GmxDump.cpp CXX Traj_GmxTng.cpp CXX Traj_GmxTrX.cpp CXX Traj_GmxXtc.cpp CXX Traj_Gro.cpp CXX Traj_Mol2File.cpp CXX Traj_NcEnsemble.cpp CXX Traj_PDBfile.cpp CXX Traj_SDF.cpp CXX Traj_SQM.cpp CXX Traj_Tinker.cpp CXX Traj_XYZ.cpp CXX TrajectoryFile.cpp CXX TrajectoryIO.cpp CXX TrajFrameCounter.cpp CXX TrajinList.cpp CXX Trajin_Multi.cpp CXX Trajin_Single.cpp CXX TrajIOarray.cpp CXX Trajout_Single.cpp CXX TrajoutList.cpp CXX Vec3.cpp CXX ViewRst.cpp CXX xoshiro128plusplus.cpp xoshiro128plusplus.cpp: In function 'void jump()': xoshiro128plusplus.cpp:60:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 60 | for(int i = 0; i < sizeof JUMP / sizeof *JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ xoshiro128plusplus.cpp: In function 'void long_jump()': xoshiro128plusplus.cpp:90:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 90 | for(int i = 0; i < sizeof LONG_JUMP / sizeof *LONG_JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CXX Action_Esander.cpp CXX Command.cpp CXX Cpptraj.cpp CXX Energy_Sander.cpp CXX ReadLine.cpp CXX main.cpp CC molsurf.c Skipping bundled READLINE build cd xdrfile && make all make[3]: Entering directory '/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 xdrfile_xtc.c CC tng_io.c CC tng_compress.c CC coder.c CC warnmalloc.c CC fixpoint.c CC xtc3.c CC bwlzh.c /bin/rm -f libxdrfile.a ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' CC xtc2.c CC widemuldiv.c CC huffmem.c CC vals16.c CC bwt.c CC mtf.c CC rle.c CC lz77.c CC dict.c CC huffman.c CC merge_sort.c 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 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' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList CPPTRAJ: NameType class unit test. 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 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 CPPTRAJ: ArgList 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 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 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 183513792 Apr 4 12:52 ../bin/cpptraj -rwxr-xr-x 1 pbuilder1 pbuilder1 183513792 Apr 4 12:52 ../bin/cpptraj make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Strip ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_General ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj CPPTRAJ: One frame strip command test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TrajinOffset CPPTRAJ: Broken Traj: Running good trajectory. CPPTRAJ: General tests CPPTRAJ: Normal trajectory read with offsets. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_trajout_framerange ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD CPPTRAJ: Trajout Frame Range [Amber Restart] CPPTRAJ: Per-Residue RMSD Test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RemdTraj CPPTRAJ: CRD Replica Trajectory Run with offset CPPTRAJ: Broken Traj: Running broken trajectory. CPPTRAJ: Gzipped trajectory read with offsets CPPTRAJ: Unstrip (Lig/Rec/Complex) command test CPPTRAJ: CRD Replica Trajectory Run CPPTRAJ: Bzip2ed trajectory read with offsets CPPTRAJ: Per-Residue RMSD Test with averaging CPPTRAJ: Trajout Frame Range [Amber Coordinates] CPPTRAJ: NetCDF Replica Trajectory Run test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DSSP CPPTRAJ: Secstruct (DSSP) command test. CPPTRAJ: Per-Residue RMSD Test with residue centering. All 6 comparisons passed. CPPTRAJ: Start argument offset CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj CPPTRAJ: Compressed broken trajectory test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hbond ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Center CPPTRAJ: Solute Hbond test CPPTRAJ: Center command test. All 4 comparisons passed. CPPTRAJ: Multi frame strip command test. CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj All 2 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NCrestart CPPTRAJ: NetCDF Restart Test - TXT->NetCDF CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. CPPTRAJ: Strip topology with PDB info ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf CPPTRAJ: Center origin command test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Image CPPTRAJ: Surface calculation test CPPTRAJ: Orthorhombic imaged distance test. CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj CPPTRAJ: NetCDF Restart Test - NetCDF->TXT All 11 comparisons passed. CPPTRAJ: Non-orthorhombic imaged distance test. CPPTRAJ: Solute Hbond test with disk caching CPPTRAJ: Center origin mass command test. CPPTRAJ: CRD Replica Trajectory Run with remdout ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radgyr CPPTRAJ: Secstruct (DSSP) command with changing number of residues. CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF CPPTRAJ: Radius of gyration command test CPPTRAJ: Orthorhombic coordinate imaging test CPPTRAJ: Solute-solvent hbond test CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt CPPTRAJ: Secstruct (DSSP): SS assign output test All 15 comparisons passed. All 2 comparisons passed. CPPTRAJ: Center reference command test. All 8 comparisons passed. CPPTRAJ: Nonorthorhombic coordinate imaging test CPPTRAJ: FtuFabI Assignment test All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Parallel CPPTRAJ: Parallel tests. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mask CPPTRAJ: Hbond, no intramolecular hydrogen bonds test CPPTRAJ: Mask single frame test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Jcoupling CPPTRAJ: J-Coupling single frame test CPPTRAJ: Center point test. CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diffusion CPPTRAJ: Diffusion test, no imaging. All 5 comparisons passed. All 10 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. Skipped test: J-Coupling extended test All 1 comparisons passed. 1 comparisons skipped. CPPTRAJ: RMSD Test with outtraj. CPPTRAJ: Mask longer command test. CPPTRAJ: Hbond, specified solute masks CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm CPPTRAJ: Diffusion test, old syntax. CPPTRAJ: Parallel test with trajectory offset CPPTRAJ: CHARMM PSF/DCD test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotdif CPPTRAJ: Rotational diffusion calculation test All 6 comparisons passed. CPPTRAJ: CHARMM DCD Write, step 1. All 5 comparisons passed. CPPTRAJ: CHARMM DCD Write, step 2. CPPTRAJ: Diffusion test, new syntax. CPPTRAJ: Hbond, no angle cutoff test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj CPPTRAJ: Partial Surface calculation test CPPTRAJ: Convert mdcrd -> NetCDF ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Runavg CPPTRAJ: Coordinate Running Average test. CPPTRAJ: Outtraj Test with maxmin. All 4 comparisons passed. All 7 comparisons passed. CPPTRAJ: Hbond, Bridge nointramol test CPPTRAJ: CHAMBER topology read/strip test. g++ -o a.out main.o NameType.o CpptrajStdio.o CPPTRAJ: Diffusion test, nonorthogonal box All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RMSD CPPTRAJ: Coordinate Running Average Traj Write CPPTRAJ: Convert NetCDF -> mdcrd CPPTRAJ: Basic RMSD tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_2DRMS CPPTRAJ: 2D RMSD Test. CPPTRAJ: Read CHARMM restart ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mol2 CPPTRAJ: Mol2 Parm/Traj Read/Write Test. All 2 comparisons passed. CPPTRAJ: 2D RMSD Test, mass-weighted. 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: STFC Diffusion Test CPPTRAJ: CHARMM PSF write CPPTRAJ: 2D RMSD Test with reference trajectory ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Average ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct CPPTRAJ: NAstruct command test. CPPTRAJ: STFC Diffusion Test with individual distances CPPTRAJ: LCPO test with GAFF atom types CPPTRAJ: PDB => Mol2 CPPTRAJ: Average Test. All 1 comparisons passed. CPPTRAJ: CHARMM COORdinates test CPPTRAJ: RMS coordinate rotation/rotation matrices test CPPTRAJ: 2D DME Test. All 6 comparisons passed. CPPTRAJ: STFC Diffusion Test with COM ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pucker CPPTRAJ: Amber Top/Rst => Mol2 All 3 comparisons passed. CPPTRAJ: Pucker command test All 2 comparisons passed. CPPTRAJ: 2D RMSD with reference mask test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CharmmParams CPPTRAJ: Test updating topology with Charmm parameters (single residue) CPPTRAJ: STFC Diffusion Test with second mask ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Datafile CPPTRAJ: RMS fit with no coordinates modification test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomMap 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. CPPTRAJ: Data file output precision test 1 comparisons skipped. All 2 comparisons passed. CPPTRAJ: 2D RMSD test, no fitting. CPPTRAJ: AtomMap Test CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial CPPTRAJ: Standard -> Grace Data ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist CPPTRAJ: Radial test, non-orthogonal imaging CPPTRAJ: 1D/2D Histogram Analysis test CPPTRAJ: NAstruct command test, single strand CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. CPPTRAJ: Hbond with imaging All 16 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest All 3 comparisons passed. CPPTRAJ: RMS fit to previous test CPPTRAJ: Closest command test using first solvent atom. CPPTRAJ: Grace -> Standard Data All 11 comparisons passed. CPPTRAJ: AtomMap with 'rmsfit' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DRMSD CPPTRAJ: RMS: imaging after unit cell rotation ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct_8OG CPPTRAJ: NA test (8OG) CPPTRAJ: Distance RMSD test CPPTRAJ: Atom map charmm->amber atom order CPPTRAJ: Hbond, orthogonal imaging CPPTRAJ: Cluster command test, in-memory pairwise distances. CPPTRAJ: X column format/precision test. All 12 comparisons passed. CPPTRAJ: Atom map charmm->amber atom order, by residue CPPTRAJ: 3D histogram test. CPPTRAJ: Closest command test using all solvent atoms. All 23 comparisons passed. CPPTRAJ: Data file group by name test All 9 comparisons passed. All 7 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_IRED All 3 comparisons passed. CPPTRAJ: IRED vector/matrix test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Molsurf CPPTRAJ: Molsurf test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons CPPTRAJ: randomizeions test (original algorithm) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Corr All 1 comparisons passed. CPPTRAJ: Correlation test CPPTRAJ: Data file group by aspect test ******************************************************************************** CPPTRAJ: Cluster command test, read pairwise distances. 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_CheckStructure CPPTRAJ: Structure Check CPPTRAJ: Radial test, orthogonal and no imaging All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Contacts CPPTRAJ: Cluster command test, read NetCDF pairwise distances. CPPTRAJ: Contacts test. All 6 comparisons passed. CPPTRAJ: RmsAvgCorr First CPPTRAJ: Structure Check with Around and Skip ******************************************************************************** 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_Principal All 9 comparisons passed. CPPTRAJ: Principal Test CPPTRAJ: Cluster command test, write ASCII pairwise distances. All 3 comparisons passed. All 3 comparisons passed. CPPTRAJ: Closest command test, using mask center All 1 comparisons passed. CPPTRAJ: Cluster command test, read ASCII pairwise distances. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Vector ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. CPPTRAJ: Basic vector tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Matrix All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Grid CPPTRAJ: Matrix Tests CPPTRAJ: Dipole test CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. All 9 comparisons passed. CPPTRAJ: Closest command test, using mask center and solvent mask CPPTRAJ: Structure Check with PBC ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Unwrap CPPTRAJ: Unwrap non-orthogonal test CPPTRAJ: Grid test CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve CPPTRAJ: Cluster, nosieve CPPTRAJ: Closest command test, solvent mask, water oxygen only CPPTRAJ: Randomize (around, overlap) CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. CPPTRAJ: Unwrap orthogonal test CPPTRAJ: Test vector center with magnitude All 3 comparisons passed. CPPTRAJ: OpenDX Grid read test CPPTRAJ: Atomicfluct test with ADP output CPPTRAJ: Cluster, sieve5 All 2 comparisons passed. CPPTRAJ: Momentum/velocity vector test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Project CPPTRAJ: Grid with specified center test. CPPTRAJ: Projection ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes CPPTRAJ: Modes analysis, RMS fluctuations ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Watershell CPPTRAJ: Watershell Test, non-orthorhombic imaging. CPPTRAJ: Grid with box center offset test. g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o All 1 comparisons passed. CPPTRAJ: Force vector test. CPPTRAJ: Cluster, nosieve savepairdist CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. CPPTRAJ: Modes analysis, displacements All 8 comparisons passed. CPPTRAJ: Structure Check with Around CPPTRAJ: Grid with mask center offset test. All 14 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AnalysisRunAvg CPPTRAJ: Analysis Running Average CPPTRAJ: Generate matrix with trajectory start/stop/offset CPPTRAJ: Modes analysis, dipole correlation ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volmap CPPTRAJ: VMD VolMap Algorithm test All 13 comparisons passed. CPPTRAJ: Generate matrix with action stop/start/offset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SPAM All 8 comparisons passed. CPPTRAJ: SPAM Test CPPTRAJ: Non-orthogonal grid test. All 2 comparisons passed. CPPTRAJ: Cluster, nosieve loadpairdist 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_LIE CPPTRAJ: LIE test 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' CPPTRAJ: Randomize (around) All 15 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Density CPPTRAJ: Density along axis tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidOrder CPPTRAJ: Lipid Order Parameter Test. VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. Skipped test: VMD VolMap Algorithm longer tests All 2 comparisons passed. 1 comparisons skipped. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReadData ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PairDist CPPTRAJ: Read vector data test (no origins, origins) CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test CPPTRAJ: PairDist Test. CPPTRAJ: Cluster, sieve5 savepairdist CPPTRAJ: Modes analysis, pseudo trajectory creation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST CPPTRAJ: GIST water-water interaction test CPPTRAJ: Read vector data set (origins, no origins) CPPTRAJ: Grid generation from 'bounds' test. CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test CPPTRAJ: Read Amber output test CPPTRAJ: Pairdist test, orthogonal imaging. CPPTRAJ: Multi-frame density along axis test All 6 comparisons passed. All 1 comparisons passed. CPPTRAJ: Read CHARMM output test All 13 comparisons passed. All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidSCD ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_systemVF CPPTRAJ: Basic lipid order parameter test CPPTRAJ: 3D data read/write test CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicCorr CPPTRAJ: Atomic Correlation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr CPPTRAJ: Randomize (overlap) CPPTRAJ: Cluster, sieve5 loadpairdist CPPTRAJ: AutoCorr test. CPPTRAJ: Standard 3D data write test CPPTRAJ: Total system density test All 1 comparisons passed. CPPTRAJ: Standard 3D data read test CPPTRAJ: Randomize (no restrictions) All 7 comparisons passed. CPPTRAJ: Cluster, nosieve pairwisecache none CPPTRAJ: Standard 3D data read/append test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Box CPPTRAJ: New Lipid Order Parameter Test, DOPC. CPPTRAJ: Box Test (Add box info) All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomTypeSelect CPPTRAJ: Selection by atom type test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AvgRef CPPTRAJ: RMSD Test with averaged reference coordinates. CPPTRAJ: Box test (remove box info) CPPTRAJ: Standard 3D data, sparse All 1 comparisons passed. All 5 comparisons passed. All 4 comparisons passed. CPPTRAJ: Box test (Modify box length) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Crank_Stat CPPTRAJ: Nonorthogonal grid standard write/read tests. All 1 comparisons passed. CPPTRAJ: Crankshaft test ******************************************************************************** CPPTRAJ: Cluster, sieve5 pairwisecache none TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateCrd CPPTRAJ: COORDS data set creation and CRDFLUCT test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LoadCrd CPPTRAJ: LoadCrd test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoImage CPPTRAJ: AutoImage test (split DNA duplex) All 3 comparisons passed. CPPTRAJ: COORDS data set creation with velocities test CPPTRAJ: Box test (auto orthogonal box, no radii) CPPTRAJ: LoadTraj test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MultiVector CPPTRAJ: Cluster, random CPPTRAJ: Box test (auto orthogonal box, VDW radii) CPPTRAJ: Multivector test CPPTRAJ: Pairdist test, nonorthogonal imaging. CPPTRAJ: Watershell Test, orthorhombic imaging. All 7 comparisons passed. CPPTRAJ: AutoImage test, use anchor mask CPPTRAJ: LoadTraj from trajin test. CPPTRAJ: TRAJ data set creation and CRDFLUCT test. All 1 comparisons passed. All 28 comparisons passed. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Lifetime CPPTRAJ: LoadCrd append from multiple files test CPPTRAJ: Lifetime test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FFT CPPTRAJ: TRAJ data set creation with velocities test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve CPPTRAJ: FFT test. CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Timecorr CPPTRAJ: Timecorr test. All 4 comparisons passed. CPPTRAJ: COORDS data set append test CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CrossCorr CPPTRAJ: CrossCorr test CPPTRAJ: COORDS test storing frame metadata CPPTRAJ: Watershell Test, no imaging. All 5 comparisons passed. CPPTRAJ: Lifetime test with data set caching. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multidihedral All 7 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SymmRmsd CPPTRAJ: SymmRmsd All 4 comparisons passed. CPPTRAJ: Multidihedral test CPPTRAJ: Read specific columns test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ensemble_MREMD CPPTRAJ: M-REMD sort test. CPPTRAJ: Write non-square matrix ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet CPPTRAJ: TRAJ test storing frame metadata All 1 comparisons passed. CPPTRAJ: Clustering, One DataSet CPPTRAJ: ASP symmetry-corrected RMSD test CPPTRAJ: Lifetime average and cumulative average test. CPPTRAJ: Multidihedral Nucleotide CHI test All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MakeStructure CPPTRAJ: Basic makestructure test CPPTRAJ: Read non-square matrix CPPTRAJ: Multidihedral protein dihedrals test CPPTRAJ: Pairdist test, 2 masks. All 12 comparisons passed. CPPTRAJ: GIST test, orthogonal cell CPPTRAJ: Clustering, Two DataSets CPPTRAJ: GLU symmetry-corrected RMSD test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotate All 8 comparisons passed. CPPTRAJ: Rotation (and inverse) of coords from matrices All 4 comparisons passed. CPPTRAJ: Read square matrix ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckChiral CPPTRAJ: Makestructure test with reference. CPPTRAJ: Multidihedral cyclic molecule test CPPTRAJ: M-REMD actions test. CPPTRAJ: Check chirality test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Integrate ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts CPPTRAJ: TYR symmetry-corrected RMSD test CPPTRAJ: Integration test. CPPTRAJ: Clustering, dihedral DataSet CPPTRAJ: Rotate with defined axis CPPTRAJ: NativeContacts test. All 15 comparisons passed. All 5 comparisons passed. All 6 comparisons passed. All 1 comparisons passed. All 2 comparisons passed. CPPTRAJ: Clustering, two dihedral DataSets All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Energy CPPTRAJ: Longer symmetry-corrected RMSD test. CPPTRAJ: Simple energy tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LESsplit ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PermuteDihedrals CPPTRAJ: PermuteDihedrals interval -120, phi psi CPPTRAJ: LES split/average test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CCP4 CPPTRAJ: CCP4 read/write and DX conversion test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CurveFit CPPTRAJ: Curve fitting test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihCovar CPPTRAJ: Dihedral Covariance Matrix Test CPPTRAJ: M-REMD ensemble outtraj test. All 8 comparisons passed. CPPTRAJ: Clustering, dihedral DataSet, K-means CPPTRAJ: PermuteDihedrals, random rotations ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetAverage CPPTRAJ: Curve fitting multi-exponential tests. All 2 comparisons passed. CPPTRAJ: Data set averaging and averaging over all sets test. CPPTRAJ: Clustering, two dihedral DataSets, K-means ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VectorMath CPPTRAJ: M-REMD no sort, running average test CPPTRAJ: Vector dot/cross product test All 4 comparisons passed. All 3 comparisons passed. All 8 comparisons passed. CPPTRAJ: NativeContacts test, save non-native contacts, residue time series All 2 comparisons passed. CPPTRAJ: Test kinetic energy calculation CPPTRAJ: M-REMD, generate RMS data ******************************************************************************** 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) All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Temperature CPPTRAJ: DBSCAN test CPPTRAJ: Curve fitting, custom output range. CPPTRAJ: Temperature test. CPPTRAJ: M-REMD, meltcurve analysis CPPTRAJ: Test total energy calculation ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Spline CPPTRAJ: Spline test All 17 comparisons passed. CPPTRAJ: DBSCAN automatic parameter determination test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Wavelet ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander_Short ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_KDE Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. CPPTRAJ: Wavelet analysis test SKIP: Energy via sander API short tests (GB/PME) All 6 comparisons passed. CPPTRAJ: KDE test. CPPTRAJ: Temperature with SHAKE on hydrogens. All 1 comparisons passed. CPPTRAJ: Test partial energy calculation ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CIF CPPTRAJ: CIF read test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PDB CPPTRAJ: Temperature with SHAKE on all atoms. CPPTRAJ: DBSCAN kdist map test CPPTRAJ: PDB format read/write test CPPTRAJ: NativeContacts test, orthorhombic imaging. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Align ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multicurve CPPTRAJ: Align Tests. CPPTRAJ: Multicurve test CPPTRAJ: Wavelet WAFEX test CPPTRAJ: DBSCAN with sieve CPPTRAJ: KDE with Kullback-Leibler divergence test CPPTRAJ: Generate offset traj from PDB All 6 comparisons passed. All 1 comparisons passed. CPPTRAJ: Temperature calc with extra points. CPPTRAJ: PQR file write with various radii All 4 comparisons passed. CPPTRAJ: Generate offset traj from CIF ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelocityAutoCorr CPPTRAJ: Velocity autocorrelation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelFrc All 17 comparisons passed. All 4 comparisons passed. CPPTRAJ: Test combining coordinates, velocities, and forces. CPPTRAJ: Align, unit cell rotation/imaging test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans All 3 comparisons passed. CPPTRAJ: Cpptraj Kmeans CPPTRAJ: Test using velocities as coordinates. ******************************************************************************** All 5 comparisons passed. TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RotateDihedral ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetCmd CPPTRAJ: Rotate dihedral to target value. All 2 comparisons passed. CPPTRAJ: Data Set commands test CPPTRAJ: PDB filter alternate atom location IDs test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remap CPPTRAJ: Remap Test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CompareTop ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Filter All 3 comparisons passed. CPPTRAJ: Compare topology test CPPTRAJ: Rotate dihedral by increment CPPTRAJ: Basic filter test CPPTRAJ: Test writing velocities (MDVEL) All 1 comparisons passed. All 1 comparisons passed. CPPTRAJ: Test using forces as coordinates. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CombineCrd CPPTRAJ: Adding PDB info to topology CPPTRAJ: Combine COORDS test. CPPTRAJ: Rotate dihedral in TRAJ data set CPPTRAJ: Cpptraj Kmeans random ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TopInfo CPPTRAJ: Topology info print test. CPPTRAJ: Data filter test. All 10 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTrr CPPTRAJ: TRR force/velocity read -> NetCDF write test CPPTRAJ: Test writing forces (MDFRC) CPPTRAJ: Combine COORDS test with box info. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ewald CPPTRAJ: Direct sum test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TI CPPTRAJ: TI analysis test. CPPTRAJ: Filter matrix test. All 6 comparisons passed. CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. All 10 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_SymmRMSD CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds CPPTRAJ: Fix imaged bonds test (Ortho.) All 5 comparisons passed. CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. CPPTRAJ: Split coords and recombine test. CPPTRAJ: TRR force/velocity read -> TRR write test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Distance CPPTRAJ: Distance tests All 5 comparisons passed. All 5 comparisons passed. CPPTRAJ: CRD => TRR CPPTRAJ: Fix imaged bonds test (Non-ortho.) CPPTRAJ: Topology info with reference coords test CPPTRAJ: Orthogonal imaged distance ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites CPPTRAJ: Cluster command test, coordinate writes. All 12 comparisons passed. All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volume CPPTRAJ: Volume tests CPPTRAJ: Non-orthogonal imaged distance CPPTRAJ: TRR => CRD All 2 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_SetVelocity CPPTRAJ: Cluster command test, coordinate writes using info file. CPPTRAJ: Set Velocity test CPPTRAJ: Replica log read/analyze test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AreaPerMol All 1 comparisons passed. All 4 comparisons passed. All 3 comparisons passed. CPPTRAJ: Area per molecule test CPPTRAJ: Ewald test (NaCl crystal) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DistBasedMask ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Calc CPPTRAJ: Distance-based atom mask tests (atom, residue) CPPTRAJ: CRD(1-5) => TRR CPPTRAJ: Calc test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CalcState CPPTRAJ: Calcstate test CPPTRAJ: Ewald test (trunc. oct) CPPTRAJ: Scale velocity test CPPTRAJ: Calc test with data sets All 7 comparisons passed. 1 out of 3 comparisons failed. All 4 comparisons passed. CPPTRAJ: Distance-based atom mask tests (molecule) All 6 comparisons passed. CPPTRAJ: Test math functions CPPTRAJ: CRD(6-10) => TRR ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Change All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateReservoir CPPTRAJ: Create RREMD NetCDF reservoir test CPPTRAJ: Change atom and residue name tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixAtomOrder All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LowestCurve CPPTRAJ: LowestCurve test CPPTRAJ: Out of order molecules test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Dpeaks CPPTRAJ: Density peaks clustering test CPPTRAJ: GIST test, nonorthogonal cell CPPTRAJ: TRR (appended) => CRD CPPTRAJ: Change chain ID test All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MinImage CPPTRAJ: Minimum Image test. All 2 comparisons passed. All 1 comparisons passed. CPPTRAJ: Change chain ID of COORDS set test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Regress All 1 comparisons passed. CPPTRAJ: Linear regression test. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rst CPPTRAJ: Generate restraints (rst) test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pairwise All 3 comparisons passed. CPPTRAJ: Pairwise tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Nreps CPPTRAJ: GMX: CRD with offset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ParmBox CPPTRAJ: Parmbox test CPPTRAJ: Clustering with specified # reps All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Solvent All 1 comparisons passed. CPPTRAJ: Test solvent command with closest All 3 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Translate CPPTRAJ: Translate test CPPTRAJ: Ewald test (partial system, trunc. oct) All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ScaleDihedralK CPPTRAJ: GMX: TRR with offset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReplicateCell CPPTRAJ: Scale dihedral force constant test CPPTRAJ: Replicate cell test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PhiPsi CPPTRAJ: Phipsi test All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Control All 1 comparisons passed. CPPTRAJ: Loop tests All 1 comparisons passed. CPPTRAJ: Scale dihedral force constant with 'useall' CPPTRAJ: Pairwise test, partial system ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_InfraredSpec All 5 comparisons passed. CPPTRAJ: Infrared spectrum calculation test 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. All 1 comparisons passed. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CmdLine ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cphstats CPPTRAJ: Command line trajectory args test, part 1 CPPTRAJ: Explicit pH REMD ensemble data read / sort ******************************************************************************** CPPTRAJ: Command line test trajectory args test, part 2 TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XYZformat CPPTRAJ: XTC read test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LibPME CPPTRAJ: XYZ format write CPPTRAJ: Particle mesh Ewald test (NaCl crystal) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hausdorff All 2 comparisons passed. CPPTRAJ: Simple Hausdorff distance test. All 10 comparisons passed. CPPTRAJ: Command line wildcard test, part 1 CPPTRAJ: Test set command CPPTRAJ: Atom XYZ format read, test 1 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CatCrd CPPTRAJ: Particle mesh Ewald test (trunc. oct) CPPTRAJ: Concatenate COORDS data set test CPPTRAJ: Command line wildcard test, part 2 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XtalSymm CPPTRAJ: XtalSymm Reference CPPTRAJ: Constant pH stats test CPPTRAJ: Hausdorff distance of 2D rms output test. CPPTRAJ: CRD => XTC CPPTRAJ: Test reading comma-separated list of strings All 2 comparisons passed. CPPTRAJ: Atom XYZ format read, test 2 All 1 comparisons passed. All 5 comparisons passed. CPPTRAJ: Sorted implicit constant pH stats test CPPTRAJ: Test nested loops and variables in loops ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihedralRMS ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Time CPPTRAJ: Atom XYZ format read, test 3 CPPTRAJ: Add time to restart test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SplitCoords CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) CPPTRAJ: SplitCoords test CPPTRAJ: XTC => CRD CPPTRAJ: Hausdorff distance of 2D rms output test. CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats CPPTRAJ: Test loop over data set blocks CPPTRAJ: Atom XYZ format read, test 4 CPPTRAJ: Remove time from restart test All 1 comparisons passed. CPPTRAJ: Dihedral RMSD test (to previous) CPPTRAJ: Add time to trajectory test CPPTRAJ: Atom XYZ format read, test 5 CPPTRAJ: Test for filename wildcards and oversets ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Slope CPPTRAJ: Finite difference test. CPPTRAJ: Unsorted pH read/write test CPPTRAJ: CRD(1-5) => XTC CPPTRAJ: Dihedral RMS fluctuation test. All 3 comparisons passed. CPPTRAJ: Atom XYZ format read, test 6 CPPTRAJ: XtalSymm Reimaging by Atom All 1 comparisons passed. All 13 comparisons passed. CPPTRAJ: Particle mesh Ewald test (ortho) CPPTRAJ: Modify time info test. All 16 comparisons passed. All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diagmatrix All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Emin CPPTRAJ: MW covariance matrix thermo analysis test CPPTRAJ: Basic energy minimization test. CPPTRAJ: CRD(6-10) => XTC ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau CPPTRAJ: Evalulate plateau test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Graft All 4 comparisons passed. CPPTRAJ: Graft test All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Flatten CPPTRAJ: Flatten test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Random CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs All 1 comparisons passed. CPPTRAJ: Energy minimization with angle term test. All 2 comparisons passed. CPPTRAJ: XTC (appended) => CRD CPPTRAJ: PCG32 RNG test. All 1 comparisons passed. CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. CPPTRAJ: Particle mesh Ewald test (ortho, with mask) CPPTRAJ: Test Stdlib RNG CPPTRAJ: Energy minimization with nonbond term test. CPPTRAJ: GMX: CRD with offset CPPTRAJ: Test Mersenne Twister RNG CPPTRAJ: PME test (partial system, trunc. oct) All 4 comparisons passed. CPPTRAJ: GMX: XTC with offset 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 (bonds) All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LJ_PME CPPTRAJ: LJ PME test. CPPTRAJ: OpenMM basic energy minimization tests (angles) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTNG CPPTRAJ: TNG read test CPPTRAJ: LJ PME kappa sweep test, 0.25 CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) CPPTRAJ: LJ PME kappa sweep test, 0.35 CPPTRAJ: LJ PME kappa sweep test, 0.45 CPPTRAJ: TNG read test (with offset) CPPTRAJ: LJ PME kappa sweep test, 0.5 CPPTRAJ: LJ with switch function test All 5 comparisons passed. All 6 comparisons passed. CPPTRAJ: XtalSymm Reimaging by Molecule CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) All 3 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. All 9 comparisons passed. ../MasterTest.sh: line 495: 273145 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 183513792 Apr 4 12:52 ../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/210217 and its subdirectories