I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 19 22:36:35 +14 2026 I: pbuilder-time-stamp: 1795077395 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-5.dsc] I: copying [./cpptraj_5.1.0+dfsg.orig.tar.xz] I: copying [./cpptraj_5.1.0+dfsg-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./cpptraj_5.1.0+dfsg-5.dsc: no acceptable signature found 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-5.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 dpkg-source: info: applying gcc-15.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2870230/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Nov 19 08:37 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2870230/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2870230/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=1c477f9be87842068ab13708fc56674c LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2870230 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.a9RXUbC0/pbuilderrc_HcIo --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.a9RXUbC0/b2 --logfile b2/build.log cpptraj_5.1.0+dfsg-5.dsc' SUDO_GID=111 SUDO_HOME=/var/lib/jenkins SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2870230/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: amd64 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 ... 19856 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-15{a} gfortran-15-x86-64-linux-gnu{a} gfortran-x86-64-linux-gnu{a} groff-base{a} hdf5-helpers{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-quad3{a} libfftw3-single3{a} libfile-stripnondeterminism-perl{a} libgfortran-15-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} 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} liblzma-dev{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-crypto-ossl0{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} libxml2-16{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 134 MB of archives. After unpacking 548 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.2-4 [98.5 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-2 [325 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-2 [877 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b3 [56.7 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 25 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.6+dfsg-0.1 [651 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.28 [941 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libgfortran-15-dev amd64 15.2.0-4 [886 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 gfortran-15-x86-64-linux-gnu amd64 15.2.0-4 [78.8 MB] Get: 36 http://deb.debian.org/debian unstable/main amd64 gfortran-15 amd64 15.2.0-4 [17.9 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 gfortran-x86-64-linux-gnu amd64 4:15.2.0-4 [1276 B] Get: 38 http://deb.debian.org/debian unstable/main amd64 gfortran amd64 4:15.2.0-4 [1436 B] Get: 39 http://deb.debian.org/debian unstable/main amd64 hdf5-helpers amd64 1.14.5+repack-4 [26.7 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 43 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.4-2 [23.8 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.4-2 [8108 B] Get: 52 http://deb.debian.org/debian unstable/main amd64 libaec-dev amd64 1.1.4-2 [21.5 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libarpack2t64 amd64 3.9.1-6 [104 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-7 [229 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.1-7 [5894 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libarpack2-dev amd64 3.9.1-6 [120 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.12.0-1 [68.4 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.16.0-1 [136 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.9-2 [443 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-10 [19.8 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-10 [57.8 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.16.0-1 [25.2 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.16.0-4 [400 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.24.0-2 [614 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.10-2 [458 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.10-2 [458 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-4 [103 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.9-2 [220 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-5 [330 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-5 [658 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.2-1 [1322 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.10-2 [1423 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.10+dfsg-1 [312 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1+b1 [117 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.12.0-1 [95.5 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.16.0-1 [25.2 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.16.0-1 [193 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-3 [67.9 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.5.4-1 [2980 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-2 [375 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.16.0-4 [522 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-ossl0 amd64 1.16.0-1 [27.5 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.16.0-4 [408 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libfftw3-double3 amd64 3.3.10-2+b1 [781 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libfftw3-long3 amd64 3.3.10-2+b1 [347 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libfftw3-quad3 amd64 3.3.10-2+b1 [618 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libfftw3-single3 amd64 3.3.10-2+b1 [809 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libfftw3-bin amd64 3.3.10-2+b1 [51.3 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libfftw3-dev amd64 3.3.10-2+b1 [2118 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libhdf5-310 amd64 1.14.5+repack-4 [1448 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libhdf5-cpp-310 amd64 1.14.5+repack-4 [146 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libhdf5-fortran-310 amd64 1.14.5+repack-4 [122 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-4 [72.6 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-fortran-310 amd64 1.14.5+repack-4 [47.9 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-cpp-310 amd64 1.14.5+repack-4 [24.9 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-4 [292 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-4 [72.2 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libhdf5-dev amd64 1.14.5+repack-4 [3327 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.8.1-2 [349 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5+20250216-2 [353 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libnetcdf22 amd64 1:4.9.3-1+b1 [517 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.14.6+dfsg-0.1 [756 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libnetcdf-dev amd64 1:4.9.3-1+b1 [116 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-12 [1052 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libopenmm-dev amd64 8.1.2+dfsg-12 [344 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libreadline-dev amd64 8.3-3 [175 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 netcdf-bin amd64 1:4.9.3-1+b1 [261 kB] Fetched 134 MB in 15s (9157 kB/s) Preconfiguring packages ... 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Unpacking libgnutls30t64:amd64 (3.8.10-2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../068-libsasl2-modules-db_2.1.28+dfsg1-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../069-libsasl2-2_2.1.28+dfsg1-10_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-10) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../070-libldap2_2.6.10+dfsg-1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../071-libnghttp2-14_1.64.0-1.1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:amd64. Preparing to unpack .../072-libngtcp2-crypto-gnutls8_1.16.0-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls8:amd64 (1.16.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../073-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../074-librtmp1_2.4+20151223.gitfa8646d.1-3_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../075-libssh2-1t64_1.11.1-1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. Preparing to unpack .../076-libcurl3t64-gnutls_8.16.0-4_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.16.0-4) ... Selecting previously unselected package libevent-2.1-7t64:amd64. Preparing to unpack .../077-libevent-2.1-7t64_2.1.12-stable-10+b1_amd64.deb ... Unpacking libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:amd64. 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libreadline-dev:amd64. Preparing to unpack .../131-libreadline-dev_8.3-3_amd64.deb ... Unpacking libreadline-dev:amd64 (8.3-3) ... Selecting previously unselected package netcdf-bin. Preparing to unpack .../132-netcdf-bin_1%3a4.9.3-1+b1_amd64.deb ... Unpacking netcdf-bin (1:4.9.3-1+b1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libkeyutils1:amd64 (1.6.3-6) ... Setting up libfftw3-single3:amd64 (3.3.10-2+b1) ... Setting up libzstd-dev:amd64 (1.5.7+dfsg-2) ... Setting up bsdextrautils (2.41.2-4) ... Setting up hdf5-helpers (1.14.5+repack-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.6+dfsg-0.1) ... Setting up libdebhelper-perl (13.28) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up libfftw3-long3:amd64 (3.3.10-2+b1) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-2) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libcom-err2:amd64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up libaec0:amd64 (1.1.4-2) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-10) ... Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libunbound8:amd64 (1.24.0-2) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-5) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-4) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-4) ... Setting up libncurses6:amd64 (6.5+20250216-2) ... Setting up libfftw3-quad3:amd64 (3.3.10-2+b1) ... Setting up comerr-dev:amd64 (2.1-1.47.2-3+b3) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up libssl-dev:amd64 (3.5.4-1) ... Setting up autopoint (0.23.1-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libfftw3-double3:amd64 (3.3.10-2+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-10) ... Setting up libgfortran5:amd64 (15.2.0-4) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.12.0-1) ... Setting up libnghttp3-dev:amd64 (1.12.0-1) ... Setting up liblzma-dev:amd64 (5.8.1-2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libngtcp2-16:amd64 (1.16.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up libopenmm8.1 (8.1.2+dfsg-12) ... Setting up readline-common (8.3-3) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libblas-dev:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libsz2:amd64 (1.1.4-2) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.18.1-2) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up liblapack3:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libncurses-dev:amd64 (6.5+20250216-2) ... Setting up gettext (0.23.1-2+b1) ... Setting up libarpack2t64:amd64 (3.9.1-6) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-5) ... Setting up nettle-dev:amd64 (3.10.2-1) ... Setting up libtool (2.5.4-5) ... Setting up libfftw3-bin (3.3.10-2+b1) ... Setting up libaec-dev:amd64 (1.1.4-2) ... Setting up libjpeg-dev:amd64 (1:2.1.5-4) ... Setting up libidn2-0:amd64 (2.3.8-4) ... Setting up libngtcp2-dev:amd64 (1.16.0-1) ... Setting up libgfortran-15-dev:amd64 (15.2.0-4) ... Setting up libopenmm-dev (8.1.2+dfsg-12) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libxml2-dev:amd64 (2.14.6+dfsg-0.1) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.9-2) ... Setting up liblapack-dev:amd64 (3.12.1-7) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libidn2-dev:amd64 (2.3.8-4) ... Setting up libngtcp2-crypto-ossl0:amd64 (1.16.0-1) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libfftw3-dev:amd64 (3.3.10-2+b1) ... Setting up libp11-kit-dev:amd64 (0.25.9-2) ... Setting up libgnutls30t64:amd64 (3.8.10-2) ... Setting up libgnutls-openssl27t64:amd64 (3.8.10-2) ... Setting up gfortran-15-x86-64-linux-gnu (15.2.0-4) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1+b1) ... Setting up libarpack2-dev:amd64 (3.9.1-6) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libreadline-dev:amd64 (8.3-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran-x86-64-linux-gnu (4:15.2.0-4) ... Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.10-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.16.0-1) ... Setting up gfortran-15 (15.2.0-4) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libgnutls28-dev:amd64 (3.8.10-2) ... Setting up libcurl4t64:amd64 (8.16.0-4) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up libcurl3t64-gnutls:amd64 (8.16.0-4) ... Setting up debhelper (13.28) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.16.0-1) ... Setting up gfortran (4:15.2.0-4) ... 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 librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libhdf5-310:amd64 (1.14.5+repack-4) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up libhdf5-fortran-310:amd64 (1.14.5+repack-4) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libhdf5-cpp-310:amd64 (1.14.5+repack-4) ... Setting up libhdf5-hl-310:amd64 (1.14.5+repack-4) ... Setting up libnetcdf22:amd64 (1:4.9.3-1+b1) ... Setting up netcdf-bin (1:4.9.3-1+b1) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up libhdf5-hl-cpp-310:amd64 (1.14.5+repack-4) ... Setting up libhdf5-hl-fortran-310:amd64 (1.14.5+repack-4) ... Setting up libcurl4-gnutls-dev:amd64 (8.16.0-4) ... Setting up libhdf5-dev (1.14.5+repack-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libnetcdf-dev (1:4.9.3-1+b1) ... Processing triggers for libc-bin (2.41-12) ... 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: user script /srv/workspace/pbuilder/2870230/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/2870230/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/cpptraj-5.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../cpptraj_5.1.0+dfsg-5_source.changes dpkg-buildpackage: info: source package cpptraj dpkg-buildpackage: info: source version 5.1.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Santiago Vila dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' touch config.h external.config.h dh_auto_clean make -j42 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/x86_64-linux-gnu --with-fftw3=/usr/lib/x86_64-linux-gnu --with-readline=/usr/lib/x86_64-linux-gnu --with-openmm=/usr/lib/x86_64-linux-gnu arpack specified: /usr/lib/x86_64-linux-gnu fftw3 specified: /usr/lib/x86_64-linux-gnu readline specified: /usr/lib/x86_64-linux-gnu openmm specified: /usr/lib/x86_64-linux-gnu Testing C++ compiler: OK Testing C compiler: OK Testing basic C++11 support: OK Testing system headers for C++11 support: OK Warning: Compilation of sanderlib requires AMBERHOME to be set Warning: if --with-sanderlib not specified. Checking BZLIB: OK Checking ZLIB: OK Checking NetCDF: OK Checking LAPACK/BLAS: OK Checking ARPACK: OK Checking FFTW3: OK Checking Readline: OK Checking OpenMM: OK vmdplugin disabled due to nonfree source. Configuration summary: Build type: Serial Options: netcdf bzlib tng zlib arpack lapack blas fftw3 readline xdrfile openmm Target platform: Linux, 64-bit. gnu compilers in use. C++11 support enabled. PME support enabled. Compiler optimizations are on. Cleaning source directory. -------------------------------------------------------------------------------- An environment resource file for CPPTRAJ has been created: /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 -j42 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 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 In file included from Ewald_ParticleMesh.h:5, from Action_Energy.cpp:4: helpme_standalone.h:2324: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2324 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:2344: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2344 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3015: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3015 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3121: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3121 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3248: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3248 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3702: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3702 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3740: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3740 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3803: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3803 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3841: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3841 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4045: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4045 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4053: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4053 | #pragma omp for helpme_standalone.h:4098: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4098 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4146: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4146 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4173: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4173 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4225: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4225 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4229: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4229 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4276: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4276 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4389: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4389 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4420: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4420 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4504: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4504 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4511: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4511 | #pragma omp for CXX Action_LESsplit.cpp CXX Action_LIE.cpp CXX Action_LipidOrder.cpp CXX Action_MakeStructure.cpp CXX Action_Mask.cpp CXX Action_Matrix.cpp CXX Action_MinImage.cpp CXX Action_Molsurf.cpp CXX Action_MultiDihedral.cpp CXX Action_MultiVector.cpp CXX Action_NAstruct.cpp CXX Action_NativeContacts.cpp CXX Action_NMRrst.cpp CXX Action_OrderParameter.cpp CXX Action_Outtraj.cpp CXX Action_PairDist.cpp CXX Action_Pairwise.cpp CXX Action_Principal.cpp CXX Action_Projection.cpp CXX Action_Pucker.cpp CXX Action_Radgyr.cpp CXX Action_Radial.cpp CXX Action_RandomizeIons.cpp CXX Action_Remap.cpp CXX Action_ReplicateCell.cpp CXX Action_Rmsd.cpp CXX Action_Rotate.cpp 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:76:57: 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: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:76:23: 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:76:57: 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]; | ^~~ 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 CXX Analysis_Matrix.cpp CXX Analysis_MeltCurve.cpp CXX Analysis_Modes.cpp CXX Analysis_Multicurve.cpp CXX Analysis_MultiHist.cpp CXX Analysis_Overlap.cpp CXX Analysis_PhiPsi.cpp CXX Analysis_Regression.cpp CXX Analysis_RemLog.cpp CXX Analysis_Rms2d.cpp CXX Analysis_RmsAvgCorr.cpp CXX Analysis_Rotdif.cpp CXX Analysis_RunningAvg.cpp CXX Analysis_Slope.cpp CXX Analysis_Spline.cpp CXX Analysis_State.cpp CXX Analysis_Statistics.cpp CXX Analysis_TI.cpp CXX Analysis_Timecorr.cpp CXX Analysis_VectorMath.cpp CXX Analysis_Wavelet.cpp CXX ArgList.cpp CXX Array1D.cpp CXX AssociatedData.cpp CXX Atom.cpp CXX AtomMap.cpp CXX AtomMask.cpp CXX AxisType.cpp CXX BondSearch.cpp CXX Box.cpp CXX BoxArgs.cpp CXX BufferedFrame.cpp CXX BufferedLine.cpp CXX ByteRoutines.cpp CXX CharMask.cpp CXX CharmmParamFile.cpp CXX CIFfile.cpp CXX ClusterDist.cpp CXX ClusterList.cpp CXX ClusterMap.cpp CXX ClusterMatrix.cpp CXX ClusterNode.cpp CXX ClusterSieve.cpp CXX Cluster_DBSCAN.cpp CXX Cluster_DPeaks.cpp CXX Cluster_HierAgglo.cpp CXX Cluster_Kmeans.cpp CXX Cluster_ReadInfo.cpp CXX Cmd.cpp CXX CmdInput.cpp CXX CmdList.cpp CXX CompactFrameArray.cpp CXX ComplexArray.cpp CXX Constraints.cpp CXX ControlBlock_For.cpp CXX CoordinateInfo.cpp CXX Corr.cpp CXX Cph.cpp CXX CpptrajFile.cpp CXX CpptrajState.cpp CXX CpptrajStdio.cpp CXX CurveFit.cpp CXX DataFile.cpp CXX DataFileList.cpp CXX DataFilter.cpp CXX DataIO.cpp CXX DataIO_CCP4.cpp CXX DataIO_CharmmFastRep.cpp CXX DataIO_CharmmOutput.cpp CXX DataIO_CharmmRepLog.cpp CXX DataIO_CharmmRtfPrm.cpp CXX DataIO_Cmatrix.cpp CXX DataIO_Cpout.cpp CXX DataIO_Evecs.cpp CXX DataIO_Gnuplot.cpp CXX DataIO_Grace.cpp CXX DataIO_OpenDx.cpp CXX DataIO_Peaks.cpp CXX DataIO_Mdout.cpp CXX DataIO_NC_Cmatrix.cpp CXX DataIO_RemLog.cpp CXX DataIO_Std.cpp CXX DataIO_VecTraj.cpp CXX DataIO_Xplor.cpp In file included from /usr/include/c++/15/vector:68, 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++/15/bits/stl_vector.h:876:23: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 876 | { _M_fill_assign(__n, __val); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/15/vector:74: /usr/include/c++/15/bits/vector.tcc: In member function 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)': /usr/include/c++/15/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++/15/bits/stl_vector.h:876:23: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 876 | { _M_fill_assign(__n, __val); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/15/bits/vector.tcc: In member function 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)': /usr/include/c++/15/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 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_Multi.cpp CXX EnsembleOut.cpp CXX EnsembleOut_Single.cpp CXX EnsembleOutList.cpp CXX Ewald.cpp CXX Ewald_ParticleMesh.cpp CXX Ewald_Regular.cpp In file included from Ewald_ParticleMesh.h:5, from Ewald_ParticleMesh.cpp:4: helpme_standalone.h:2324: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2324 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:2344: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2344 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3015: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3015 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3121: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3121 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3248: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3248 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3702: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3702 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3740: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3740 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3803: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3803 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3841: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3841 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4045: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4045 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4053: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4053 | #pragma omp for helpme_standalone.h:4098: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4098 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4146: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4146 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4173: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4173 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4225: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4225 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4229: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4229 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4276: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4276 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4389: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4389 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4420: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4420 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4504: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4504 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4511: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4511 | #pragma omp for CXX ExclusionArray.cpp CXX Exec_AddMissingRes.cpp CXX Exec_Analyze.cpp CXX Exec_Calc.cpp CXX Exec_CatCrd.cpp CXX Exec_Change.cpp CXX Exec_ClusterMap.cpp CXX Exec_CombineCoords.cpp CXX Exec_Commands.cpp CXX Exec_CompareTop.cpp CXX Exec_CrdAction.cpp CXX Exec_CrdOut.cpp CXX Exec_CreateSet.cpp CXX Exec_DataFile.cpp CXX Exec_DataFilter.cpp CXX Exec_DataSetCmd.cpp CXX Exec_Emin.cpp CXX Exec_Flatten.cpp CXX Exec_GenerateAmberRst.cpp CXX Exec_Graft.cpp CXX Exec_Help.cpp CXX Exec_LoadCrd.cpp helpme_standalone.h: In instantiation of 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]': helpme_standalone.h:3899:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3899 | 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:1011:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 1011 | for (int val = 0; val < nRows_; ++val) eigenPairs.push_back({eigenValues[val][0], unsortedEigenVectors[val]}); | ~~~~^~~~~~~~ helpme_standalone.h:1014:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 1014 | for (int val = 0; val < nRows_; ++val) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::PMEInstance >::sanityChecks(int, const RealMat&, const RealMat&, int) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h: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 | sanityChecks(parameterAngMom, parameters, coordinates); | ^~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3199:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3199 | 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:5020:9: 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]' 5020 | filterAtomsAndBuildSplineCache(parameterAngMom, coordinates); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3747:45: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3747 | for (size_t row = threadID; row < gridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~ helpme_standalone.h:3754:37: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3754 | for (int atom = 0; atom < nAtoms; ++atom) { | ~~~~~^~~~~~~~ helpme_standalone.h:3762:61: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3762 | if (cGridIterator.size() && thisAtomsThread == threadID) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~ helpme_standalone.h:3751:25: warning: unused variable 'gridIteratorC' [-Wunused-variable] 3751 | const auto &gridIteratorC = threadedGridIteratorC_[threadID]; | ^~~~~~~~~~~~~ helpme_standalone.h:3795:55: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3795 | for (int atom = splineCache_.size(); atom < newSize; ++atom) | ~~~~~^~~~~~~~~ helpme_standalone.h:3811:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3811 | 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:5021:25: 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]' 5021 | 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:3709:45: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3709 | 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:5024:32: 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]' 5024 | auto gridAddress = forwardTransform(realGrid); | ^~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:4005:28: warning: variable 'realCBA' set but not used [-Wunused-but-set-variable] 4005 | Real *__restrict__ realCBA; | ^~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::Matrix::assertSymmetric(const Real&) const [with Real = double]': helpme_standalone.h:1001:9: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 1001 | assertSymmetric(); | ^~~~~~~~~~~~~~~ helpme_standalone.h:3899:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3899 | 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:797:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 797 | 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:1007:42: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 1007 | JacobiCyclicDiagonalization(eigenValues[0], unsortedEigenVectors[0], cbegin(), nRows_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3899:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3899 | 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:214:20: warning: variable 'cos_2phi' set but not used [-Wunused-but-set-variable] 214 | 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:786:26: required from 'helpme::Matrix helpme::Matrix::inverse() const [with Real = double]' 786 | return this->applyOperation([](Real& element) { element = 1 / element; }); | ~~~~~~^~~~~~~~~~~~~~ helpme_standalone.h:3911:44: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3911 | 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:825:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 825 | 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:3830:47: required from 'void helpme::PMEInstance >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 3830 | atomSplines.aSpline.update(aStartingGridPoint, gridDimensionA_ * aCoord - aStartingGridPoint, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3831 | splineOrder_, splineDerivativeLevel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:5020:9: 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]' 5020 | filterAtomsAndBuildSplineCache(parameterAngMom, coordinates); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:2209:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 2209 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:2209:72: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2209 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~ CXX Exec_LoadTraj.cpp helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::multiply(const helpme::Matrix&) const [with Real = double]': helpme_standalone.h:878:64: required from 'helpme::Matrix helpme::Matrix::operator*(const helpme::Matrix&) const [with Real = double]' 878 | Matrix operator*(const Matrix& other) const { return this->multiply(other); } | ~~~~~~^~~~~~~~ helpme_standalone.h:830:22: required from 'helpme::Matrix helpme::Matrix::applyOperation(const std::function&) const [with Real = double]' 830 | return evecs * evecsT; | ~~~~~~^~~~~~~~ helpme_standalone.h:786:26: required from 'helpme::Matrix helpme::Matrix::inverse() const [with Real = double]' 786 | return this->applyOperation([](Real& element) { element = 1 / element; }); | ~~~~~~^~~~~~~~~~~~~~ helpme_standalone.h:3911:44: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3911 | 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:861:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 861 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h:863:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 863 | for (int col = 0; col < other.nCols_; ++col) { | ~~~~^~~~~~~~~~~~~~ helpme_standalone.h:864:41: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 864 | for (int link = 0; link < nCols_; ++link) { | ~~~~~^~~~~~~~ CXX Exec_ParallelAnalysis.cpp CXX Exec_ParmBox.cpp CXX Exec_ParmSolvent.cpp CXX Exec_ParmStrip.cpp CXX Exec_ParmWrite.cpp CXX Exec_PermuteDihedrals.cpp CXX Exec_Precision.cpp CXX Exec_PrepareForLeap.cpp CXX Exec_PrintData.cpp CXX Exec_Random.cpp CXX Exec_ReadData.cpp CXX Exec_ReadEnsembleData.cpp CXX Exec_ReadInput.cpp CXX Exec_RotateDihedral.cpp CXX Exec_RunAnalysis.cpp CXX Exec_ScaleDihedralK.cpp CXX Exec_Set.cpp CXX Exec_SequenceAlign.cpp CXX Exec_Show.cpp CXX Exec_SortEnsembleData.cpp CXX Exec_SplitCoords.cpp CXX Exec_System.cpp CXX Exec_Top.cpp CXX Exec_Traj.cpp CXX Exec_UpdateParameters.cpp CXX Exec_ViewRst.cpp CXX File_TempName.cpp CXX FileIO_Bzip2.cpp CXX FileIO_Gzip.cpp CXX FileIO_Mpi.cpp CXX FileIO_MpiShared.cpp CXX FileIO_Std.cpp CXX FileName.cpp CXX FileType.cpp CXX FileTypes.cpp CXX ForLoop.cpp CXX ForLoop_dataSetBlocks.cpp CXX ForLoop_integer.cpp CXX ForLoop_list.cpp CXX ForLoop_mask.cpp CXX ForLoop_overSets.cpp CXX Frame.cpp CXX GridAction.cpp CXX HistBin.cpp CXX Hungarian.cpp CXX ImageRoutines.cpp CXX Image_List_Mask.cpp CXX Image_List_Pair.cpp CXX Image_List_Unit.cpp CXX InputTrajCommon.cpp CXX KDE.cpp CXX MapAtom.cpp CXX MaskArray.cpp CXX MaskToken.cpp CXX Matrix_3x3.cpp CXX MdOpts.cpp CXX MetaData.cpp CXX Minimize_SteepestDescent.cpp CXX Mol.cpp CXX Mol2File.cpp CXX NameType.cpp CXX NC_Cmatrix.cpp CXX NC_Routines.cpp CXX NetcdfFile.cpp CXX OMM_helpers.cpp CXX OutputTrajCommon.cpp CXX ParameterSet.cpp CXX PDBfile.cpp CXX PairList.cpp CXX Parallel.cpp CXX ParallelNetcdf.cpp CXX ParmFile.cpp CXX Parm_Amber.cpp CXX Parm_CharmmPsf.cpp CXX Parm_CIF.cpp CXX Parm_Gromacs.cpp CXX Parm_Mol2.cpp CXX Parm_PDB.cpp CXX Parm_SDF.cpp CXX Parm_Tinker.cpp CXX PotentialFunction.cpp CXX PotentialTerm.cpp CXX PotentialTerm_Angle.cpp CXX PotentialTerm_Bond.cpp CXX PotentialTerm_Dihedral.cpp CXX PotentialTerm_LJ_Coulomb.cpp CXX PotentialTerm_OpenMM.cpp CXX ProgressBar.cpp CXX ProgressTimer.cpp CXX PubFFT.cpp CXX ExternalFxn.cpp CXX Random.cpp CXX Range.cpp CXX RNG.cpp CXX RNG_Marsaglia.cpp CXX RNG_MersenneTwister.cpp CXX RNG_PCG32.cpp CXX RNG_Stdlib.cpp CXX RNG_Xoshiro128pp.cpp CXX RPNcalc.cpp CXX ReferenceAction.cpp CXX RemdReservoirNC.cpp CXX Residue.cpp CXX SDFfile.cpp CXX SimplexMin.cpp CXX Spline.cpp CXX SplineFxnTable.cpp CXX StringRoutines.cpp CXX StructureCheck.cpp CXX StructureMapper.cpp CXX SymmetricRmsdCalc.cpp CXX TextFormat.cpp CXX Timer.cpp CXX TinkerFile.cpp CXX TopInfo.cpp CXX Topology.cpp CXX TorsionRoutines.cpp CXX Traj_AmberCoord.cpp CXX Traj_AmberNetcdf.cpp CXX Traj_AmberRestart.cpp CXX Traj_AmberRestartNC.cpp CXX Traj_Binpos.cpp CXX Traj_CharmmCor.cpp CXX Traj_CharmmDcd.cpp CXX Traj_CharmmRestart.cpp CXX Traj_CIF.cpp CXX Traj_Conflib.cpp CXX Traj_DTR.cpp CXX Traj_GmxDump.cpp CXX Traj_GmxTng.cpp CXX Traj_GmxTrX.cpp CXX Traj_GmxXtc.cpp CXX Traj_Gro.cpp CXX Traj_Mol2File.cpp CXX Traj_NcEnsemble.cpp CXX Traj_PDBfile.cpp CXX Traj_SDF.cpp 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:3471:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3471 | fftHelperA_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3471:31: note: '' declared here 3471 | fftHelperA_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3472:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3472 | fftHelperB_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3472:31: note: '' declared here 3472 | fftHelperB_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3473:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3473 | fftHelperC_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3473:31: note: '' declared here 3473 | 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:3504:43: helpme_standalone.h:520:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] 520 | 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 | 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:3505:43: helpme_standalone.h:520:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] 520 | 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 | 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:3506:43: helpme_standalone.h:520:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] 520 | 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:3506:45: note: '' declared here 3506 | compressionCoefficientsC_ = RealMat(); | ^~~~~~~~~ CXX Traj_SQM.cpp CXX Traj_Tinker.cpp CXX Traj_XYZ.cpp CXX TrajectoryFile.cpp CXX TrajectoryIO.cpp CXX TrajFrameCounter.cpp CXX TrajinList.cpp CXX Trajin_Multi.cpp CXX Trajin_Single.cpp CXX TrajIOarray.cpp CXX Trajout_Single.cpp CXX TrajoutList.cpp CXX Vec3.cpp CXX ViewRst.cpp CXX xoshiro128plusplus.cpp CXX Action_Esander.cpp xoshiro128plusplus.cpp: In function 'void jump()': xoshiro128plusplus.cpp:60:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 60 | for(int i = 0; i < sizeof JUMP / sizeof *JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ xoshiro128plusplus.cpp: In function 'void long_jump()': xoshiro128plusplus.cpp:90:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 90 | for(int i = 0; i < sizeof LONG_JUMP / sizeof *LONG_JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CXX Command.cpp CXX Cpptraj.cpp CXX Energy_Sander.cpp CXX ReadLine.cpp CXX main.cpp CC molsurf.c Skipping bundled READLINE build cd xdrfile && make all make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' CC xdrfile.c CC xdr_seek.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 xdrfile_trr.c CC tng_io.c CC xdrfile_xtc.c CC tng_compress.c CC coder.c CC warnmalloc.c CC fixpoint.c CC xtc3.c CC bwlzh.c CC xtc2.c CC widemuldiv.c CC huffmem.c CC vals16.c CC bwt.c CC mtf.c CC rle.c CC lz77.c CC dict.c CC huffman.c 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:5032:16: warning: 'energy' may be used uninitialized [-Wmaybe-uninitialized] 5032 | return energy; | ^~~~~~ helpme_standalone.h:5022:14: note: 'energy' was declared here 5022 | Real energy; | ^~~~~~ CC merge_sort.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' 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/x86_64-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/x86_64-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/x86_64-linux-gnu/lib -lfftw3 -L/usr/lib/x86_64-linux-gnu/lib -lOpenMM -lnetcdf -lbz2 tng/libtng_io.a -lz xdrfile/libxdrfile.a -Wl,-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 -j42 test TESTSUITEFLAGS="-j42 --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/ArgList TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType 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 -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp CPPTRAJ: ArgList class unit test. g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' 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 -fcf-protection -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++ -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 pbuilder2 pbuilder2 184920736 Nov 19 08:41 ../bin/cpptraj make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' -rwxr-xr-x 1 pbuilder2 pbuilder2 184920736 Nov 19 08:41 ../bin/cpptraj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_General ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Strip CPPTRAJ: One frame strip command test CPPTRAJ: General tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_trajout_framerange ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RemdTraj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TrajinOffset CPPTRAJ: Trajout Frame Range [Amber Restart] ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DSSP ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj CPPTRAJ: CRD Replica Trajectory Run with offset CPPTRAJ: Normal trajectory read with offsets. CPPTRAJ: Broken Traj: Running good trajectory. CPPTRAJ: Secstruct (DSSP) command test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Center ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Image ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hbond CPPTRAJ: Orthorhombic imaged distance test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD CPPTRAJ: Center command test. CPPTRAJ: Per-Residue RMSD Test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mask CPPTRAJ: Surface calculation test CPPTRAJ: Solute Hbond test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radgyr ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NCrestart CPPTRAJ: Radius of gyration command test CPPTRAJ: Mask single frame test CPPTRAJ: NetCDF Restart Test - TXT->NetCDF ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Jcoupling CPPTRAJ: J-Coupling single frame test ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diffusion TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm CPPTRAJ: Diffusion test, no imaging. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj CPPTRAJ: CHARMM PSF/DCD test CPPTRAJ: RMSD Test with outtraj. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotdif ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj CPPTRAJ: Rotational diffusion calculation test CPPTRAJ: Convert mdcrd -> NetCDF ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pucker ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RMSD ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomMap ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Average ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_2DRMS TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Runavg ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct CPPTRAJ: Basic RMSD tests CPPTRAJ: 2D RMSD Test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mol2 CPPTRAJ: Gzipped trajectory read with offsets CPPTRAJ: Pucker command test CPPTRAJ: AtomMap Test CPPTRAJ: Average Test. CPPTRAJ: NAstruct command test. CPPTRAJ: Coordinate Running Average test. CPPTRAJ: Mol2 Parm/Traj Read/Write Test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Datafile CPPTRAJ: Data file output precision test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DRMSD CPPTRAJ: CRD Replica Trajectory Run CPPTRAJ: Distance RMSD test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist CPPTRAJ: Cluster command test, in-memory pairwise distances. ******************************************************************************** CPPTRAJ: Closest command test using first solvent atom. TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial CPPTRAJ: Non-orthorhombic imaged distance test. CPPTRAJ: Radial test, non-orthogonal imaging CPPTRAJ: 1D/2D Histogram Analysis test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_IRED CPPTRAJ: Trajout Frame Range [Amber Coordinates] CPPTRAJ: NetCDF Restart Test - NetCDF->TXT CPPTRAJ: IRED vector/matrix test CPPTRAJ: Broken Traj: Running broken trajectory. 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: Secstruct (DSSP) command test, Ptraj Format. CPPTRAJ: Unstrip (Lig/Rec/Complex) command test CPPTRAJ: Per-Residue RMSD Test with averaging CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons CPPTRAJ: CHARMM DCD Write, step 1. CPPTRAJ: randomizeions test (original algorithm) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Molsurf CPPTRAJ: 2D RMSD Test, mass-weighted. CPPTRAJ: Solute Hbond test with disk caching CPPTRAJ: Bzip2ed trajectory read with offsets CPPTRAJ: Molsurf test CPPTRAJ: Coordinate Running Average Traj Write CPPTRAJ: Center origin command test. All 2 comparisons passed. CPPTRAJ: NetCDF Replica Trajectory Run test All 4 comparisons passed. All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Corr CPPTRAJ: RMS coordinate rotation/rotation matrices test CPPTRAJ: Diffusion test, old syntax. CPPTRAJ: Correlation test CPPTRAJ: Mask longer command test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckStructure CPPTRAJ: Structure Check CPPTRAJ: AtomMap with 'rmsfit' CPPTRAJ: PDB => Mol2 CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Contacts CPPTRAJ: Standard -> Grace Data ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RmsAvgCorr CPPTRAJ: Orthorhombic coordinate imaging test CPPTRAJ: Contacts test. CPPTRAJ: Secstruct (DSSP) command with changing number of residues. CPPTRAJ: RmsAvgCorr Reference CPPTRAJ: Cluster command test, read pairwise distances. CPPTRAJ: CHARMM DCD Write, step 2. CPPTRAJ: Start argument offset All 1 comparisons passed. All 2 comparisons passed. CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj CPPTRAJ: Per-Residue RMSD Test with residue centering. CPPTRAJ: 2D RMSD Test with reference trajectory All 2 comparisons passed. CPPTRAJ: Solute-solvent hbond test CPPTRAJ: Center origin mass command test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Principal CPPTRAJ: Closest command test using all solvent atoms. All 3 comparisons passed. CPPTRAJ: Principal Test CPPTRAJ: NAstruct command test, single strand CPPTRAJ: Amber Top/Rst => Mol2 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ClusterDihedral ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Vector CPPTRAJ: Structure Check with Around and Skip CPPTRAJ: 3D histogram test. CPPTRAJ: Basic vector tests CPPTRAJ: Atom map charmm->amber atom order CPPTRAJ: clusterdihedral test CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Matrix CPPTRAJ: RMS fit with no coordinates modification test. All 5 comparisons passed. CPPTRAJ: Matrix Tests CPPTRAJ: Secstruct (DSSP): SS assign output test CPPTRAJ: CHAMBER topology read/strip test. CPPTRAJ: Cluster command test, read NetCDF pairwise distances. CPPTRAJ: Grace -> Standard Data CPPTRAJ: Convert NetCDF -> mdcrd CPPTRAJ: Multi frame strip command test. All 3 comparisons passed. All 7 comparisons passed. ******************************************************************************** CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct CPPTRAJ: RmsAvgCorr First ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Grid CPPTRAJ: 2D DME Test. CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. CPPTRAJ: Center reference command test. CPPTRAJ: Dipole test All 11 comparisons passed. CPPTRAJ: Nonorthorhombic coordinate imaging test Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. Skipped test: Amber Top/Rst => Mol2, SYBYL atom types All 4 comparisons passed. ******************************************************************************** 1 comparisons skipped. TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Project CPPTRAJ: Projection All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Unwrap CPPTRAJ: Diffusion test, new syntax. CPPTRAJ: Atom map charmm->amber atom order, by residue CPPTRAJ: Unwrap non-orthogonal test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct_8OG CPPTRAJ: Hbond, no intramolecular hydrogen bonds test All 3 comparisons passed. CPPTRAJ: NA test (8OG) CPPTRAJ: Read CHARMM restart CPPTRAJ: Strip topology with PDB info ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes CPPTRAJ: Modes analysis, RMS fluctuations CPPTRAJ: 2D RMSD with reference mask test. CPPTRAJ: Compressed broken trajectory test CPPTRAJ: Cluster command test, write ASCII pairwise distances. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Watershell CPPTRAJ: Watershell Test, non-orthorhombic imaging. CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj CPPTRAJ: X column format/precision test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AnalysisRunAvg CPPTRAJ: FtuFabI Assignment test CPPTRAJ: Analysis Running Average CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. All 3 comparisons passed. All 1 comparisons passed. All 2 comparisons passed. CPPTRAJ: Test vector center with magnitude All 9 comparisons passed. CPPTRAJ: 2D RMSD test, no fitting. CPPTRAJ: CHARMM PSF write ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volmap All 11 comparisons passed. CPPTRAJ: VMD VolMap Algorithm test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SPAM CPPTRAJ: Center point test. CPPTRAJ: SPAM Test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LIE CPPTRAJ: Modes analysis, displacements CPPTRAJ: LIE test CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj CPPTRAJ: Cluster command test, read ASCII pairwise distances. CPPTRAJ: Grid test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidOrder ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Density CPPTRAJ: Lipid Order Parameter Test. CPPTRAJ: Density along axis tests CPPTRAJ: Diffusion test, nonorthogonal box All 2 comparisons passed. CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar All 3 comparisons passed. CPPTRAJ: CHARMM COORdinates test All 2 comparisons passed. CPPTRAJ: Unwrap orthogonal test CPPTRAJ: Data file group by name test CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. All 6 comparisons passed. CPPTRAJ: RMS fit to previous test All 5 comparisons passed. CPPTRAJ: Momentum/velocity vector test. CPPTRAJ: Hbond, specified solute masks ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PairDist CPPTRAJ: PairDist Test. ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_systemVF CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test CPPTRAJ: GIST water-water interaction test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReadData ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicCorr CPPTRAJ: Atomic Correlation test CPPTRAJ: Read vector data test (no origins, origins) CPPTRAJ: Modes analysis, dipole correlation CPPTRAJ: CRD Replica Trajectory Run with remdout All 10 comparisons passed. All 6 comparisons passed. CPPTRAJ: Closest command test, using mask center All 9 comparisons passed. CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. CPPTRAJ: RMS: imaging after unit cell rotation 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_CharmmParams CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM CPPTRAJ: Test updating topology with Charmm parameters (single residue) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr CPPTRAJ: AutoCorr test. CPPTRAJ: Force vector test. CPPTRAJ: STFC Diffusion Test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve CPPTRAJ: Cluster, nosieve CPPTRAJ: Hbond, no angle cutoff test All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Box CPPTRAJ: OpenDX Grid read test CPPTRAJ: Read vector data set (origins, no origins) CPPTRAJ: Box Test (Add box info) CPPTRAJ: Data file group by aspect test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomTypeSelect CPPTRAJ: Selection by atom type test. All 1 comparisons passed. CPPTRAJ: Atomicfluct test with ADP output CPPTRAJ: Structure Check with PBC All 12 comparisons passed. All 8 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AvgRef CPPTRAJ: RMSD Test with averaged reference coordinates. All 2 comparisons passed. CPPTRAJ: Read Amber output test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Crank_Stat CPPTRAJ: Crankshaft test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateCrd CPPTRAJ: Hbond, Bridge nointramol test CPPTRAJ: COORDS data set creation and CRDFLUCT test. CPPTRAJ: Box test (remove box info) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoImage All 1 comparisons passed. All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LoadCrd All 15 comparisons passed. CPPTRAJ: AutoImage test (split DNA duplex) CPPTRAJ: LoadCrd test. CPPTRAJ: STFC Diffusion Test with individual distances CPPTRAJ: Closest command test, using mask center and solvent mask CPPTRAJ: Cluster, sieve5 All 14 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Parallel CPPTRAJ: Modes analysis, pseudo trajectory creation test CPPTRAJ: Parallel tests. CPPTRAJ: Read CHARMM output test CPPTRAJ: Box test (Modify box length) CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. CPPTRAJ: Pairdist test, orthogonal imaging. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Lifetime ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MultiVector CPPTRAJ: Lifetime test. CPPTRAJ: Multivector test CPPTRAJ: Grid with specified center test. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Timecorr CPPTRAJ: Timecorr test. All 6 comparisons passed. CPPTRAJ: COORDS data set creation with velocities test CPPTRAJ: LoadTraj test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FFT CPPTRAJ: FFT test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SymmRmsd CPPTRAJ: SymmRmsd ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CrossCorr CPPTRAJ: CrossCorr test CPPTRAJ: 3D data read/write test All 6 comparisons passed. All 1 comparisons passed. CPPTRAJ: Multi-frame density along axis test All 1 comparisons passed. CPPTRAJ: Outtraj Test with maxmin. All 13 comparisons passed. CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test CPPTRAJ: Parallel test with trajectory offset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidSCD CPPTRAJ: Box test (auto orthogonal box, no radii) CPPTRAJ: ASP symmetry-corrected RMSD test CPPTRAJ: STFC Diffusion Test with COM CPPTRAJ: Basic lipid order parameter test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ensemble_MREMD CPPTRAJ: Closest command test, solvent mask, water oxygen only ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multidihedral CPPTRAJ: Standard 3D data write test CPPTRAJ: Generate matrix with trajectory start/stop/offset CPPTRAJ: M-REMD sort test. CPPTRAJ: LoadTraj from trajin test. CPPTRAJ: Multidihedral test CPPTRAJ: SPAM Pure Solvent Test All 7 comparisons passed. All 1 comparisons passed. CPPTRAJ: Partial Surface calculation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MakeStructure CPPTRAJ: Cluster, nosieve savepairdist CPPTRAJ: Basic makestructure test CPPTRAJ: Lifetime test with data set caching. CPPTRAJ: Grid with box center offset test. CPPTRAJ: GLU symmetry-corrected RMSD test CPPTRAJ: Box test (auto orthogonal box, VDW radii) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Integrate ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotate CPPTRAJ: Integration test. CPPTRAJ: Rotation (and inverse) of coords from matrices All 6 comparisons passed. All 5 comparisons passed. CPPTRAJ: STFC Diffusion Test with second mask CPPTRAJ: Generate matrix with action stop/start/offset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckChiral ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts CPPTRAJ: Check chirality test CPPTRAJ: Standard 3D data read test CPPTRAJ: NativeContacts test. CPPTRAJ: LoadCrd append from multiple files test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Energy CPPTRAJ: Simple energy tests All 1 comparisons passed. All 7 comparisons passed. CPPTRAJ: TYR symmetry-corrected RMSD test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LESsplit CPPTRAJ: LES split/average test CPPTRAJ: Multidihedral Nucleotide CHI test All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PermuteDihedrals CPPTRAJ: PermuteDihedrals interval -120, phi psi All 15 comparisons passed. CPPTRAJ: Radial test, orthogonal and no imaging ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CCP4 CPPTRAJ: Makestructure test with reference. All 2 comparisons passed. CPPTRAJ: CCP4 read/write and DX conversion test. All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihCovar All 1 comparisons passed. CPPTRAJ: Grid with mask center offset test. CPPTRAJ: M-REMD actions test. CPPTRAJ: Total system density test CPPTRAJ: Standard 3D data read/append test CPPTRAJ: Lifetime average and cumulative average test. CPPTRAJ: Cluster, nosieve loadpairdist CPPTRAJ: TRAJ data set creation and CRDFLUCT test. CPPTRAJ: Dihedral Covariance Matrix Test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CurveFit CPPTRAJ: Multidihedral protein dihedrals test CPPTRAJ: Curve fitting test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetAverage CPPTRAJ: Data set averaging and averaging over all sets test. CPPTRAJ: Rotate with defined axis ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VectorMath CPPTRAJ: Vector dot/cross product test All 7 comparisons passed. CPPTRAJ: Longer symmetry-corrected RMSD test. All 9 comparisons passed. All 5 comparisons passed. ******************************************************************************** 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 12 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Temperature CPPTRAJ: Temperature test. CPPTRAJ: TRAJ data set creation with velocities test. CPPTRAJ: New Lipid Order Parameter Test, DOPC. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander_Short Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. SKIP: Energy via sander API short tests (GB/PME) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_KDE ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Spline CPPTRAJ: KDE test. CPPTRAJ: PermuteDihedrals, random rotations All 2 comparisons passed. CPPTRAJ: Spline test All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CIF CPPTRAJ: Standard 3D data, sparse ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Wavelet CPPTRAJ: Multidihedral cyclic molecule test CPPTRAJ: M-REMD ensemble outtraj test. CPPTRAJ: Wavelet analysis test ******************************************************************************** All 8 comparisons passed. TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Align CPPTRAJ: CIF read test CPPTRAJ: Align Tests. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PDB CPPTRAJ: PDB format read/write test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelocityAutoCorr All 2 comparisons passed. CPPTRAJ: Velocity autocorrelation test CPPTRAJ: Temperature with SHAKE on hydrogens. CPPTRAJ: Curve fitting multi-exponential tests. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelFrc CPPTRAJ: Test combining coordinates, velocities, and forces. All 3 comparisons passed. CPPTRAJ: Cluster, sieve5 savepairdist All 7 comparisons passed. CPPTRAJ: Non-orthogonal grid test. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetCmd ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RotateDihedral ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remap All 6 comparisons passed. CPPTRAJ: Rotate dihedral to target value. CPPTRAJ: Remap Test CPPTRAJ: Data Set commands test CPPTRAJ: Test using velocities as coordinates. CPPTRAJ: M-REMD no sort, running average test All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CompareTop CPPTRAJ: Compare topology test CPPTRAJ: Temperature with SHAKE on all atoms. CPPTRAJ: Nonorthogonal grid standard write/read tests. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Filter CPPTRAJ: Basic filter test CPPTRAJ: COORDS data set append test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CombineCrd CPPTRAJ: Combine COORDS test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TopInfo CPPTRAJ: Topology info print test. CPPTRAJ: Test writing velocities (MDVEL) All 1 comparisons passed. CPPTRAJ: Temperature calc with extra points. CPPTRAJ: Align, unit cell rotation/imaging test. CPPTRAJ: M-REMD, generate RMS data CPPTRAJ: Rotate dihedral by increment ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTrr CPPTRAJ: COORDS test storing frame metadata CPPTRAJ: TRR force/velocity read -> NetCDF write test CPPTRAJ: Test kinetic energy calculation All 1 comparisons passed. All 4 comparisons passed. CPPTRAJ: Combine COORDS test with box info. All 10 comparisons passed. All 3 comparisons passed. CPPTRAJ: NativeContacts test, save non-native contacts, residue time series ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds All 16 comparisons passed. CPPTRAJ: Curve fitting, custom output range. CPPTRAJ: Test using forces as coordinates. CPPTRAJ: Fix imaged bonds test (Ortho.) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TI CPPTRAJ: AutoImage test, use anchor mask CPPTRAJ: TI analysis test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Distance CPPTRAJ: M-REMD, meltcurve analysis ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ewald CPPTRAJ: Distance tests CPPTRAJ: Direct sum test CPPTRAJ: Rotate dihedral in TRAJ data set ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volume CPPTRAJ: Randomize (around, overlap) CPPTRAJ: Volume tests CPPTRAJ: Wavelet WAFEX test CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test CPPTRAJ: PQR file write with various radii CPPTRAJ: Cluster, sieve5 loadpairdist CPPTRAJ: LCPO test with GAFF atom types CPPTRAJ: Data filter test. All 1 comparisons passed. CPPTRAJ: KDE with Kullback-Leibler divergence test All 17 comparisons passed. All 6 comparisons passed. CPPTRAJ: Test writing forces (MDFRC) CPPTRAJ: Generate offset traj from PDB All 5 comparisons passed. CPPTRAJ: NativeContacts test, orthorhombic imaging. CPPTRAJ: Orthogonal imaged distance ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SetVelocity CPPTRAJ: Set Velocity test All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remlog CPPTRAJ: TRAJ test storing frame metadata CPPTRAJ: Test total energy calculation ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AreaPerMol CPPTRAJ: Replica log read/analyze test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multicurve CPPTRAJ: Area per molecule test CPPTRAJ: Multicurve test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DistBasedMask CPPTRAJ: Distance-based atom mask tests (atom, residue) All 3 comparisons passed. CPPTRAJ: PDB filter alternate atom location IDs test CPPTRAJ: Fix imaged bonds test (Non-ortho.) CPPTRAJ: Generate offset traj from CIF CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. All 2 comparisons passed. CPPTRAJ: Scale velocity test CPPTRAJ: Split coords and recombine test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Calc CPPTRAJ: Filter matrix test. CPPTRAJ: Non-orthogonal imaged distance CPPTRAJ: Calc test All 4 comparisons passed. All 5 comparisons passed. All 1 comparisons passed. CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CalcState ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateReservoir CPPTRAJ: Cluster, nosieve pairwisecache none CPPTRAJ: Test partial energy calculation CPPTRAJ: Calcstate test CPPTRAJ: Create RREMD NetCDF reservoir test CPPTRAJ: Grid generation from 'bounds' test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Change All 7 comparisons passed. All 1 comparisons passed. CPPTRAJ: Change atom and residue name tests CPPTRAJ: Distance-based atom mask tests (molecule) All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LowestCurve All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixAtomOrder CPPTRAJ: LowestCurve test CPPTRAJ: Out of order molecules test CPPTRAJ: TRR force/velocity read -> TRR write test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Regress CPPTRAJ: Linear regression test. CPPTRAJ: Calc test with data sets ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MinImage ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pairwise CPPTRAJ: Minimum Image test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rst CPPTRAJ: Pairwise tests CPPTRAJ: Generate restraints (rst) test CPPTRAJ: Adding PDB info to topology All 5 comparisons passed. All 2 comparisons passed. All 3 comparisons passed. CPPTRAJ: Change chain ID test CPPTRAJ: Hbond with imaging ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Solvent CPPTRAJ: Test solvent command with closest ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ParmBox All 2 comparisons passed. CPPTRAJ: Test math functions All 4 comparisons passed. CPPTRAJ: Parmbox test All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Translate CPPTRAJ: CRD => TRR CPPTRAJ: Translate test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ScaleDihedralK CPPTRAJ: Scale dihedral force constant test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReplicateCell CPPTRAJ: Replicate cell test All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PhiPsi CPPTRAJ: Topology info with reference coords test All 10 comparisons passed. CPPTRAJ: Phipsi test All 2 comparisons passed. All 1 comparisons passed. All 4 comparisons passed. CPPTRAJ: Change chain ID of COORDS set test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Control CPPTRAJ: Loop tests All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_InfraredSpec CPPTRAJ: Pairwise test, partial system CPPTRAJ: Infrared spectrum calculation test All 1 comparisons passed. All 5 comparisons passed. CPPTRAJ: Hbond, orthogonal imaging CPPTRAJ: Scale dihedral force constant with 'useall' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XYZformat ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CmdLine All 1 comparisons passed. CPPTRAJ: Command line trajectory args test, part 1 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cphstats All 1 comparisons passed. CPPTRAJ: XYZ format write ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hausdorff All 1 comparisons passed. CPPTRAJ: Explicit pH REMD ensemble data read / sort CPPTRAJ: Simple Hausdorff distance test. All 6 comparisons passed. All 13 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SplitCoords ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XtalSymm ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CatCrd All 1 comparisons passed. CPPTRAJ: SplitCoords test CPPTRAJ: XtalSymm Reference All 3 comparisons passed. CPPTRAJ: Concatenate COORDS data set test All 12 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihedralRMS All 2 comparisons passed. CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Time CPPTRAJ: Add time to restart test CPPTRAJ: Structure Check with Around ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Slope All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diagmatrix CPPTRAJ: Finite difference test. CPPTRAJ: TRR => CRD CPPTRAJ: MW covariance matrix thermo analysis test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Emin CPPTRAJ: Command line test trajectory args test, part 2 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau CPPTRAJ: Basic energy minimization test. CPPTRAJ: Evalulate plateau test ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Graft TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Flatten CPPTRAJ: Graft test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Random CPPTRAJ: Flatten test. All 17 comparisons passed. CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs CPPTRAJ: Test set command CPPTRAJ: Cluster, sieve5 pairwisecache none CPPTRAJ: Hausdorff distance of 2D rms output test. CPPTRAJ: Atom XYZ format read, test 1 All 10 comparisons passed. All 1 comparisons passed. All 1 comparisons passed. CPPTRAJ: Remove time from restart test All 23 comparisons passed. All 1 comparisons passed. CPPTRAJ: Constant pH stats test All 1 comparisons passed. All 1 comparisons passed. CPPTRAJ: PCG32 RNG test. CPPTRAJ: Command line wildcard test, part 1 All 2 comparisons passed. All 1 comparisons passed. CPPTRAJ: Dihedral RMSD test (to previous) CPPTRAJ: Energy minimization with angle term test. All 2 comparisons passed. CPPTRAJ: Add time to trajectory test CPPTRAJ: Test Stdlib RNG CPPTRAJ: Command line wildcard test, part 2 CPPTRAJ: Atom XYZ format read, test 2 All 1 comparisons passed. CPPTRAJ: Ewald test (NaCl crystal) CPPTRAJ: Test reading comma-separated list of strings CPPTRAJ: Sorted implicit constant pH stats test CPPTRAJ: CRD(1-5) => TRR All 6 comparisons passed. CPPTRAJ: Dihedral RMS fluctuation test. CPPTRAJ: Test Mersenne Twister RNG CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. All 2 comparisons passed. CPPTRAJ: Cluster, random CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats CPPTRAJ: Atom XYZ format read, test 3 All 4 comparisons passed. CPPTRAJ: Ewald test (trunc. oct) CPPTRAJ: Hausdorff distance of 2D rms output test. CPPTRAJ: Test nested loops and variables in loops CPPTRAJ: Modify time info test. All 5 comparisons passed. CPPTRAJ: Energy minimization with nonbond term test. CPPTRAJ: Pairdist test, nonorthogonal imaging. CPPTRAJ: Atom XYZ format read, test 4 All 4 comparisons passed. CPPTRAJ: CRD(6-10) => TRR CPPTRAJ: Unsorted pH read/write test All 28 comparisons passed. CPPTRAJ: Test loop over data set blocks ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). CPPTRAJ: Atom XYZ format read, test 5 All 16 comparisons passed. All 8 comparisons passed. CPPTRAJ: TRR (appended) => CRD CPPTRAJ: Atom XYZ format read, test 6 CPPTRAJ: Test for filename wildcards and oversets All 6 comparisons passed. CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). All 13 comparisons passed. g++ -o a.out main.o NameType.o CpptrajStdio.o All 3 comparisons passed. CPPTRAJ: OpenMM basic energy minimization tests (bonds) CPPTRAJ: GMX: CRD with offset CPPTRAJ: Randomize (around) CPPTRAJ: OpenMM basic energy minimization tests (angles) All 4 comparisons passed. CPPTRAJ: Ewald test (partial system, trunc. oct) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet CPPTRAJ: Clustering, One DataSet make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' CPPTRAJ: XtalSymm Reimaging by Atom CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) '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: OpenMM basic energy minimization tests (nonbonds) CPPTRAJ: Clustering, Two DataSets All 4 comparisons passed. CPPTRAJ: GMX: TRR with offset CPPTRAJ: Watershell Test, orthorhombic imaging. CPPTRAJ: Clustering, dihedral DataSet All 1 comparisons passed. CPPTRAJ: Clustering, two dihedral DataSets Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: Ewald test (trunc. oct), 10 frames Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: Ewald test (ortho), 10 frames All 4 comparisons passed. 2 comparisons skipped. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LibPME CPPTRAJ: Particle mesh Ewald test (NaCl crystal) CPPTRAJ: Clustering, dihedral DataSet, K-means All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc CPPTRAJ: XTC read test CPPTRAJ: Particle mesh Ewald test (trunc. oct) CPPTRAJ: Clustering, two dihedral DataSets, K-means All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN CPPTRAJ: DBSCAN test CPPTRAJ: CRD => XTC CPPTRAJ: Randomize (overlap) CPPTRAJ: DBSCAN automatic parameter determination test. CPPTRAJ: Read specific columns test. CPPTRAJ: XTC => CRD CPPTRAJ: DBSCAN kdist map test CPPTRAJ: Write non-square matrix CPPTRAJ: DBSCAN with sieve CPPTRAJ: Randomize (no restrictions) CPPTRAJ: Watershell Test, no imaging. All 4 comparisons passed. CPPTRAJ: Read non-square matrix CPPTRAJ: Pairdist test, 2 masks. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans CPPTRAJ: Cpptraj Kmeans CPPTRAJ: Read square matrix All 4 comparisons passed. CPPTRAJ: CRD(1-5) => XTC All 15 comparisons passed. CPPTRAJ: Particle mesh Ewald test (ortho) CPPTRAJ: Cpptraj Kmeans random CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) All 5 comparisons passed. CPPTRAJ: CRD(6-10) => XTC All 6 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) All 3 comparisons passed. CPPTRAJ: XTC (appended) => CRD CPPTRAJ: Particle mesh Ewald test (ortho, with mask) CPPTRAJ: PME test (partial system, trunc. oct) All 5 comparisons passed. CPPTRAJ: GMX: CRD 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. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LJ_PME CPPTRAJ: LJ PME test. CPPTRAJ: LJ PME kappa sweep test, 0.25 All 5 comparisons passed. CPPTRAJ: GMX: XTC with offset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites CPPTRAJ: Cluster command test, coordinate writes. CPPTRAJ: LJ PME kappa sweep test, 0.35 CPPTRAJ: GIST test, orthogonal cell CPPTRAJ: XtalSymm Reimaging by Molecule All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTNG CPPTRAJ: TNG read test CPPTRAJ: Cluster command test, coordinate writes using info file. CPPTRAJ: LJ PME kappa sweep test, 0.45 CPPTRAJ: LJ PME kappa sweep test, 0.5 All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Dpeaks CPPTRAJ: Density peaks clustering test CPPTRAJ: TNG read test (with offset) CPPTRAJ: LJ with switch function test All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Nreps CPPTRAJ: Clustering with specified # reps All 5 comparisons passed. All 2 comparisons passed. All 6 comparisons passed. g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' Unit test passed. make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' All 5 comparisons passed. All 3 comparisons passed. All 9 comparisons passed. CPPTRAJ: GIST test, nonorthogonal cell 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. 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 pbuilder2 pbuilder2 184920736 Nov 19 08:41 ../bin/cpptraj ===================== TEST SUMMARY ====================== 853 out of 859 comparisons OK (0 failed, 0 warnings, 6 skipped). 480 out of 480 program executions completed. 170 out of 173 tests completed with no issues. 2 tests skipped. ========================================================= make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/cpptraj/ make -j42 install DESTDIR=/build/reproducible-path/cpptraj-5.1.0\+dfsg/debian/cpptraj AM_UPDATE_INFO_DIR=no 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' Skipping bundled ARPACK build Skipping bundled READLINE build g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o -L/usr/lib/x86_64-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/x86_64-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/x86_64-linux-gnu/lib -lfftw3 -L/usr/lib/x86_64-linux-gnu/lib -lOpenMM -lnetcdf -lbz2 tng/libtng_io.a -lz xdrfile/libxdrfile.a -Wl,-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' dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libreadline8t64 from: /lib/x86_64-linux-gnu/libreadline.so.8 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libreadline8t64 to: /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'cpptraj-dbgsym' in '../cpptraj-dbgsym_5.1.0+dfsg-5_amd64.deb'. dpkg-deb: building package 'cpptraj' in '../cpptraj_5.1.0+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../cpptraj_5.1.0+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../cpptraj_5.1.0+dfsg-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2870230/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2870230/tmp/hooks/B01_cleanup finished 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/2870230 and its subdirectories I: Current time: Thu Nov 19 22:43:18 +14 2026 I: pbuilder-time-stamp: 1795077798