I: pbuilder: network access will be disabled during build I: Current time: Sun Mar 9 04:50:00 +14 2025 I: pbuilder-time-stamp: 1741445400 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [cpptraj_5.1.0+dfsg-4.dsc] I: copying [./cpptraj_5.1.0+dfsg.orig.tar.xz] I: copying [./cpptraj_5.1.0+dfsg-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./cpptraj_5.1.0+dfsg-4.dsc: unsupported subcommand dpkg-source: info: extracting cpptraj in cpptraj-5.1.0+dfsg dpkg-source: info: unpacking cpptraj_5.1.0+dfsg.orig.tar.xz dpkg-source: info: unpacking cpptraj_5.1.0+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-system-libraries.patch dpkg-source: info: applying skip-failing-test.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/120576/tmp/hooks/D01_modify_environment starting debug: Running on infom01-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 Mar 8 14:50 /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/120576/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/120576/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]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(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=12 ' 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=d352701befd147be92532c4f13d18ebf 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=120576 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.bEZqnmUs/pbuilderrc_SfiF --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.bEZqnmUs/b2 --logfile b2/build.log cpptraj_5.1.0+dfsg-4.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.1.0-31-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/120576/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 ... 19783 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on libarpack2-dev; however: Package libarpack2-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on libnetcdf-dev; however: Package libnetcdf-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmm-dev; however: Package libopenmm-dev is not installed. pbuilder-satisfydepends-dummy depends on libreadline-dev; however: Package libreadline-dev is not installed. pbuilder-satisfydepends-dummy depends on netcdf-bin; however: Package netcdf-bin is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran{a} gfortran-14{a} gfortran-14-x86-64-linux-gnu{a} gfortran-x86-64-linux-gnu{a} groff-base{a} hdf5-helpers{a} icu-devtools{a} intltool-debian{a} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarpack2-dev{a} libarpack2t64{a} libblas-dev{a} libblas3{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libffi8{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-quad3{a} libfftw3-single3{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-310{a} libhdf5-cpp-310{a} libhdf5-dev{a} libhdf5-fortran-310{a} libhdf5-hl-310{a} libhdf5-hl-cpp-310{a} libhdf5-hl-fortran-310{a} libicu-dev{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-dev{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnetcdf-dev{a} libnetcdf22{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libopenmm-dev{a} libopenmm8.1{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} libreadline-dev{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsz2{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2{a} libxml2-dev{a} libzstd-dev{a} m4{a} man-db{a} netcdf-bin{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 134 newly installed, 0 to remove and 0 not upgraded. Need to get 83.9 MB of archives. After unpacking 333 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 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 2.13.0-1 [1420 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 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 1.14.1-2 [19.7 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 25 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libgfortran-14-dev amd64 14.2.0-17 [879 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-17 [11.7 MB] Get: 37 http://deb.debian.org/debian unstable/main amd64 gfortran-14 amd64 14.2.0-17 [14.0 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1 [1284 B] Get: 39 http://deb.debian.org/debian unstable/main amd64 gfortran amd64 4:14.2.0-1 [1436 B] Get: 40 http://deb.debian.org/debian unstable/main amd64 hdf5-helpers amd64 1.14.5+repack-3 [26.6 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-6 [210 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 45 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-4 [60.0 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-4 [42.2 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-4 [42.4 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-4 [54.2 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-4 [126 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 54 http://deb.debian.org/debian unstable/main amd64 libaec-dev amd64 1.1.3-1+b1 [21.5 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libarpack2t64 amd64 3.9.1-4 [104 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-2 [170 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.1-2 [4998 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libarpack2-dev amd64 3.9.1-4 [120 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 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 3.8.9-2 [1464 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.12.1-3 [365 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-4 [15.9 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.9+dfsg-1 [307 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.4.1-1 [2787 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.12.1-3 [480 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.12.1-3 [369 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libfftw3-double3 amd64 3.3.10-2+b1 [781 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libfftw3-long3 amd64 3.3.10-2+b1 [347 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libfftw3-quad3 amd64 3.3.10-2+b1 [618 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libfftw3-single3 amd64 3.3.10-2+b1 [809 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libfftw3-bin amd64 3.3.10-2+b1 [51.3 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libfftw3-dev amd64 3.3.10-2+b1 [2118 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libhdf5-cpp-310 amd64 1.14.5+repack-3 [133 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libhdf5-fortran-310 amd64 1.14.5+repack-3 [111 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [69.3 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-fortran-310 amd64 1.14.5+repack-3 [43.9 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-cpp-310 amd64 1.14.5+repack-3 [24.4 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3.1 [292 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-3.1 [72.0 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libhdf5-dev amd64 1.14.5+repack-3 [3165 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-6 [10.4 MB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5+20250216-2 [353 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libnetcdf22 amd64 1:4.9.3-1 [517 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [794 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libnetcdf-dev amd64 1:4.9.3-1 [116 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-4+b1 [1058 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libopenmm-dev amd64 8.1.2+dfsg-4+b1 [346 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libreadline-dev amd64 8.2-6 [153 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 netcdf-bin amd64 1:4.9.3-1 [260 kB] Fetched 83.9 MB in 1s (60.0 MB/s) Preconfiguring packages ... 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Unpacking libbrotli-dev:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../062-libbz2-dev_1.0.8-6_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.8-6) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../063-libidn2-0_2.3.7-2+b1_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.7-2+b1) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../064-libffi8_3.4.7-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.7-1) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../065-libp11-kit0_0.25.5-3_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../066-libtasn1-6_4.20.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:amd64. Preparing to unpack .../067-libgnutls30t64_3.8.9-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.9-2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../068-libsasl2-modules-db_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../069-libsasl2-2_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../070-libldap2_2.6.9+dfsg-1_amd64.deb ... Unpacking libldap2:amd64 (2.6.9+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../071-libnghttp2-14_1.64.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../072-libnghttp3-9_1.8.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.8.0-1) ... Selecting previously unselected package libngtcp2-16: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 (8.2-6) ... Selecting previously unselected package libreadline-dev:amd64. Preparing to unpack .../132-libreadline-dev_8.2-6_amd64.deb ... Unpacking libreadline-dev:amd64 (8.2-6) ... Selecting previously unselected package netcdf-bin. Preparing to unpack .../133-netcdf-bin_1%3a4.9.3-1_amd64.deb ... Unpacking netcdf-bin (1:4.9.3-1) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libfftw3-single3:amd64 (3.3.10-2+b1) ... Setting up libicu72:amd64 (72.1-6) ... Setting up libzstd-dev:amd64 (1.5.6+dfsg-2) ... Setting up bsdextrautils (2.40.4-5) ... Setting up hdf5-helpers (1.14.5+repack-3) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.1) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libfftw3-long3:amd64 (3.3.10-2+b1) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-7) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libcom-err2:amd64 (1.47.2-1) ... Setting up file (1:5.45-3+b1) ... Setting up libaec0:amd64 (1.1.3-1+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-4) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libunbound8:amd64 (1.22.0-1+b1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-3) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3.1) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-3.1) ... Setting up libncurses6:amd64 (6.5+20250216-2) ... Setting up libfftw3-quad3:amd64 (3.3.10-2+b1) ... Setting up comerr-dev:amd64 (2.1-1.47.2-1) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up libssl-dev:amd64 (3.4.1-1) ... Setting up autopoint (0.23.1-1) ... Setting up icu-devtools (72.1-6) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-4) ... Setting up libfftw3-double3:amd64 (3.3.10-2+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:amd64 (14.2.0-17) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libnghttp3-dev:amd64 (1.8.0-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.4.7-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-4) ... 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-4+b1) ... Setting up readline-common (8.2-6) ... Setting up libicu-dev:amd64 (72.1-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Setting up libldap2:amd64 (2.6.9+dfsg-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libblas-dev:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libsz2:amd64 (1.1.3-1+b1) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:amd64 (14.2.0-17) ... Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libncurses-dev:amd64 (6.5+20250216-2) ... Setting up gettext (0.23.1-1) ... Setting up libarpack2t64:amd64 (3.9.1-4) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libtool (2.5.4-4) ... Setting up libfftw3-bin (3.3.10-2+b1) ... Setting up libaec-dev:amd64 (1.1.3-1+b1) ... Setting up libjpeg-dev:amd64 (1:2.1.5-3.1) ... Setting up libidn2-0:amd64 (2.3.7-2+b1) ... Setting up libngtcp2-dev:amd64 (1.11.0-1) ... Setting up libopenmm-dev (8.1.2+dfsg-4+b1) ... Setting up gfortran-14-x86-64-linux-gnu (14.2.0-17) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libxml2-dev:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ... Setting up libldap-dev:amd64 (2.6.9+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up liblapack-dev:amd64 (3.12.1-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libidn2-dev:amd64 (2.3.7-2+b1) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up gfortran-14 (14.2.0-17) ... Setting up libfftw3-dev:amd64 (3.3.10-2+b1) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libgnutls30t64:amd64 (3.8.9-2) ... Setting up libgnutls-openssl27t64:amd64 (3.8.9-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1) ... Setting up libarpack2-dev:amd64 (3.9.1-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libreadline-dev:amd64 (8.2-6) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran-x86-64-linux-gnu (4:14.2.0-1) ... Setting up gfortran (4:14.2.0-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.9-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:amd64 (1.21.3-4) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-4) ... Setting up libgnutls28-dev:amd64 (3.8.9-2) ... Setting up libcurl4t64:amd64 (8.12.1-3) ... Setting up libkdb5-10t64:amd64 (1.21.3-4) ... Setting up libcurl3t64-gnutls:amd64 (8.12.1-3) ... Setting up debhelper (13.24.1) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.11.0-1) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhdf5-310:amd64 (1.14.5+repack-3) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-4) ... Setting up libhdf5-fortran-310:amd64 (1.14.5+repack-3) ... Setting up krb5-multidev:amd64 (1.21.3-4) ... Setting up libhdf5-cpp-310:amd64 (1.14.5+repack-3) ... Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3) ... Setting up libnetcdf22:amd64 (1:4.9.3-1) ... Setting up netcdf-bin (1:4.9.3-1) ... Setting up libkrb5-dev:amd64 (1.21.3-4) ... Setting up libhdf5-hl-cpp-310:amd64 (1.14.5+repack-3) ... Setting up libhdf5-hl-fortran-310:amd64 (1.14.5+repack-3) ... Setting up libcurl4-gnutls-dev:amd64 (8.12.1-3) ... Setting up libhdf5-dev (1.14.5+repack-3) ... 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) ... Processing triggers for libc-bin (2.41-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/120576/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/120576/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-4_source.changes dpkg-buildpackage: info: source package cpptraj dpkg-buildpackage: info: source version 5.1.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture 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 -j12 clean make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' /bin/rm -f SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o cpptraj *.LIBCPPTRAJ.o libcpptraj # cd readline && make clean cd xdrfile && make clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' /bin/rm -f *.o libxdrfile.a a.out test.trr test.xtc test.xdr make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' # cd arpack && make clean cd cuda_kernels && make clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/cuda_kernels' /bin/rm -f *.o libcpptraj_cuda.a make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/cuda_kernels' cd tng && make clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' /bin/rm -f *.o libtng_io.a tng_io_testing.o a.out tng_example_out.tng tng_test.tng make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' cd test && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' Cleaning all test directories: make test.complete test.libcpptraj OPT=clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' cd unitTests && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' Cleaning unit tests. make test.complete OPT=clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' rm -rf bin make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' ./configure gnu --with-arpack=/usr/lib/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 -j12 make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make install make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' CXX SpaceGroup.cpp CXX ActionFrameCounter.cpp CXX ActionList.cpp CXX ActionTopWriter.cpp CXX Action_Align.cpp CXX Action_Angle.cpp CXX Action_AreaPerMol.cpp CXX Action_AtomMap.cpp CXX Action_AtomicCorr.cpp CXX Action_AtomicFluct.cpp CXX Action_AutoImage.cpp CXX Action_Average.cpp CXX Action_Bounds.cpp CXX Action_Box.cpp CXX Action_Center.cpp CXX Action_Channel.cpp CXX Action_CheckChirality.cpp CXX Action_CheckStructure.cpp CXX Action_Closest.cpp CXX Action_ClusterDihedral.cpp CXX Action_Contacts.cpp CXX Action_CreateCrd.cpp CXX Action_CreateReservoir.cpp CXX Action_DNAionTracker.cpp CXX Action_DSSP.cpp CXX Action_Density.cpp CXX Action_Diffusion.cpp CXX Action_Dihedral.cpp CXX Action_DihedralRMS.cpp CXX Action_Dipole.cpp CXX Action_Distance.cpp CXX Action_DistRmsd.cpp CXX Action_Energy.cpp In file included from Ewald_ParticleMesh.h:5, from Action_Energy.cpp:4: helpme_standalone.h:2323: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2323 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:2343: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2343 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3014: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3014 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3120: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3120 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3247: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3247 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3701: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3701 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3739: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3739 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3802: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3802 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3840: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3840 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4044: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4044 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4052: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4052 | #pragma omp for helpme_standalone.h:4097: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4097 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4145: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4145 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4172: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4172 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4224: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4224 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4228: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4228 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4275: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4275 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4388: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4388 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4419: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4503: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4503 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4510: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4510 | #pragma omp for CXX Action_FilterByData.cpp CXX Action_FixAtomOrder.cpp CXX Action_FixImagedBonds.cpp CXX Action_GIST.cpp CXX Action_Grid.cpp CXX Action_GridFreeEnergy.cpp CXX Action_HydrogenBond.cpp CXX Action_Image.cpp CXX Action_InfraredSpectrum.cpp CXX Action_Jcoupling.cpp CXX Action_LESsplit.cpp CXX Action_LIE.cpp CXX Action_LipidOrder.cpp CXX Action_MakeStructure.cpp CXX Action_Mask.cpp In file included from Matrix_3x3.h:3, from Box.h:3, from Frame.h:5, from Topology.h:10, from DataSet_Coords.h:4, from DataSet_Coords_REF.h:3, from ReferenceFrame.h:3, from DataSetList.h:4, from DataFile.h:4, from DataFileList.h:3, from ActionState.h:3, from Action.h:5, from Action_GIST.h:3, from Action_GIST.cpp:3: In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:814:31: Vec3.h:76:57: 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_Matrix.cpp CXX Action_MinImage.cpp CXX Action_Molsurf.cpp CXX Action_MultiDihedral.cpp CXX Action_MultiVector.cpp CXX Action_NAstruct.cpp CXX Action_NativeContacts.cpp CXX Action_NMRrst.cpp CXX Action_OrderParameter.cpp CXX Action_Outtraj.cpp CXX Action_PairDist.cpp CXX Action_Pairwise.cpp CXX Action_Principal.cpp CXX Action_Projection.cpp CXX Action_Pucker.cpp CXX Action_Radgyr.cpp CXX Action_Radial.cpp CXX Action_RandomizeIons.cpp CXX Action_Remap.cpp CXX Action_ReplicateCell.cpp CXX Action_Rmsd.cpp CXX Action_Rotate.cpp CXX Action_RunningAvg.cpp CXX Action_STFC_Diffusion.cpp CXX Action_Scale.cpp CXX Action_SetVelocity.cpp CXX Action_Spam.cpp CXX Action_Strip.cpp CXX Action_Surf.cpp CXX Action_SymmetricRmsd.cpp CXX Action_Temperature.cpp CXX Action_Time.cpp CXX Action_Translate.cpp CXX Action_Unstrip.cpp CXX Action_Unwrap.cpp CXX Action_Vector.cpp CXX Action_VelocityAutoCorr.cpp CXX Action_Volmap.cpp CXX Action_Volume.cpp CXX Action_Watershell.cpp CXX Action_XtalSymm.cpp CXX AnalysisList.cpp CXX Analysis_AmdBias.cpp CXX Analysis_AutoCorr.cpp CXX Analysis_Average.cpp CXX Analysis_Clustering.cpp CXX Analysis_Corr.cpp CXX Analysis_ConstantPHStats.cpp CXX Analysis_CrankShaft.cpp CXX Analysis_CrdFluct.cpp CXX Analysis_CrossCorr.cpp CXX Analysis_CurveFit.cpp CXX Analysis_Divergence.cpp CXX Analysis_EvalPlateau.cpp CXX Analysis_FFT.cpp CXX Analysis_HausdorffDistance.cpp CXX Analysis_Hist.cpp CXX Analysis_Integrate.cpp CXX Analysis_IRED.cpp CXX Analysis_KDE.cpp CXX Analysis_Lifetime.cpp CXX Analysis_LowestCurve.cpp In file included from /usr/include/c++/14/vector:66, from ArgList.h:3, from Action.h:4, from Action_XtalSymm.h:3, from Action_XtalSymm.cpp:1: In member function 'void std::vector<_Tp, _Alloc>::assign(size_type, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]', inlined from 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)' at Action_XtalSymm.cpp:57:12: /usr/include/c++/14/bits/stl_vector.h:809:23: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 809 | { _M_fill_assign(__n, __val); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:72: /usr/include/c++/14/bits/vector.tcc: In member function 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)': /usr/include/c++/14/bits/vector.tcc:270:5: note: by argument 3 of type 'const std::vector::value_type&' {aka 'const Vec3&'} to 'void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]' declared here 270 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ Action_XtalSymm.cpp:57:33: note: '' declared here 57 | T_.assign( nCopyTotal, Vec3()); | ^ In member function 'void std::vector<_Tp, _Alloc>::assign(size_type, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]', inlined from 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)' at Action_XtalSymm.cpp:58:15: /usr/include/c++/14/bits/stl_vector.h:809:23: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 809 | { _M_fill_assign(__n, __val); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/14/bits/vector.tcc: In member function 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)': /usr/include/c++/14/bits/vector.tcc:270:5: note: by argument 3 of type 'const std::vector::value_type&' {aka 'const Vec3&'} to 'void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]' declared here 270 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ Action_XtalSymm.cpp:58:33: note: '' declared here 58 | RefT_.assign(nCopyTotal, Vec3()); | ^ CXX Analysis_Matrix.cpp CXX Analysis_MeltCurve.cpp CXX Analysis_Modes.cpp CXX Analysis_Multicurve.cpp CXX Analysis_MultiHist.cpp CXX Analysis_Overlap.cpp CXX Analysis_PhiPsi.cpp CXX Analysis_Regression.cpp CXX Analysis_RemLog.cpp CXX Analysis_Rms2d.cpp CXX Analysis_RmsAvgCorr.cpp CXX Analysis_Rotdif.cpp CXX Analysis_RunningAvg.cpp CXX Analysis_Slope.cpp CXX Analysis_Spline.cpp CXX Analysis_State.cpp CXX Analysis_Statistics.cpp CXX Analysis_TI.cpp CXX Analysis_Timecorr.cpp CXX Analysis_VectorMath.cpp CXX Analysis_Wavelet.cpp CXX ArgList.cpp CXX Array1D.cpp CXX AssociatedData.cpp CXX Atom.cpp CXX AtomMap.cpp CXX AtomMask.cpp CXX AxisType.cpp CXX BondSearch.cpp CXX Box.cpp CXX BoxArgs.cpp CXX BufferedFrame.cpp CXX BufferedLine.cpp CXX ByteRoutines.cpp CXX CharMask.cpp CXX CharmmParamFile.cpp CXX CIFfile.cpp CXX ClusterDist.cpp CXX ClusterList.cpp CXX ClusterMap.cpp CXX ClusterMatrix.cpp CXX ClusterNode.cpp CXX ClusterSieve.cpp CXX Cluster_DBSCAN.cpp CXX Cluster_DPeaks.cpp CXX Cluster_HierAgglo.cpp CXX Cluster_Kmeans.cpp CXX Cluster_ReadInfo.cpp CXX Cmd.cpp CXX CmdInput.cpp CXX CmdList.cpp CXX CompactFrameArray.cpp CXX ComplexArray.cpp CXX Constraints.cpp CXX ControlBlock_For.cpp CXX CoordinateInfo.cpp CXX Corr.cpp CXX Cph.cpp CXX CpptrajFile.cpp CXX CpptrajState.cpp CXX CpptrajStdio.cpp CXX CurveFit.cpp CXX DataFile.cpp CXX DataFileList.cpp CXX DataFilter.cpp CXX DataIO.cpp CXX DataIO_CCP4.cpp CXX DataIO_CharmmFastRep.cpp CXX DataIO_CharmmOutput.cpp CXX DataIO_CharmmRepLog.cpp CXX DataIO_CharmmRtfPrm.cpp CXX DataIO_Cmatrix.cpp CXX DataIO_Cpout.cpp CXX DataIO_Evecs.cpp CXX DataIO_Gnuplot.cpp CXX DataIO_Grace.cpp CXX DataIO_OpenDx.cpp CXX DataIO_Peaks.cpp CXX DataIO_Mdout.cpp CXX DataIO_NC_Cmatrix.cpp CXX DataIO_RemLog.cpp CXX DataIO_Std.cpp CXX DataIO_VecTraj.cpp CXX DataIO_Xplor.cpp CXX DataIO_XVG.cpp CXX DataSet.cpp CXX DataSetList.cpp CXX DataSet_1D.cpp CXX DataSet_3D.cpp CXX DataSet_Cmatrix.cpp CXX DataSet_Cmatrix_DISK.cpp CXX DataSet_Cmatrix_MEM.cpp CXX DataSet_Cmatrix_NOMEM.cpp CXX DataSet_Coords.cpp CXX DataSet_Coords_CRD.cpp CXX DataSet_Coords_REF.cpp CXX DataSet_Coords_TRJ.cpp CXX DataSet_GridDbl.cpp CXX DataSet_GridFlt.cpp CXX DataSet_Mat3x3.cpp CXX DataSet_MatrixDbl.cpp CXX DataSet_MatrixFlt.cpp CXX DataSet_Mesh.cpp CXX DataSet_Modes.cpp CXX DataSet_Parameters.cpp CXX DataSet_pH.cpp CXX DataSet_PHREMD_Explicit.cpp CXX DataSet_PHREMD_Implicit.cpp CXX DataSet_RemLog.cpp CXX DataSet_Topology.cpp CXX DataSet_Vector.cpp CXX DataSet_Vector_Scalar.cpp CXX DataSet_double.cpp CXX DataSet_float.cpp CXX DataSet_integer_disk.cpp CXX DataSet_integer_mem.cpp CXX DataSet_string.cpp CXX DataSet_StringVar.cpp CXX DataSet_Tensor.cpp CXX DataSet_unsignedInt.cpp CXX Deprecated.cpp CXX DihedralSearch.cpp CXX DistRoutines.cpp CXX Energy.cpp CXX EnergyArray.cpp CXX EnsembleIn.cpp CXX EnsembleIn_Multi.cpp CXX EnsembleIn_Single.cpp CXX EnsembleNavigator.cpp CXX EnsembleOut.cpp CXX EnsembleOut_Multi.cpp CXX EnsembleOut_Single.cpp CXX EnsembleOutList.cpp CXX Ewald.cpp CXX Ewald_ParticleMesh.cpp In file included from Ewald_ParticleMesh.h:5, from Ewald_ParticleMesh.cpp:4: helpme_standalone.h:2323: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2323 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:2343: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2343 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3014: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3014 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3120: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3120 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3247: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3247 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3701: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3701 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3739: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3739 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3802: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3802 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3840: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3840 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4044: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4044 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4052: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4052 | #pragma omp for helpme_standalone.h:4097: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4097 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4145: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4145 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4172: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4172 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4224: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4224 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4228: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4228 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4275: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4275 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4388: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4388 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4419: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4503: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4503 | #pragma omp parallel num_threads(nThreads_) CXX Ewald_Regular.cpp helpme_standalone.h:4510: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4510 | #pragma omp for CXX ExclusionArray.cpp CXX Exec_AddMissingRes.cpp helpme_standalone.h: In instantiation of 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]': helpme_standalone.h:3898:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3898 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:1010:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 1010 | for (int val = 0; val < nRows_; ++val) eigenPairs.push_back({eigenValues[val][0], unsortedEigenVectors[val]}); | ~~~~^~~~~~~~ helpme_standalone.h:1013:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 1013 | for (int val = 0; val < nRows_; ++val) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::PMEInstance >::sanityChecks(int, const RealMat&, const RealMat&, int) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5018:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5018 | sanityChecks(parameterAngMom, parameters, coordinates); | ^~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3198:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3198 | if (parameters.nCols() != (nCartesian(parameterAngMom) - cartesianOffset)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::PMEInstance >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5019:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5019 | filterAtomsAndBuildSplineCache(parameterAngMom, coordinates); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3746:45: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3746 | for (size_t row = threadID; row < gridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~ helpme_standalone.h:3753:37: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3753 | for (int atom = 0; atom < nAtoms; ++atom) { | ~~~~~^~~~~~~~ helpme_standalone.h:3761:61: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3761 | if (cGridIterator.size() && thisAtomsThread == threadID) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~ helpme_standalone.h:3750:25: warning: unused variable 'gridIteratorC' [-Wunused-variable] 3750 | const auto &gridIteratorC = threadedGridIteratorC_[threadID]; | ^~~~~~~~~~~~~ helpme_standalone.h:3794:55: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3794 | for (int atom = splineCache_.size(); atom < newSize; ++atom) | ~~~~~^~~~~~~~~ helpme_standalone.h:3810:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3810 | for (size_t cRow = threadID; cRow < gridDimensionC_; cRow += nThreads_) { | ~~~~~^~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'Real* helpme::PMEInstance >::spreadParameters(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5020:25: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5020 | auto realGrid = spreadParameters(parameterAngMom, parameters); | ^~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3708:45: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3708 | for (size_t row = threadID; row < myGridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'helpme::PMEInstance >::Complex* helpme::PMEInstance >::forwardTransform(Real*) [with Real = double; typename std::enable_if::value, int>::type = 0; Complex = std::complex]': helpme_standalone.h:5023:32: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5023 | auto gridAddress = forwardTransform(realGrid); | ^~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:4004:28: warning: variable 'realCBA' set but not used [-Wunused-but-set-variable] 4004 | Real *__restrict__ realCBA; | ^~~~~~~ CXX Exec_Analyze.cpp helpme_standalone.h: In instantiation of 'void helpme::Matrix::assertSymmetric(const Real&) const [with Real = double]': helpme_standalone.h:1000:9: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 1000 | assertSymmetric(); | ^~~~~~~~~~~~~~~ helpme_standalone.h:3898:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3898 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:796:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 796 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::JacobiCyclicDiagonalization(Real*, Real*, const Real*, int) [with Real = double]': helpme_standalone.h:1006:42: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 1006 | JacobiCyclicDiagonalization(eigenValues[0], unsortedEigenVectors[0], cbegin(), nRows_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3898:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3898 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:213:20: warning: variable 'cos_2phi' set but not used [-Wunused-but-set-variable] 213 | Real sin_2phi, cos_2phi, cot_2phi; | ^~~~~~~~ helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::applyOperation(const std::function&) const [with Real = double]': helpme_standalone.h:785:26: required from 'helpme::Matrix helpme::Matrix::inverse() const [with Real = double]' 785 | return this->applyOperation([](Real& element) { element = 1 / element; }); | ~~~~~~^~~~~~~~~~~~~~ helpme_standalone.h:3910:44: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3910 | recVecs_ = boxVecs_.inverse(); | ~~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:824:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 824 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::BSpline::update(short int, Real, short int, short int) [with Real = double]': helpme_standalone.h:3829:47: required from 'void helpme::PMEInstance >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 3829 | atomSplines.aSpline.update(aStartingGridPoint, gridDimensionA_ * aCoord - aStartingGridPoint, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3830 | splineOrder_, splineDerivativeLevel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:5019:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5019 | filterAtomsAndBuildSplineCache(parameterAngMom, coordinates); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:2208:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 2208 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:2208:72: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2208 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::multiply(const helpme::Matrix&) const [with Real = double]': helpme_standalone.h:877:64: required from 'helpme::Matrix helpme::Matrix::operator*(const helpme::Matrix&) const [with Real = double]' 877 | Matrix operator*(const Matrix& other) const { return this->multiply(other); } | ~~~~~~^~~~~~~~ helpme_standalone.h:829:22: required from 'helpme::Matrix helpme::Matrix::applyOperation(const std::function&) const [with Real = double]' 829 | return evecs * evecsT; | ~~~~~~^~~~~~~~ helpme_standalone.h:785:26: required from 'helpme::Matrix helpme::Matrix::inverse() const [with Real = double]' 785 | return this->applyOperation([](Real& element) { element = 1 / element; }); | ~~~~~~^~~~~~~~~~~~~~ helpme_standalone.h:3910:44: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3910 | recVecs_ = boxVecs_.inverse(); | ~~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:860:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 860 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h:862:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 862 | for (int col = 0; col < other.nCols_; ++col) { | ~~~~^~~~~~~~~~~~~~ helpme_standalone.h:863:41: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 863 | for (int link = 0; link < nCols_; ++link) { | ~~~~~^~~~~~~~ CXX Exec_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 CXX Exec_LoadTraj.cpp helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3470:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3470 | fftHelperA_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3470:31: note: '' declared here 3470 | fftHelperA_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3471:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3471 | fftHelperB_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3471:31: note: '' declared here 3471 | fftHelperB_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3472:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3472 | fftHelperC_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3472:31: note: '' declared here 3472 | fftHelperC_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3503:43: helpme_standalone.h:519:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] 519 | class Matrix { | ^~~~~~ helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3503:45: note: '' declared here 3503 | compressionCoefficientsA_ = RealMat(); | ^~~~~~~~~ In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3504:43: helpme_standalone.h:519:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] 519 | class Matrix { | ^~~~~~ helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3504:45: note: '' declared here 3504 | compressionCoefficientsB_ = RealMat(); | ^~~~~~~~~ In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3505:43: helpme_standalone.h:519:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] 519 | class Matrix { | ^~~~~~ helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3505:45: note: '' declared here 3505 | compressionCoefficientsC_ = RealMat(); | ^~~~~~~~~ CXX Exec_ParallelAnalysis.cpp CXX Exec_ParmBox.cpp helpme_standalone.h: In member function 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:5031:16: warning: 'energy' may be used uninitialized [-Wmaybe-uninitialized] 5031 | return energy; | ^~~~~~ helpme_standalone.h:5021:14: note: 'energy' was declared here 5021 | Real energy; | ^~~~~~ CXX Exec_ParmSolvent.cpp CXX Exec_ParmStrip.cpp CXX Exec_ParmWrite.cpp CXX Exec_PermuteDihedrals.cpp CXX Exec_Precision.cpp CXX Exec_PrepareForLeap.cpp CXX Exec_PrintData.cpp CXX Exec_Random.cpp CXX Exec_ReadData.cpp CXX Exec_ReadEnsembleData.cpp CXX Exec_ReadInput.cpp CXX Exec_RotateDihedral.cpp CXX Exec_RunAnalysis.cpp CXX Exec_ScaleDihedralK.cpp CXX Exec_Set.cpp CXX Exec_SequenceAlign.cpp CXX Exec_Show.cpp CXX Exec_SortEnsembleData.cpp CXX Exec_SplitCoords.cpp CXX Exec_System.cpp CXX Exec_Top.cpp CXX Exec_Traj.cpp CXX Exec_UpdateParameters.cpp CXX Exec_ViewRst.cpp CXX File_TempName.cpp CXX FileIO_Bzip2.cpp CXX FileIO_Gzip.cpp CXX FileIO_Mpi.cpp CXX FileIO_MpiShared.cpp CXX FileIO_Std.cpp CXX FileName.cpp CXX FileType.cpp CXX FileTypes.cpp CXX ForLoop.cpp CXX ForLoop_dataSetBlocks.cpp CXX ForLoop_integer.cpp CXX ForLoop_list.cpp CXX ForLoop_mask.cpp CXX ForLoop_overSets.cpp CXX Frame.cpp CXX GridAction.cpp CXX HistBin.cpp CXX Hungarian.cpp CXX ImageRoutines.cpp CXX Image_List_Mask.cpp CXX Image_List_Pair.cpp CXX Image_List_Unit.cpp CXX InputTrajCommon.cpp CXX KDE.cpp CXX MapAtom.cpp CXX MaskArray.cpp CXX MaskToken.cpp CXX Matrix_3x3.cpp CXX MdOpts.cpp CXX MetaData.cpp CXX Minimize_SteepestDescent.cpp CXX Mol.cpp CXX Mol2File.cpp CXX NameType.cpp CXX NC_Cmatrix.cpp CXX NC_Routines.cpp CXX NetcdfFile.cpp CXX OMM_helpers.cpp CXX OutputTrajCommon.cpp CXX ParameterSet.cpp CXX PDBfile.cpp CXX PairList.cpp CXX Parallel.cpp CXX ParallelNetcdf.cpp CXX ParmFile.cpp CXX Parm_Amber.cpp CXX Parm_CharmmPsf.cpp CXX Parm_CIF.cpp CXX Parm_Gromacs.cpp CXX Parm_Mol2.cpp CXX Parm_PDB.cpp CXX Parm_SDF.cpp CXX Parm_Tinker.cpp CXX PotentialFunction.cpp CXX PotentialTerm.cpp CXX PotentialTerm_Angle.cpp CXX PotentialTerm_Bond.cpp CXX PotentialTerm_Dihedral.cpp CXX PotentialTerm_LJ_Coulomb.cpp CXX PotentialTerm_OpenMM.cpp CXX ProgressBar.cpp CXX ProgressTimer.cpp CXX PubFFT.cpp CXX ExternalFxn.cpp CXX Random.cpp CXX Range.cpp CXX RNG.cpp CXX RNG_Marsaglia.cpp CXX RNG_MersenneTwister.cpp CXX RNG_PCG32.cpp CXX RNG_Stdlib.cpp CXX RNG_Xoshiro128pp.cpp CXX RPNcalc.cpp CXX ReferenceAction.cpp CXX RemdReservoirNC.cpp CXX Residue.cpp CXX SDFfile.cpp CXX SimplexMin.cpp CXX Spline.cpp CXX SplineFxnTable.cpp CXX StringRoutines.cpp CXX StructureCheck.cpp CXX StructureMapper.cpp CXX SymmetricRmsdCalc.cpp CXX TextFormat.cpp CXX Timer.cpp CXX TinkerFile.cpp CXX TopInfo.cpp CXX Topology.cpp CXX TorsionRoutines.cpp CXX Traj_AmberCoord.cpp CXX Traj_AmberNetcdf.cpp CXX Traj_AmberRestart.cpp CXX Traj_AmberRestartNC.cpp CXX Traj_Binpos.cpp CXX Traj_CharmmCor.cpp CXX Traj_CharmmDcd.cpp CXX Traj_CharmmRestart.cpp CXX Traj_CIF.cpp CXX Traj_Conflib.cpp CXX Traj_DTR.cpp CXX Traj_GmxDump.cpp CXX Traj_GmxTng.cpp CXX Traj_GmxTrX.cpp CXX Traj_GmxXtc.cpp CXX Traj_Gro.cpp CXX Traj_Mol2File.cpp CXX Traj_NcEnsemble.cpp CXX Traj_PDBfile.cpp CXX Traj_SDF.cpp CXX Traj_SQM.cpp CXX Traj_Tinker.cpp CXX Traj_XYZ.cpp CXX TrajectoryFile.cpp CXX TrajectoryIO.cpp CXX TrajFrameCounter.cpp CXX TrajinList.cpp CXX Trajin_Multi.cpp CXX Trajin_Single.cpp CXX TrajIOarray.cpp CXX Trajout_Single.cpp CXX TrajoutList.cpp CXX Vec3.cpp CXX ViewRst.cpp CXX xoshiro128plusplus.cpp xoshiro128plusplus.cpp: In function 'void jump()': xoshiro128plusplus.cpp:60:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 60 | for(int i = 0; i < sizeof JUMP / sizeof *JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ xoshiro128plusplus.cpp: In function 'void long_jump()': xoshiro128plusplus.cpp:90:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 90 | for(int i = 0; i < sizeof LONG_JUMP / sizeof *LONG_JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CXX Action_Esander.cpp CXX Command.cpp CXX Cpptraj.cpp CXX Energy_Sander.cpp CXX ReadLine.cpp CXX main.cpp CC molsurf.c Skipping bundled READLINE build cd xdrfile && make all make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' CC xdrfile.c Skipping bundled ARPACK build cd tng && make all make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' CC md5.c CC tng_io.c CC xdr_seek.c CC xdrfile_trr.c CC tng_compress.c CC coder.c CC xdrfile_xtc.c CC warnmalloc.c CC fixpoint.c CC xtc3.c CC bwlzh.c CC xtc2.c CC widemuldiv.c tng_io.c: In function 'tng_gen_data_block_add': tng_io.c:12600:9: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tng_io.c:12600:47: note: length computed here 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ CC huffmem.c /bin/rm -f libxdrfile.a CC vals16.c ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' CC bwt.c CC mtf.c CC rle.c CC lz77.c CC dict.c CC huffman.c CC merge_sort.c /bin/rm -f libtng_io.a ar cqs libtng_io.a md5.o tng_io.o tng_compress.o coder.o warnmalloc.o fixpoint.o xtc3.o bwlzh.o xtc2.o widemuldiv.o huffmem.o vals16.o bwt.o mtf.o rle.o lz77.o dict.o huffman.o merge_sort.o make[3]: Leaving directory '/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 -j12 test "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 check unittest make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' make[2]: Nothing to be done for 'test'. cd test && make test.complete summary cd unitTests && make test.complete summary make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList CPPTRAJ: NameType class unit test. CPPTRAJ: ArgList 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 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++ -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 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 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 186114960 Mar 8 14:52 ../bin/cpptraj -rwxr-xr-x 1 pbuilder2 pbuilder2 186114960 Mar 8 14:52 ../bin/cpptraj make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Strip CPPTRAJ: One frame strip command test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_General ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TrajinOffset CPPTRAJ: General tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RemdTraj CPPTRAJ: Normal trajectory read with offsets. CPPTRAJ: CRD Replica Trajectory Run with offset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj CPPTRAJ: Broken Traj: Running good trajectory. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_trajout_framerange CPPTRAJ: Trajout Frame Range [Amber Restart] CPPTRAJ: Gzipped trajectory read with offsets CPPTRAJ: CRD Replica Trajectory Run CPPTRAJ: Unstrip (Lig/Rec/Complex) command test CPPTRAJ: Broken Traj: Running broken trajectory. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD CPPTRAJ: Per-Residue RMSD Test. CPPTRAJ: Trajout Frame Range [Amber Coordinates] CPPTRAJ: Bzip2ed trajectory read with offsets All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DSSP CPPTRAJ: Secstruct (DSSP) command test. CPPTRAJ: Per-Residue RMSD Test with averaging CPPTRAJ: NetCDF Replica Trajectory Run test CPPTRAJ: Multi frame strip command test. CPPTRAJ: Start argument offset CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj CPPTRAJ: Strip topology with PDB info All 4 comparisons passed. CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Center All 11 comparisons passed. CPPTRAJ: Center command test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hbond CPPTRAJ: Solute Hbond test CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj CPPTRAJ: Compressed broken trajectory test CPPTRAJ: Center origin command test. CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj CPPTRAJ: Per-Residue RMSD Test with residue centering. CPPTRAJ: Secstruct (DSSP) command with changing number of residues. All 2 comparisons passed. CPPTRAJ: Solute Hbond test with disk caching All 15 comparisons passed. CPPTRAJ: CRD Replica Trajectory Run with remdout ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NCrestart CPPTRAJ: NetCDF Restart Test - TXT->NetCDF ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Parallel CPPTRAJ: Parallel tests. CPPTRAJ: Center origin mass command test. All 3 comparisons passed. CPPTRAJ: Secstruct (DSSP): SS assign output test CPPTRAJ: NetCDF Restart Test - NetCDF->TXT ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Image CPPTRAJ: Orthorhombic imaged distance test. CPPTRAJ: Solute-solvent hbond test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf CPPTRAJ: Surface calculation test All 8 comparisons passed. CPPTRAJ: Parallel test with trajectory offset CPPTRAJ: Center reference command test. CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radgyr CPPTRAJ: Radius of gyration command test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mask CPPTRAJ: Non-orthorhombic imaged distance test. CPPTRAJ: Mask single frame test CPPTRAJ: Hbond, no intramolecular hydrogen bonds test CPPTRAJ: FtuFabI Assignment test CPPTRAJ: Center point test. All 2 comparisons passed. CPPTRAJ: Orthorhombic coordinate imaging test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Jcoupling CPPTRAJ: J-Coupling single frame test CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt CPPTRAJ: Mask longer command test. All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diffusion CPPTRAJ: Diffusion test, no imaging. All 7 comparisons passed. CPPTRAJ: Hbond, specified solute masks ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj CPPTRAJ: RMSD Test with outtraj. CPPTRAJ: Nonorthorhombic coordinate imaging test All 10 comparisons passed. J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. Skipped test: J-Coupling extended test All 1 comparisons passed. 1 comparisons skipped. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm All 5 comparisons passed. CPPTRAJ: CHARMM PSF/DCD test CPPTRAJ: Diffusion test, old syntax. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotdif CPPTRAJ: Hbond, no angle cutoff test CPPTRAJ: Rotational diffusion calculation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj CPPTRAJ: Convert mdcrd -> NetCDF CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar CPPTRAJ: CHARMM DCD Write, step 1. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Runavg CPPTRAJ: Coordinate Running Average test. CPPTRAJ: Hbond, Bridge nointramol test CPPTRAJ: Diffusion test, new syntax. CPPTRAJ: CHARMM DCD Write, step 2. CPPTRAJ: Coordinate Running Average Traj Write CPPTRAJ: Convert NetCDF -> mdcrd CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM All 2 comparisons passed. All 4 comparisons passed. CPPTRAJ: Diffusion test, nonorthogonal box ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RMSD CPPTRAJ: Basic RMSD tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_2DRMS CPPTRAJ: 2D RMSD Test. All 6 comparisons passed. CPPTRAJ: STFC Diffusion Test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mol2 CPPTRAJ: Mol2 Parm/Traj Read/Write Test. CPPTRAJ: 2D RMSD Test, mass-weighted. All 1 comparisons passed. CPPTRAJ: RMS coordinate rotation/rotation matrices test CPPTRAJ: Outtraj Test with maxmin. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct CPPTRAJ: NAstruct command test. CPPTRAJ: STFC Diffusion Test with individual distances CPPTRAJ: PDB => Mol2 CPPTRAJ: Amber Top/Rst => Mol2 CPPTRAJ: RMS fit with no coordinates modification test. CPPTRAJ: STFC Diffusion Test with COM All 4 comparisons passed. CPPTRAJ: CHAMBER topology read/strip test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Average CPPTRAJ: 2D RMSD Test with reference trajectory 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. CPPTRAJ: Average Test. CPPTRAJ: NAstruct command test, single strand CPPTRAJ: STFC Diffusion Test with second mask CPPTRAJ: Partial Surface calculation test CPPTRAJ: Read CHARMM restart All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pucker CPPTRAJ: Pucker command test CPPTRAJ: RMS fit to previous test CPPTRAJ: 2D DME Test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomMap CPPTRAJ: AtomMap Test All 11 comparisons passed. g++ -o a.out main.o NameType.o CpptrajStdio.o CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test CPPTRAJ: CHARMM PSF write CPPTRAJ: Hbond with imaging CPPTRAJ: 2D RMSD with reference mask test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct_8OG CPPTRAJ: NA test (8OG) CPPTRAJ: RMS: imaging after unit cell rotation CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. CPPTRAJ: AtomMap with 'rmsfit' CPPTRAJ: Hbond, orthogonal imaging All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Datafile CPPTRAJ: CHARMM COORdinates test CPPTRAJ: Data file output precision test CPPTRAJ: 2D RMSD test, no fitting. All 12 comparisons passed. make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial CPPTRAJ: Atom map charmm->amber atom order CPPTRAJ: Radial test, non-orthogonal imaging ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist CPPTRAJ: 1D/2D Histogram Analysis test All 6 comparisons passed. '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. All 6 comparisons passed. All 16 comparisons passed. CPPTRAJ: Standard -> Grace Data All 23 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CharmmParams ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest CPPTRAJ: Test updating topology with Charmm parameters (single residue) CPPTRAJ: Closest command test using first solvent atom. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DRMSD CPPTRAJ: Distance RMSD test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_IRED CPPTRAJ: IRED vector/matrix test CPPTRAJ: Grace -> Standard Data ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster CPPTRAJ: Atom map charmm->amber atom order, by residue CPPTRAJ: Cluster command test, in-memory pairwise distances. All 2 comparisons passed. CPPTRAJ: X column format/precision test. All 9 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons CPPTRAJ: Closest command test using all solvent atoms. CPPTRAJ: randomizeions test (original algorithm) CPPTRAJ: 3D histogram test. CPPTRAJ: Cluster command test, read pairwise distances. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Corr CPPTRAJ: LCPO test with GAFF atom types CPPTRAJ: Correlation test CPPTRAJ: Data file group by name test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Molsurf CPPTRAJ: Molsurf test All 7 comparisons passed. All 3 comparisons passed. All 2 comparisons passed. CPPTRAJ: Data file group by aspect test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckStructure CPPTRAJ: Structure Check CPPTRAJ: Cluster command test, read NetCDF pairwise distances. CPPTRAJ: Closest command test, using mask center ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RmsAvgCorr All 6 comparisons passed. CPPTRAJ: RmsAvgCorr Reference ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Contacts CPPTRAJ: Contacts test. CPPTRAJ: Cluster command test, write ASCII pairwise distances. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Principal CPPTRAJ: Principal Test CPPTRAJ: Structure Check with Around and Skip CPPTRAJ: Cluster command test, read ASCII pairwise distances. CPPTRAJ: Closest command test, using mask center and solvent mask CPPTRAJ: RmsAvgCorr First All 9 comparisons passed. All 3 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve CPPTRAJ: Cluster, nosieve ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Vector CPPTRAJ: Basic vector tests CPPTRAJ: Closest command test, solvent mask, water oxygen only CPPTRAJ: Radial test, orthogonal and no imaging ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Matrix CPPTRAJ: Matrix Tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ClusterDihedral CPPTRAJ: clusterdihedral test CPPTRAJ: Cluster, sieve5 CPPTRAJ: Structure Check with PBC All 4 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. All 9 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Grid CPPTRAJ: Dipole test CPPTRAJ: Cluster, nosieve savepairdist CPPTRAJ: Test vector center with magnitude CPPTRAJ: Randomize (around, overlap) CPPTRAJ: Grid test CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Unwrap CPPTRAJ: Unwrap non-orthogonal test All 1 comparisons passed. CPPTRAJ: Cluster, nosieve loadpairdist CPPTRAJ: Generate matrix with trajectory start/stop/offset CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes CPPTRAJ: Modes analysis, RMS fluctuations CPPTRAJ: Momentum/velocity vector test. CPPTRAJ: OpenDX Grid read test CPPTRAJ: Generate matrix with action stop/start/offset CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. CPPTRAJ: Modes analysis, displacements CPPTRAJ: Unwrap orthogonal test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Project All 15 comparisons passed. CPPTRAJ: Cluster, sieve5 savepairdist CPPTRAJ: Modes analysis, dipole correlation ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Watershell CPPTRAJ: Force vector test. CPPTRAJ: Watershell Test, non-orthorhombic imaging. CPPTRAJ: Grid with specified center test. CPPTRAJ: Atomicfluct test with ADP output CPPTRAJ: Projection All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AnalysisRunAvg CPPTRAJ: Analysis Running Average All 8 comparisons passed. All 1 comparisons passed. CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. CPPTRAJ: Grid with box center offset test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volmap All 14 comparisons passed. CPPTRAJ: VMD VolMap Algorithm test All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SPAM CPPTRAJ: SPAM Test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Density CPPTRAJ: Density along axis tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LIE CPPTRAJ: LIE test CPPTRAJ: Grid with mask center offset test. All 13 comparisons passed. 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_LipidOrder CPPTRAJ: Lipid Order Parameter Test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PairDist CPPTRAJ: PairDist Test. CPPTRAJ: Cluster, sieve5 loadpairdist CPPTRAJ: Modes analysis, pseudo trajectory creation test CPPTRAJ: Multi-frame density along axis test CPPTRAJ: Randomize (around) CPPTRAJ: Non-orthogonal grid test. CPPTRAJ: Cluster, nosieve pairwisecache none CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test CPPTRAJ: Total system density test CPPTRAJ: Pairdist test, orthogonal imaging. CPPTRAJ: SPAM Pure Solvent Test CPPTRAJ: Structure Check with Around CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test All 7 comparisons passed. All 6 comparisons passed. All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReadData CPPTRAJ: Read vector data test (no origins, origins) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidSCD CPPTRAJ: Basic lipid order parameter test CPPTRAJ: Grid generation from 'bounds' test. CPPTRAJ: Read vector data set (origins, no origins) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST CPPTRAJ: GIST water-water interaction test g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o CPPTRAJ: Read Amber output test All 13 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_systemVF CPPTRAJ: Read CHARMM output test CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test CPPTRAJ: New Lipid Order Parameter Test, DOPC. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicCorr CPPTRAJ: Atomic Correlation test All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr CPPTRAJ: AutoCorr test. CPPTRAJ: 3D data read/write test CPPTRAJ: Cluster, sieve5 pairwisecache none make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' CPPTRAJ: Standard 3D data write test Unit test passed. make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' All 1 comparisons passed. CPPTRAJ: Randomize (overlap) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Box ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomTypeSelect CPPTRAJ: Box Test (Add box info) CPPTRAJ: Selection by atom type test. All 4 comparisons passed. CPPTRAJ: Cluster, random CPPTRAJ: Standard 3D data read test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AvgRef CPPTRAJ: RMSD Test with averaged reference coordinates. All 1 comparisons passed. All 1 comparisons passed. ******************************************************************************** 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: Standard 3D data read/append test CPPTRAJ: COORDS data set creation and CRDFLUCT test. All 1 comparisons passed. CPPTRAJ: Box test (remove box info) CPPTRAJ: Randomize (no restrictions) All 28 comparisons passed. All 3 comparisons passed. CPPTRAJ: COORDS data set creation with velocities test CPPTRAJ: Box test (Modify box length) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LoadCrd CPPTRAJ: LoadCrd test. CPPTRAJ: Standard 3D data, sparse ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoImage CPPTRAJ: AutoImage test (split DNA duplex) CPPTRAJ: Nonorthogonal grid standard write/read tests. CPPTRAJ: Box test (auto orthogonal box, no radii) All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MultiVector CPPTRAJ: Multivector test CPPTRAJ: LoadTraj test. CPPTRAJ: Pairdist test, nonorthogonal imaging. CPPTRAJ: TRAJ data set creation and CRDFLUCT test. All 1 comparisons passed. CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Lifetime CPPTRAJ: LoadTraj from trajin test. CPPTRAJ: Lifetime test. CPPTRAJ: Box test (auto orthogonal box, VDW radii) CPPTRAJ: TRAJ data set creation with velocities test. All 7 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FFT CPPTRAJ: FFT test. CPPTRAJ: LoadCrd append from multiple files test CPPTRAJ: Lifetime test with data set caching. CPPTRAJ: AutoImage test, use anchor mask All 4 comparisons passed. CPPTRAJ: COORDS data set append test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet All 4 comparisons passed. CPPTRAJ: Clustering, One DataSet CPPTRAJ: Watershell Test, orthorhombic imaging. All 2 comparisons passed. All 5 comparisons passed. CPPTRAJ: Lifetime average and cumulative average test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Timecorr CPPTRAJ: Timecorr test. CPPTRAJ: COORDS test storing frame metadata CPPTRAJ: Clustering, Two DataSets All 12 comparisons passed. ******************************************************************************** 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 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multidihedral CPPTRAJ: CrossCorr test CPPTRAJ: Multidihedral test CPPTRAJ: Clustering, dihedral DataSet CPPTRAJ: ASP symmetry-corrected RMSD test CPPTRAJ: Multidihedral Nucleotide CHI test All 1 comparisons passed. All 7 comparisons passed. CPPTRAJ: TRAJ test storing frame metadata CPPTRAJ: Clustering, two dihedral DataSets ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MakeStructure CPPTRAJ: Read specific columns test. CPPTRAJ: Basic makestructure test CPPTRAJ: GLU symmetry-corrected RMSD test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ensemble_MREMD CPPTRAJ: Clustering, dihedral DataSet, K-means CPPTRAJ: Multidihedral protein dihedrals test CPPTRAJ: M-REMD sort test. CPPTRAJ: Write non-square matrix CPPTRAJ: Makestructure test with reference. CPPTRAJ: Clustering, two dihedral DataSets, K-means CPPTRAJ: Watershell Test, no imaging. CPPTRAJ: Multidihedral cyclic molecule test All 8 comparisons passed. CPPTRAJ: Read non-square matrix CPPTRAJ: TYR symmetry-corrected RMSD test All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotate CPPTRAJ: Rotation (and inverse) of coords from matrices ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Integrate CPPTRAJ: Integration test. All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN All 6 comparisons passed. CPPTRAJ: Longer symmetry-corrected RMSD test. CPPTRAJ: DBSCAN test CPPTRAJ: Read square matrix All 1 comparisons passed. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckChiral CPPTRAJ: Check chirality test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Energy CPPTRAJ: M-REMD actions test. CPPTRAJ: Simple energy tests All 8 comparisons passed. All 15 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts CPPTRAJ: Rotate with defined axis All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PermuteDihedrals ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LESsplit CPPTRAJ: PermuteDihedrals interval -120, phi psi CPPTRAJ: LES split/average test CPPTRAJ: NativeContacts test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CCP4 CPPTRAJ: CCP4 read/write and DX conversion test. CPPTRAJ: DBSCAN automatic parameter determination test. All 3 comparisons passed. CPPTRAJ: PermuteDihedrals, random rotations ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihCovar All 3 comparisons passed. All 2 comparisons passed. CPPTRAJ: Dihedral Covariance Matrix Test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CurveFit ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetAverage CPPTRAJ: Curve fitting test. CPPTRAJ: DBSCAN kdist map test CPPTRAJ: M-REMD ensemble outtraj test. CPPTRAJ: Data set averaging and averaging over all sets test. CPPTRAJ: Test kinetic energy calculation All 4 comparisons passed. All 2 comparisons passed. CPPTRAJ: Curve fitting multi-exponential tests. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VectorMath CPPTRAJ: Vector dot/cross product test CPPTRAJ: M-REMD no sort, running average test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander SANDER energy tests (long) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. SKIP: SANDER energy tests (long) All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander_Short Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. SKIP: Energy via sander API short tests (GB/PME) CPPTRAJ: Pairdist test, 2 masks. CPPTRAJ: Test total energy calculation CPPTRAJ: DBSCAN with sieve ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Temperature CPPTRAJ: Temperature test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Spline CPPTRAJ: Spline test All 2 comparisons passed. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_KDE ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Wavelet CPPTRAJ: KDE test. CPPTRAJ: Wavelet analysis test All 1 comparisons passed. CPPTRAJ: Temperature with SHAKE on hydrogens. All 4 comparisons passed. CPPTRAJ: M-REMD, generate RMS data All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CIF CPPTRAJ: Test partial energy calculation CPPTRAJ: CIF read test CPPTRAJ: Curve fitting, custom output range. CPPTRAJ: GIST test, orthogonal cell ******************************************************************************** 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_Cluster_Kmeans CPPTRAJ: Temperature with SHAKE on all atoms. CPPTRAJ: M-REMD, meltcurve analysis All 6 comparisons passed. CPPTRAJ: Cpptraj Kmeans CPPTRAJ: Wavelet WAFEX test All 6 comparisons passed. CPPTRAJ: NativeContacts test, save non-native contacts, residue time series CPPTRAJ: Temperature calc with extra points. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Align ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multicurve CPPTRAJ: Align Tests. All 17 comparisons passed. CPPTRAJ: Multicurve test CPPTRAJ: PQR file write with various radii ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelocityAutoCorr CPPTRAJ: Velocity autocorrelation test CPPTRAJ: KDE with Kullback-Leibler divergence test CPPTRAJ: Generate offset traj from PDB CPPTRAJ: Cpptraj Kmeans random CPPTRAJ: Align, unit cell rotation/imaging test. All 1 comparisons passed. All 5 comparisons passed. CPPTRAJ: PDB filter alternate atom location IDs test CPPTRAJ: Generate offset traj from CIF CPPTRAJ: NativeContacts test, orthorhombic imaging. All 4 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RotateDihedral ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelFrc CPPTRAJ: Rotate dihedral to target value. CPPTRAJ: Test combining coordinates, velocities, and forces. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remap CPPTRAJ: Remap Test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CompareTop CPPTRAJ: Compare topology test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetCmd CPPTRAJ: Data Set commands test CPPTRAJ: Test using velocities as coordinates. CPPTRAJ: Rotate dihedral by increment CPPTRAJ: Adding PDB info to topology All 6 comparisons passed. All 2 comparisons passed. All 1 comparisons passed. All 1 comparisons passed. CPPTRAJ: Test writing velocities (MDVEL) All 10 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Filter ******************************************************************************** CPPTRAJ: Rotate dihedral in TRAJ data set TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_SymmRMSD ******************************************************************************** CPPTRAJ: Basic filter test TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CombineCrd CPPTRAJ: Combine COORDS test. CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTrr CPPTRAJ: TRR force/velocity read -> NetCDF write test All 17 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TopInfo CPPTRAJ: Test using forces as coordinates. CPPTRAJ: Topology info print test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ewald CPPTRAJ: Combine COORDS test with box info. CPPTRAJ: Direct sum test All 3 comparisons passed. CPPTRAJ: Data filter test. CPPTRAJ: Test writing forces (MDFRC) All 10 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TI CPPTRAJ: TI analysis test. CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. CPPTRAJ: Split coords and recombine test. CPPTRAJ: Filter matrix test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. CPPTRAJ: Fix imaged bonds test (Ortho.) All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Distance CPPTRAJ: Distance tests All 5 comparisons passed. CPPTRAJ: TRR force/velocity read -> TRR write test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volume CPPTRAJ: Volume tests CPPTRAJ: Orthogonal imaged distance All 1 comparisons passed. CPPTRAJ: CRD => TRR All 5 comparisons passed. CPPTRAJ: Topology info with reference coords test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SetVelocity CPPTRAJ: Set Velocity test CPPTRAJ: Fix imaged bonds test (Non-ortho.) All 5 comparisons passed. All 12 comparisons passed. CPPTRAJ: Non-orthogonal imaged distance ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remlog CPPTRAJ: Scale velocity test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AreaPerMol CPPTRAJ: Replica log read/analyze test. CPPTRAJ: Cluster command test, coordinate writes. CPPTRAJ: Area per molecule test CPPTRAJ: TRR => CRD All 3 comparisons passed. All 3 comparisons passed. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DistBasedMask CPPTRAJ: Distance-based atom mask tests (atom, residue) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Calc CPPTRAJ: Calc test CPPTRAJ: Cluster command test, coordinate writes using info file. All 4 comparisons passed. CPPTRAJ: Distance-based atom mask tests (molecule) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CalcState CPPTRAJ: Calcstate test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Change CPPTRAJ: Change atom and residue name tests CPPTRAJ: Calc test with data sets All 7 comparisons passed. All 6 comparisons passed. CPPTRAJ: CRD(1-5) => TRR CPPTRAJ: Ewald test (NaCl crystal) CPPTRAJ: Change chain ID test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixAtomOrder CPPTRAJ: Out of order molecules test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateReservoir CPPTRAJ: Test math functions CPPTRAJ: Ewald test (trunc. oct) CPPTRAJ: Create RREMD NetCDF reservoir test All 4 comparisons passed. CPPTRAJ: Change chain ID of COORDS set test All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LowestCurve CPPTRAJ: CRD(6-10) => TRR CPPTRAJ: LowestCurve test All 6 comparisons passed. All 4 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MinImage CPPTRAJ: Minimum Image test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rst CPPTRAJ: Generate restraints (rst) test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Regress CPPTRAJ: Linear regression test. CPPTRAJ: TRR (appended) => CRD All 8 comparisons passed. All 1 comparisons passed. All 1 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pairwise CPPTRAJ: Pairwise tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Dpeaks ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ParmBox CPPTRAJ: Parmbox test CPPTRAJ: Density peaks clustering test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Translate ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Solvent CPPTRAJ: Test solvent command with closest CPPTRAJ: Translate test All 1 comparisons passed. All 1 comparisons passed. All 3 comparisons passed. CPPTRAJ: GMX: CRD with offset All 1 comparisons passed. ******************************************************************************** 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_ScaleDihedralK CPPTRAJ: Scale dihedral force constant test CPPTRAJ: Pairwise test, partial system CPPTRAJ: Scale dihedral force constant with 'useall' All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Control All 5 comparisons passed. CPPTRAJ: Loop tests CPPTRAJ: GMX: TRR with offset CPPTRAJ: Ewald test (partial system, trunc. oct) All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_InfraredSpec ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PhiPsi All 2 comparisons passed. CPPTRAJ: Infrared spectrum calculation test All 10 comparisons passed. CPPTRAJ: Phipsi test All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cphstats ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Nreps CPPTRAJ: Explicit pH REMD ensemble data read / sort CPPTRAJ: Clustering with specified # reps 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_CmdLine ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XYZformat CPPTRAJ: Command line trajectory args test, part 1 All 5 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CatCrd CPPTRAJ: XYZ format write CPPTRAJ: Command line test trajectory args test, part 2 CPPTRAJ: Concatenate COORDS data set test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hausdorff All 2 comparisons passed. CPPTRAJ: Simple Hausdorff distance test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LibPME ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc CPPTRAJ: Particle mesh Ewald test (NaCl crystal) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Time CPPTRAJ: Add time to restart test CPPTRAJ: XTC read test All 1 comparisons passed. CPPTRAJ: Test set command CPPTRAJ: Command line wildcard test, part 1 CPPTRAJ: Atom XYZ format read, test 1 All 2 comparisons passed. CPPTRAJ: Constant pH stats test CPPTRAJ: Particle mesh Ewald test (trunc. oct) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XtalSymm CPPTRAJ: XtalSymm Reference ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SplitCoords ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihedralRMS CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) CPPTRAJ: CRD => XTC CPPTRAJ: SplitCoords test CPPTRAJ: Remove time from restart test CPPTRAJ: Hausdorff distance of 2D rms output test. CPPTRAJ: Atom XYZ format read, test 2 CPPTRAJ: Sorted implicit constant pH stats test CPPTRAJ: Command line wildcard test, part 2 CPPTRAJ: Test reading comma-separated list of strings CPPTRAJ: Add time to trajectory test CPPTRAJ: XTC => CRD All 1 comparisons passed. All 2 comparisons passed. CPPTRAJ: Atom XYZ format read, test 3 CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats CPPTRAJ: Dihedral RMSD test (to previous) CPPTRAJ: Test nested loops and variables in loops CPPTRAJ: Hausdorff distance of 2D rms output test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Slope CPPTRAJ: Finite difference test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diagmatrix CPPTRAJ: Dihedral RMS fluctuation test. CPPTRAJ: MW covariance matrix thermo analysis test CPPTRAJ: Test loop over data set blocks CPPTRAJ: Particle mesh Ewald test (ortho) CPPTRAJ: CRD(1-5) => XTC CPPTRAJ: Atom XYZ format read, test 4 All 1 comparisons passed. All 5 comparisons passed. CPPTRAJ: XtalSymm Reimaging by Atom All 1 comparisons passed. CPPTRAJ: Modify time info test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau CPPTRAJ: Evalulate plateau test CPPTRAJ: CRD(6-10) => XTC ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Emin CPPTRAJ: Basic energy minimization test. CPPTRAJ: Atom XYZ format read, test 5 CPPTRAJ: Test for filename wildcards and oversets ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Graft CPPTRAJ: Graft test All 2 comparisons passed. All 4 comparisons passed. CPPTRAJ: Unsorted pH read/write test CPPTRAJ: XTC (appended) => CRD CPPTRAJ: Energy minimization with angle term test. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Random CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs CPPTRAJ: Particle mesh Ewald test (ortho, with mask) All 13 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Flatten All 3 comparisons passed. All 16 comparisons passed. CPPTRAJ: Flatten test. CPPTRAJ: Atom XYZ format read, test 6 CPPTRAJ: PCG32 RNG test. CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. CPPTRAJ: Energy minimization with nonbond term test. CPPTRAJ: Test Stdlib RNG All 6 comparisons passed. CPPTRAJ: PME test (partial system, trunc. oct) CPPTRAJ: GIST test, nonorthogonal cell CPPTRAJ: Test Mersenne Twister RNG All 1 comparisons passed. CPPTRAJ: GMX: CRD with offset All 4 comparisons passed. CPPTRAJ: GMX: XTC with offset PME test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: PME test (trunc. oct), 10 frames All 5 comparisons passed. 1 comparisons skipped. CPPTRAJ: OpenMM basic energy minimization tests (bonds) All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LJ_PME ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTNG CPPTRAJ: OpenMM basic energy minimization tests (angles) CPPTRAJ: LJ PME test. CPPTRAJ: TNG read test CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) CPPTRAJ: LJ PME kappa sweep test, 0.25 CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) CPPTRAJ: LJ PME kappa sweep test, 0.35 CPPTRAJ: TNG read test (with offset) CPPTRAJ: LJ PME kappa sweep test, 0.45 CPPTRAJ: XtalSymm Reimaging by Molecule CPPTRAJ: LJ PME kappa sweep test, 0.5 CPPTRAJ: LJ with switch function test All 6 comparisons passed. All 5 comparisons passed. CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) All 3 comparisons passed. All 11 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST_Order CPPTRAJ: TIP3P water cluster test CPPTRAJ: TIP4P water cluster test CPPTRAJ: TIP5P water cluster test All 4 comparisons passed. All 9 comparisons passed. 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 186114960 Mar 8 14:52 ../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 -j12 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 READLINE build Skipping bundled ARPACK build g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o -L/usr/lib/x86_64-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/x86_64-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/x86_64-linux-gnu/lib -lfftw3 -L/usr/lib/x86_64-linux-gnu/lib -lOpenMM -lnetcdf -lbz2 tng/libtng_io.a -lz xdrfile/libxdrfile.a -Wl,-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' in '../cpptraj_5.1.0+dfsg-4_amd64.deb'. dpkg-deb: building package 'cpptraj-dbgsym' in '../cpptraj-dbgsym_5.1.0+dfsg-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../cpptraj_5.1.0+dfsg-4_amd64.buildinfo dpkg-genchanges --build=binary -O../cpptraj_5.1.0+dfsg-4_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/120576/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/120576/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/120576 and its subdirectories I: Current time: Sun Mar 9 04:52:47 +14 2025 I: pbuilder-time-stamp: 1741445567