I: pbuilder: network access will be disabled during build I: Current time: Thu Feb 26 21:28:37 -12 2026 I: pbuilder-time-stamp: 1772184517 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: using eatmydata during job 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/112505/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='6bdda9c586d64f79b64fdddaefee8e3b' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='112505' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.HcEnNzdT/pbuilderrc_tcpi --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HcEnNzdT/b1 --logfile b1/build.log cpptraj_5.1.0+dfsg-4.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos6-i386 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/112505/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: i386 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, 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 ... 19818 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 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-i686-linux-gnu{a} gfortran-i686-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} libnetcdf19t64{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} 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, 132 newly installed, 0 to remove and 0 not upgraded. Need to get 85.7 MB of archives. After unpacking 328 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-6 [69.4 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.23.1-1 [245 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-7 [1199 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.4-1 [96.1 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-5 [301 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 autopoint all 0.23.1-1 [770 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.2-1 [24.3 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 comerr-dev i386 2.1-1.47.2-1 [56.2 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 libtool all 2.5.4-2 [539 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 25 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 libunistring5 i386 1.3-1 [458 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-6 [9582 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 gettext i386 0.23.1-1 [1714 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 debhelper all 13.24.1 [920 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.2.0-14 [735 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 libgfortran-14-dev i386 14.2.0-14 [800 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 gfortran-14-i686-linux-gnu i386 14.2.0-14 [12.5 MB] Get: 37 http://deb.debian.org/debian unstable/main i386 gfortran-14 i386 14.2.0-14 [13.5 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 gfortran-i686-linux-gnu i386 4:14.2.0-1 [1280 B] Get: 39 http://deb.debian.org/debian unstable/main i386 gfortran i386 4:14.2.0-1 [1432 B] Get: 40 http://deb.debian.org/debian unstable/main i386 hdf5-helpers i386 1.14.5+repack-3 [26.6 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 icu-devtools i386 72.1-6 [218 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-4 [35.0 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-4 [83.7 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 45 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-4 [354 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-4 [149 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 libgssrpc4t64 i386 1.21.3-4 [63.4 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 libkadm5clnt-mit12 i386 1.21.3-4 [44.1 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 libkdb5-10t64 i386 1.21.3-4 [45.3 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 libkadm5srv-mit12 i386 1.21.3-4 [57.7 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 krb5-multidev i386 1.21.3-4 [126 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 libaec0 i386 1.1.3-1+b1 [25.0 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 libsz2 i386 1.1.3-1+b1 [8128 B] Get: 54 http://deb.debian.org/debian unstable/main i386 libaec-dev i386 1.1.3-1+b1 [23.0 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 libblas3 i386 3.12.0-4 [143 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 liblapack3 i386 3.12.0-4 [2194 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 libarpack2t64 i386 3.9.1-4 [102 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 libblas-dev i386 3.12.0-4 [155 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 liblapack-dev i386 3.12.0-4 [4452 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 libarpack2-dev i386 3.9.1-4 [122 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 libbrotli-dev i386 1.1.0-2+b6 [313 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 libbz2-dev i386 1.0.8-6 [32.1 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 libidn2-0 i386 2.3.7-2+b1 [130 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 libffi8 i386 3.4.6-1 [21.2 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 libp11-kit0 i386 0.25.5-3 [423 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 libtasn1-6 i386 4.19.0-3+b3 [51.1 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 libgnutls30t64 i386 3.8.8-2 [1451 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8+b1 [20.9 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-8+b1 [61.3 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 libldap2 i386 2.6.9+dfsg-1 [205 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 libnghttp3-9 i386 1.6.0-2 [75.9 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 libngtcp2-16 i386 1.9.1-1 [151 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 libngtcp2-crypto-gnutls8 i386 1.9.1-1 [19.1 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 libcurl3t64-gnutls i386 8.11.1-1+b1 [404 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 libevent-2.1-7t64 i386 2.1.12-stable-10+b1 [195 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 libunbound8 i386 1.22.0-1+b1 [633 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 libgnutls-dane0t64 i386 3.8.8-2 [447 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 libgnutls-openssl27t64 i386 3.8.8-2 [447 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 libidn2-dev i386 2.3.7-2+b1 [126 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 libp11-kit-dev i386 0.25.5-3 [208 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 libtasn1-6-dev i386 4.19.0-3+b3 [102 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 libgmpxx4ldbl i386 2:6.3.0+dfsg-3 [329 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 libgmp-dev i386 2:6.3.0+dfsg-3 [661 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 nettle-dev i386 3.10-1+b1 [1334 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 libgnutls28-dev i386 3.8.8-2 [1453 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 libkrb5-dev i386 1.21.3-4 [15.9 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 libldap-dev i386 2.6.9+dfsg-1 [328 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 pkgconf i386 1.8.1-4 [26.2 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 libnghttp2-dev i386 1.64.0-1 [123 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 libnghttp3-dev i386 1.6.0-2 [101 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 libngtcp2-crypto-gnutls-dev i386 1.9.1-1 [24.0 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 libngtcp2-dev i386 1.9.1-1 [202 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 libpsl-dev i386 0.21.2-1.1+b1 [78.4 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 librtmp-dev i386 2.4+20151223.gitfa8646d.1-2+b5 [72.3 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 libssl-dev i386 3.4.0-2 [2842 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 libssh2-1-dev i386 1.11.1-1 [407 kB] Get: 105 http://deb.debian.org/debian unstable/main i386 libzstd-dev i386 1.5.6+dfsg-2 [354 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 libcurl4-gnutls-dev i386 8.11.1-1+b1 [535 kB] Get: 107 http://deb.debian.org/debian unstable/main i386 libcurl4t64 i386 8.11.1-1+b1 [393 kB] Get: 108 http://deb.debian.org/debian unstable/main i386 libfftw3-double3 i386 3.3.10-2+b1 [629 kB] Get: 109 http://deb.debian.org/debian unstable/main i386 libfftw3-long3 i386 3.3.10-2+b1 [349 kB] Get: 110 http://deb.debian.org/debian unstable/main i386 libfftw3-quad3 i386 3.3.10-2+b1 [1860 kB] Get: 111 http://deb.debian.org/debian unstable/main i386 libfftw3-single3 i386 3.3.10-2+b1 [646 kB] Get: 112 http://deb.debian.org/debian unstable/main i386 libfftw3-bin i386 3.3.10-2+b1 [50.0 kB] Get: 113 http://deb.debian.org/debian unstable/main i386 libfftw3-dev i386 3.3.10-2+b1 [3254 kB] Get: 114 http://deb.debian.org/debian unstable/main i386 libhdf5-310 i386 1.14.5+repack-3 [1327 kB] Get: 115 http://deb.debian.org/debian unstable/main i386 libhdf5-cpp-310 i386 1.14.5+repack-3 [140 kB] Get: 116 http://deb.debian.org/debian unstable/main i386 libhdf5-fortran-310 i386 1.14.5+repack-3 [119 kB] Get: 117 http://deb.debian.org/debian unstable/main i386 libhdf5-hl-310 i386 1.14.5+repack-3 [81.6 kB] Get: 118 http://deb.debian.org/debian unstable/main i386 libhdf5-hl-fortran-310 i386 1.14.5+repack-3 [45.7 kB] Get: 119 http://deb.debian.org/debian unstable/main i386 libhdf5-hl-cpp-310 i386 1.14.5+repack-3 [24.9 kB] Get: 120 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo i386 1:2.1.5-3+b1 [171 kB] Get: 121 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo-dev i386 1:2.1.5-3+b1 [305 kB] Get: 122 http://deb.debian.org/debian unstable/main i386 libjpeg-dev i386 1:2.1.5-3+b1 [72.2 kB] Get: 123 http://deb.debian.org/debian unstable/main i386 libhdf5-dev i386 1.14.5+repack-3 [3319 kB] Get: 124 http://deb.debian.org/debian unstable/main i386 libicu-dev i386 72.1-6 [10.6 MB] Get: 125 http://deb.debian.org/debian unstable/main i386 libncurses6 i386 6.5-2+b1 [112 kB] Get: 126 http://deb.debian.org/debian unstable/main i386 libncurses-dev i386 6.5-2+b1 [505 kB] Get: 127 http://deb.debian.org/debian unstable/main i386 libnetcdf19t64 i386 1:4.9.2-7+b1 [529 kB] Get: 128 http://deb.debian.org/debian unstable/main i386 libxml2-dev i386 2.12.7+dfsg+really2.9.14-0.2+b1 [857 kB] Get: 129 http://deb.debian.org/debian unstable/main i386 libnetcdf-dev i386 1:4.9.2-7+b1 [104 kB] Get: 130 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-6 [173 kB] Get: 131 http://deb.debian.org/debian unstable/main i386 libreadline-dev i386 8.2-6 [166 kB] Get: 132 http://deb.debian.org/debian unstable/main i386 netcdf-bin i386 1:4.9.2-7+b1 [262 kB] Fetched 85.7 MB in 1s (63.5 MB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19818 files and directories currently installed.) Preparing to unpack .../000-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. 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Setting up file (1:5.45-3+b1) ... Setting up libaec0:i386 (1.1.3-1+b1) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up libkrb5support0:i386 (1.21.3-4) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-8+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.12.0-4) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libunbound8:i386 (1.22.0-1+b1) ... Setting up libpkgconf3:i386 (1.8.1-4) ... Setting up libgmpxx4ldbl:i386 (2:6.3.0+dfsg-3) ... Setting up libjpeg62-turbo:i386 (1:2.1.5-3+b1) ... Setting up libjpeg62-turbo-dev:i386 (1:2.1.5-3+b1) ... Setting up libncurses6:i386 (6.5-2+b1) ... Setting up libfftw3-quad3:i386 (3.3.10-2+b1) ... Setting up comerr-dev:i386 (2.1-1.47.2-1) ... Setting up libunistring5:i386 (1.3-1) ... Setting up libssl-dev:i386 (3.4.0-2) ... Setting up autopoint (0.23.1-1) ... 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Setting up libldap2:i386 (2.6.9+dfsg-1) ... Setting up libbrotli-dev:i386 (1.1.0-2+b6) ... Setting up libblas-dev:i386 (3.12.0-4) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode Setting up libsz2:i386 (1.1.3-1+b1) ... Setting up libbz2-dev:i386 (1.0.8-6) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:i386 (14.2.0-14) ... Setting up libfile-stripnondeterminism-perl (1.14.1-1) ... Setting up liblapack3:i386 (3.12.0-4) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up libncurses-dev:i386 (6.5-2+b1) ... Setting up gettext (0.23.1-1) ... Setting up libarpack2t64:i386 (3.9.1-4) ... 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Setting up libngtcp2-crypto-gnutls8:i386 (1.9.1-1) ... Setting up libkadm5clnt-mit12:i386 (1.21.3-4) ... Setting up libgnutls28-dev:i386 (3.8.8-2) ... Setting up libcurl4t64:i386 (8.11.1-1+b1) ... Setting up libkdb5-10t64:i386 (1.21.3-4) ... Setting up libcurl3t64-gnutls:i386 (8.11.1-1+b1) ... Setting up debhelper (13.24.1) ... Setting up libngtcp2-crypto-gnutls-dev:i386 (1.9.1-1) ... 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 librtmp-dev:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhdf5-310:i386 (1.14.5+repack-3) ... Setting up libkadm5srv-mit12:i386 (1.21.3-4) ... Setting up libhdf5-fortran-310:i386 (1.14.5+repack-3) ... Setting up krb5-multidev:i386 (1.21.3-4) ... Setting up libhdf5-cpp-310:i386 (1.14.5+repack-3) ... Setting up libhdf5-hl-310:i386 (1.14.5+repack-3) ... Setting up libnetcdf19t64:i386 (1:4.9.2-7+b1) ... Setting up netcdf-bin (1:4.9.2-7+b1) ... Setting up libkrb5-dev:i386 (1.21.3-4) ... Setting up libhdf5-hl-cpp-310:i386 (1.14.5+repack-3) ... Setting up libhdf5-hl-fortran-310:i386 (1.14.5+repack-3) ... Setting up libcurl4-gnutls-dev:i386 (8.11.1-1+b1) ... Setting up libhdf5-dev (1.14.5+repack-3) ... update-alternatives: using /usr/lib/i386-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/i386-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libnetcdf-dev (1:4.9.2-7+b1) ... Processing triggers for libc-bin (2.40-6) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/cpptraj-5.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../cpptraj_5.1.0+dfsg-4_source.changes dpkg-buildpackage: info: source package cpptraj dpkg-buildpackage: info: source version 5.1.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 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 -j22 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/i386-linux-gnu --with-fftw3=/usr/lib/i386-linux-gnu --with-readline=/usr/lib/i386-linux-gnu arpack specified: /usr/lib/i386-linux-gnu fftw3 specified: /usr/lib/i386-linux-gnu readline specified: /usr/lib/i386-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 vmdplugin disabled due to nonfree source. Configuration summary: Build type: Serial Options: netcdf bzlib tng zlib arpack lapack blas fftw3 readline xdrfile 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 -j22 make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make install make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' CXX SpaceGroup.cpp CXX ActionFrameCounter.cpp CXX ActionList.cpp CXX ActionTopWriter.cpp CXX Action_Align.cpp CXX Action_Angle.cpp CXX Action_AreaPerMol.cpp CXX Action_AtomMap.cpp CXX Action_AtomicCorr.cpp CXX Action_AtomicFluct.cpp CXX Action_AutoImage.cpp CXX Action_Average.cpp CXX Action_Bounds.cpp CXX Action_Box.cpp CXX Action_Center.cpp CXX Action_Channel.cpp CXX Action_CheckChirality.cpp CXX Action_CheckStructure.cpp CXX Action_Closest.cpp CXX Action_ClusterDihedral.cpp CXX Action_Contacts.cpp CXX Action_CreateCrd.cpp CXX Action_CreateReservoir.cpp CXX Action_DNAionTracker.cpp CXX Action_DSSP.cpp CXX Action_Density.cpp CXX Action_Diffusion.cpp CXX Action_Dihedral.cpp CXX Action_DihedralRMS.cpp CXX Action_Dipole.cpp CXX Action_Distance.cpp CXX Action_DistRmsd.cpp CXX Action_Energy.cpp CXX Action_FilterByData.cpp CXX Action_FixAtomOrder.cpp CXX Action_FixImagedBonds.cpp CXX Action_GIST.cpp 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_Grid.cpp CXX Action_GridFreeEnergy.cpp CXX Action_HydrogenBond.cpp CXX Action_Image.cpp CXX Action_InfraredSpectrum.cpp CXX Action_Jcoupling.cpp CXX Action_LESsplit.cpp CXX Action_LIE.cpp CXX Action_LipidOrder.cpp CXX Action_MakeStructure.cpp CXX Action_Mask.cpp CXX Action_Matrix.cpp CXX Action_MinImage.cpp CXX Action_Molsurf.cpp CXX Action_MultiDihedral.cpp CXX Action_MultiVector.cpp CXX Action_NAstruct.cpp CXX Action_NativeContacts.cpp CXX Action_NMRrst.cpp 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:76:40: 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:76:40: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:815:31: Vec3.h:76:23: 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_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 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 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 AssociatedData.cpp CXX Atom.cpp CXX AtomMap.cpp CXX AtomMask.cpp CXX AxisType.cpp CXX BondSearch.cpp CXX Box.cpp CXX BoxArgs.cpp CXX BufferedFrame.cpp CXX BufferedLine.cpp CXX ByteRoutines.cpp CXX CharMask.cpp CXX CharmmParamFile.cpp CXX CIFfile.cpp CXX ClusterDist.cpp CXX ClusterList.cpp CXX ClusterMap.cpp CXX ClusterMatrix.cpp CXX ClusterNode.cpp CXX ClusterSieve.cpp CXX Cluster_DBSCAN.cpp CXX Cluster_DPeaks.cpp CXX Cluster_HierAgglo.cpp CXX Cluster_Kmeans.cpp CXX Cluster_ReadInfo.cpp CXX Cmd.cpp CXX CmdInput.cpp CXX CmdList.cpp CXX CompactFrameArray.cpp CXX ComplexArray.cpp CXX Constraints.cpp CXX ControlBlock_For.cpp CXX CoordinateInfo.cpp CXX Corr.cpp CXX Cph.cpp CXX CpptrajFile.cpp CXX CpptrajState.cpp CXX CpptrajStdio.cpp CXX CurveFit.cpp CXX DataFile.cpp CXX DataFileList.cpp CXX DataFilter.cpp CXX DataIO.cpp CXX DataIO_CCP4.cpp CXX DataIO_CharmmFastRep.cpp CXX DataIO_CharmmOutput.cpp CXX DataIO_CharmmRepLog.cpp CXX DataIO_CharmmRtfPrm.cpp CXX DataIO_Cmatrix.cpp CXX DataIO_Cpout.cpp CXX DataIO_Evecs.cpp CXX DataIO_Gnuplot.cpp CXX DataIO_Grace.cpp CXX DataIO_OpenDx.cpp CXX DataIO_Peaks.cpp CXX DataIO_Mdout.cpp CXX DataIO_NC_Cmatrix.cpp CXX DataIO_RemLog.cpp CXX DataIO_Std.cpp CXX DataIO_VecTraj.cpp CXX DataIO_Xplor.cpp CXX DataIO_XVG.cpp CXX DataSet.cpp CXX DataSetList.cpp CXX DataSet_1D.cpp CXX DataSet_3D.cpp CXX DataSet_Cmatrix.cpp CXX DataSet_Cmatrix_DISK.cpp CXX DataSet_Cmatrix_MEM.cpp CXX DataSet_Cmatrix_NOMEM.cpp CXX DataSet_Coords.cpp CXX DataSet_Coords_CRD.cpp CXX DataSet_Coords_REF.cpp CXX DataSet_Coords_TRJ.cpp CXX DataSet_GridDbl.cpp CXX DataSet_GridFlt.cpp CXX DataSet_Mat3x3.cpp CXX DataSet_MatrixDbl.cpp CXX DataSet_MatrixFlt.cpp CXX DataSet_Mesh.cpp CXX DataSet_Modes.cpp CXX DataSet_Parameters.cpp CXX DataSet_pH.cpp CXX DataSet_PHREMD_Explicit.cpp CXX DataSet_PHREMD_Implicit.cpp CXX DataSet_RemLog.cpp CXX DataSet_Topology.cpp CXX DataSet_Vector.cpp CXX DataSet_Vector_Scalar.cpp CXX DataSet_double.cpp CXX DataSet_float.cpp CXX DataSet_integer_disk.cpp CXX DataSet_integer_mem.cpp CXX DataSet_string.cpp CXX DataSet_StringVar.cpp CXX DataSet_Tensor.cpp CXX DataSet_unsignedInt.cpp CXX Deprecated.cpp CXX DihedralSearch.cpp CXX DistRoutines.cpp CXX Energy.cpp CXX EnergyArray.cpp CXX EnsembleIn.cpp CXX EnsembleIn_Multi.cpp CXX EnsembleIn_Single.cpp CXX EnsembleNavigator.cpp CXX EnsembleOut.cpp CXX EnsembleOut_Multi.cpp CXX EnsembleOut_Single.cpp CXX EnsembleOutList.cpp CXX Ewald.cpp CXX Ewald_ParticleMesh.cpp CXX Ewald_Regular.cpp CXX ExclusionArray.cpp CXX Exec_AddMissingRes.cpp CXX Exec_Analyze.cpp In file included from Ewald_ParticleMesh.h:5, from Ewald_ParticleMesh.cpp:4: helpme_standalone.h:2323: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2323 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:2343: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2343 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3014: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3014 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3120: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3120 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3247: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3247 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3701: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3701 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3739: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3739 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3802: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3802 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3840: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3840 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4044: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4044 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4052: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4052 | #pragma omp for helpme_standalone.h:4097: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4097 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4145: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4145 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4172: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4172 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4224: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4224 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4228: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4228 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4275: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4275 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4388: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4388 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4419: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4503: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4503 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4510: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4510 | #pragma omp for CXX Exec_Calc.cpp CXX Exec_CatCrd.cpp CXX Exec_Change.cpp CXX Exec_ClusterMap.cpp CXX Exec_CombineCoords.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 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 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 '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 '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 '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 '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 '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 '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 'unsigned int'} and 'int' [-Wsign-compare] 3708 | for (size_t row = threadID; row < myGridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'helpme::PMEInstance >::Complex* helpme::PMEInstance >::forwardTransform(Real*) [with Real = double; typename std::enable_if::value, int>::type = 0; Complex = std::complex]': helpme_standalone.h:5023:32: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5023 | auto gridAddress = forwardTransform(realGrid); | ^~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:4004:28: warning: variable 'realCBA' set but not used [-Wunused-but-set-variable] 4004 | Real *__restrict__ realCBA; | ^~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::Matrix::assertSymmetric(const Real&) const [with Real = double]': helpme_standalone.h:1000:9: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 1000 | assertSymmetric(); | ^~~~~~~~~~~~~~~ helpme_standalone.h:3898:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3898 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:796:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const 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 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 '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 'unsigned int'} and 'short int' [-Wsign-compare] 2208 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~ CXX Exec_Commands.cpp CXX Exec_CompareTop.cpp CXX Exec_CrdAction.cpp helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::multiply(const helpme::Matrix&) const [with Real = double]': helpme_standalone.h:877:64: required from 'helpme::Matrix helpme::Matrix::operator*(const helpme::Matrix&) const [with Real = double]' 877 | Matrix operator*(const Matrix& other) const { return this->multiply(other); } | ~~~~~~^~~~~~~~ helpme_standalone.h:829:22: required from 'helpme::Matrix helpme::Matrix::applyOperation(const std::function&) const [with Real = double]' 829 | return evecs * evecsT; | ~~~~~~^~~~~~~~ helpme_standalone.h:785:26: required from 'helpme::Matrix helpme::Matrix::inverse() const [with Real = double]' 785 | return this->applyOperation([](Real& element) { element = 1 / element; }); | ~~~~~~^~~~~~~~~~~~~~ helpme_standalone.h:3910:44: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3910 | recVecs_ = boxVecs_.inverse(); | ~~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:860:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const 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 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 unsigned int'} [-Wsign-compare] 863 | for (int link = 0; link < nCols_; ++link) { | ~~~~~^~~~~~~~ CXX Exec_CrdOut.cpp CXX Exec_CreateSet.cpp CXX Exec_DataFile.cpp CXX Exec_DataFilter.cpp CXX Exec_DataSetCmd.cpp CXX Exec_Emin.cpp CXX Exec_Flatten.cpp CXX Exec_GenerateAmberRst.cpp CXX Exec_Graft.cpp CXX Exec_Help.cpp CXX Exec_LoadCrd.cpp CXX Exec_LoadTraj.cpp CXX Exec_ParallelAnalysis.cpp CXX Exec_ParmBox.cpp 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 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 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 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 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 RNG.cpp: In member function 'virtual unsigned int Cpptraj::RNG::Number_UpTo(unsigned int)': RNG.cpp:36:68: warning: right shift count >= width of type [-Wshift-count-overflow] 36 | return (unsigned int)(((unsigned long)exclusiveMax * Number()) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 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 '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 '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 molsurf.c: In function 'memory_usage': molsurf.c:228:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 228 | printf ("one atom %ld\n", sizeof (ATOM)); | ~~^ ~~~~~~~~~~~~~ | | | | | unsigned int | long int | %d molsurf.c:229:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 229 | printf ("atom total %ld\n", natomIn * sizeof (ATOM)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int unsigned int | %d molsurf.c:232:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 232 | printf ("one NEIGHBOR_TORUS %ld\n", sizeof (NEIGHBOR_TORUS)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | | unsigned int | long int | %d molsurf.c:233:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 233 | printf ("NEIGHBOR_TORUS total %ld\n", 60 * natomIn * sizeof (NEIGHBOR_TORUS)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int unsigned int | %d molsurf.c:236:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 236 | printf ("one NEIGHBOR %ld\n", sizeof (NEIGHBOR)); | ~~^ ~~~~~~~~~~~~~~~~~ | | | | | unsigned int | long int | %d molsurf.c:237:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 237 | printf ("NEIGHBOR total %ld\n", 60 * natomIn * sizeof (NEIGHBOR)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int unsigned int | %d molsurf.c:240:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 240 | printf ("one TORUS %ld\n", sizeof (TORUS)); | ~~^ ~~~~~~~~~~~~~~ | | | | | unsigned int | long int | %d molsurf.c:241:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 241 | printf ("TORUS total %ld\n", 5 * natomIn * sizeof (TORUS)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int unsigned int | %d molsurf.c:244:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 244 | printf ("one PROBE %ld\n", sizeof (PROBE)); | ~~^ ~~~~~~~~~~~~~~ | | | | | unsigned int | long int | %d molsurf.c:245:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 245 | printf ("PROBE total %ld\n", 5 * natomIn * sizeof (PROBE)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int unsigned int | %d molsurf.c:248:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 248 | printf ("one VERTEX %ld\n", sizeof (VERTEX)); | ~~^ ~~~~~~~~~~~~~~~ | | | | | unsigned int | long int | %d molsurf.c:249:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 249 | printf ("VERTEX total %ld\n", 10 * natomIn * sizeof (VERTEX)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int unsigned int | %d molsurf.c:252:28: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 252 | printf ("one EDGE %ld\n", sizeof (EDGE)); | ~~^ ~~~~~~~~~~~~~ | | | | | unsigned int | long int | %d molsurf.c:253:28: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 253 | printf ("EDGE total %ld\n", 10 * natomIn * sizeof (EDGE)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int unsigned int | %d molsurf.c:256:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 256 | printf ("one CIRCLE %ld\n", sizeof (CIRCLE)); | ~~^ ~~~~~~~~~~~~~~~ | | | | | unsigned int | long int | %d molsurf.c:257:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 257 | printf ("CIRCLE total %ld\n", 5 * natomIn * sizeof (CIRCLE)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int unsigned int | %d molsurf.c:260:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 260 | printf ("one CONCAVE_FACE %ld\n", sizeof (CONCAVE_FACE)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~ | | | | | unsigned int | long int | %d molsurf.c:261:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 261 | printf ("CONCAVE_FACE total %ld\n", 10 * natomIn * sizeof (CONCAVE_FACE)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int unsigned int | %d molsurf.c:264:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 264 | printf ("one SADDLE_FACE %ld\n", sizeof (SADDLE_FACE)); | ~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | | unsigned int | long int | %d molsurf.c:265:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 265 | printf ("SADDLE_FACE total %ld\n", 10 * natomIn * sizeof (SADDLE_FACE)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int unsigned int | %d molsurf.c:268:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 268 | printf ("one CYCLE %ld\n", sizeof (CYCLE)); | ~~^ ~~~~~~~~~~~~~~ | | | | | unsigned int | long int | %d molsurf.c:269:36: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'unsigned int' [-Wformat=] 269 | printf ("CYCLE total %ld\n", 10 * natomIn * sizeof (CYCLE)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int unsigned int | %d 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 CC huffmem.c CC vals16.c CC bwt.c CC mtf.c CC rle.c CC lz77.c CC dict.c CC huffman.c CC merge_sort.c /bin/rm -f libxdrfile.a ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' tng_io.c: In function 'tng_gen_data_block_add': tng_io.c:12600:9: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tng_io.c:12600:47: note: length computed here 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ /bin/rm -f libtng_io.a ar cqs libtng_io.a md5.o tng_io.o tng_compress.o coder.o warnmalloc.o fixpoint.o xtc3.o bwlzh.o xtc2.o widemuldiv.o huffmem.o vals16.o bwt.o mtf.o rle.o lz77.o dict.o huffman.o merge_sort.o make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o -L/usr/lib/i386-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/i386-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/i386-linux-gnu/lib -lfftw3 -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 -j22 test "TESTSUITEFLAGS=-j22 --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/unitTests' make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' 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 -Wformat -Werror=format-security -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 -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o StringRoutines.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/StringRoutines.cpp -rwxr-xr-x 1 pbuilder1 pbuilder1 174677108 Feb 27 09:30 ../bin/cpptraj -rwxr-xr-x 1 pbuilder1 pbuilder1 174677108 Feb 27 09:30 ../bin/cpptraj make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Strip ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_General ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TrajinOffset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DSSP ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD CPPTRAJ: One frame strip command test CPPTRAJ: Normal trajectory read with offsets. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Image CPPTRAJ: Broken Traj: Running good trajectory. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_trajout_framerange ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Center CPPTRAJ: Secstruct (DSSP) command test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radgyr ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NCrestart TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RemdTraj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hbond CPPTRAJ: Orthorhombic imaged distance test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf CPPTRAJ: Per-Residue RMSD Test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mask CPPTRAJ: Center command test. CPPTRAJ: Radius of gyration command test CPPTRAJ: Trajout Frame Range [Amber Restart] CPPTRAJ: NetCDF Restart Test - TXT->NetCDF CPPTRAJ: CRD Replica Trajectory Run with offset CPPTRAJ: Surface calculation test CPPTRAJ: Mask single frame test CPPTRAJ: Solute Hbond test CPPTRAJ: General tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Jcoupling CPPTRAJ: J-Coupling single frame test CPPTRAJ: Gzipped trajectory read with offsets CPPTRAJ: CRD Replica Trajectory Run ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diffusion CPPTRAJ: NetCDF Restart Test - NetCDF->TXT CPPTRAJ: Diffusion test, no imaging. CPPTRAJ: Center origin command test. CPPTRAJ: Trajout Frame Range [Amber Coordinates] CPPTRAJ: Non-orthorhombic imaged distance test. CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. CPPTRAJ: Broken Traj: Running broken trajectory. All 2 comparisons passed. CPPTRAJ: Per-Residue RMSD Test with averaging J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. Skipped test: J-Coupling extended test All 1 comparisons passed. 1 comparisons skipped. CPPTRAJ: NetCDF Replica Trajectory Run test CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF CPPTRAJ: Mask longer command test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj CPPTRAJ: RMSD Test with outtraj. CPPTRAJ: Bzip2ed trajectory read with offsets ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm CPPTRAJ: Diffusion test, old syntax. CPPTRAJ: Solute Hbond test with disk caching CPPTRAJ: CHARMM PSF/DCD test All 6 comparisons passed. CPPTRAJ: Secstruct (DSSP) command with changing number of residues. CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj CPPTRAJ: Center origin mass command test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotdif CPPTRAJ: Rotational diffusion calculation test CPPTRAJ: Orthorhombic coordinate imaging test CPPTRAJ: CHARMM DCD Write, step 1. CPPTRAJ: Per-Residue RMSD Test with residue centering. CPPTRAJ: Unstrip (Lig/Rec/Complex) command test All 5 comparisons passed. CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj CPPTRAJ: Solute-solvent hbond test CPPTRAJ: Center reference command test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj CPPTRAJ: Convert mdcrd -> NetCDF CPPTRAJ: Start argument offset All 4 comparisons passed. CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj CPPTRAJ: Secstruct (DSSP): SS assign output test CPPTRAJ: CHARMM DCD Write, step 2. CPPTRAJ: Diffusion test, new syntax. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Runavg CPPTRAJ: Coordinate Running Average test. CPPTRAJ: Nonorthorhombic coordinate imaging test All 4 comparisons passed. All 3 comparisons passed. CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj All 2 comparisons passed. CPPTRAJ: FtuFabI Assignment test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RMSD CPPTRAJ: Basic RMSD tests CPPTRAJ: CHAMBER topology read/strip test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_2DRMS CPPTRAJ: Coordinate Running Average Traj Write CPPTRAJ: Center point test. CPPTRAJ: 2D RMSD Test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mol2 CPPTRAJ: CRD Replica Trajectory Run with remdout CPPTRAJ: Hbond, no intramolecular hydrogen bonds test CPPTRAJ: Diffusion test, nonorthogonal box CPPTRAJ: Mol2 Parm/Traj Read/Write Test. CPPTRAJ: Read CHARMM restart CPPTRAJ: Compressed broken trajectory test All 5 comparisons passed. All 2 comparisons passed. CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar CPPTRAJ: 2D RMSD Test, mass-weighted. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct CPPTRAJ: NAstruct command test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Average CPPTRAJ: Average Test. CPPTRAJ: PDB => Mol2 All 8 comparisons passed. CPPTRAJ: Convert NetCDF -> mdcrd CPPTRAJ: Multi frame strip command test. CPPTRAJ: CHARMM PSF write CPPTRAJ: STFC Diffusion Test CPPTRAJ: RMS coordinate rotation/rotation matrices test CPPTRAJ: 2D RMSD Test with reference trajectory ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pucker CPPTRAJ: Pucker command test All 10 comparisons passed. CPPTRAJ: Amber Top/Rst => Mol2 CPPTRAJ: Hbond, specified solute masks ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomMap All 2 comparisons passed. CPPTRAJ: CHARMM COORdinates test CPPTRAJ: AtomMap Test All 2 comparisons passed. CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Datafile CPPTRAJ: Strip topology with PDB info CPPTRAJ: Data file output precision test ******************************************************************************** Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial Skipped test: Amber Top/Rst => Mol2, SYBYL atom types All 4 comparisons passed. 1 comparisons skipped. CPPTRAJ: Radial test, non-orthogonal imaging CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test CPPTRAJ: 2D DME Test. CPPTRAJ: STFC Diffusion Test with individual distances ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist CPPTRAJ: 1D/2D Histogram Analysis test All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CharmmParams CPPTRAJ: Test updating topology with Charmm parameters (single residue) CPPTRAJ: NAstruct command test, single strand CPPTRAJ: RMS fit with no coordinates modification test. All 11 comparisons passed. CPPTRAJ: Hbond, no angle cutoff test CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. CPPTRAJ: AtomMap with 'rmsfit' CPPTRAJ: 2D RMSD with reference mask test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest CPPTRAJ: Closest command test using first solvent atom. CPPTRAJ: Standard -> Grace Data All 3 comparisons passed. All 11 comparisons passed. All 2 comparisons passed. CPPTRAJ: STFC Diffusion Test with COM All 6 comparisons passed. CPPTRAJ: Hbond, Bridge nointramol test CPPTRAJ: 2D RMSD test, no fitting. CPPTRAJ: Atom map charmm->amber atom order ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct_8OG ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DRMSD CPPTRAJ: NA test (8OG) CPPTRAJ: Distance RMSD test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_IRED All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster CPPTRAJ: IRED vector/matrix test CPPTRAJ: Cluster command test, in-memory pairwise distances. CPPTRAJ: 3D histogram test. CPPTRAJ: Grace -> Standard Data ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons CPPTRAJ: randomizeions test (original algorithm) All 6 comparisons passed. CPPTRAJ: Atom map charmm->amber atom order, by residue ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Molsurf CPPTRAJ: STFC Diffusion Test with second mask CPPTRAJ: Molsurf test All 7 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Corr CPPTRAJ: Correlation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckStructure CPPTRAJ: RMS fit to previous test CPPTRAJ: Structure Check CPPTRAJ: X column format/precision test. All 9 comparisons passed. CPPTRAJ: Cluster command test, read pairwise distances. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RmsAvgCorr CPPTRAJ: RmsAvgCorr Reference CPPTRAJ: Outtraj Test with maxmin. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Contacts CPPTRAJ: Contacts test. All 15 comparisons passed. CPPTRAJ: RMS: imaging after unit cell rotation All 3 comparisons passed. All 2 comparisons passed. CPPTRAJ: Structure Check with Around and Skip CPPTRAJ: Data file group by name test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Parallel CPPTRAJ: Closest command test using all solvent atoms. CPPTRAJ: Parallel tests. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Principal ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ClusterDihedral CPPTRAJ: Principal Test CPPTRAJ: Cluster command test, read NetCDF pairwise distances. CPPTRAJ: clusterdihedral test CPPTRAJ: RmsAvgCorr First ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Vector CPPTRAJ: Basic vector tests All 12 comparisons passed. CPPTRAJ: Data file group by aspect test CPPTRAJ: Partial Surface calculation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Matrix CPPTRAJ: Matrix Tests CPPTRAJ: Parallel test with trajectory offset All 3 comparisons passed. CPPTRAJ: Cluster command test, write ASCII pairwise distances. All 4 comparisons passed. All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Unwrap All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Grid CPPTRAJ: Unwrap non-orthogonal test CPPTRAJ: Dipole test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Project CPPTRAJ: Projection CPPTRAJ: Cluster command test, read ASCII pairwise distances. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes CPPTRAJ: Modes analysis, RMS fluctuations CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. All 1 comparisons passed. CPPTRAJ: Test vector center with magnitude All 9 comparisons passed. CPPTRAJ: Modes analysis, displacements CPPTRAJ: Grid test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Watershell CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve CPPTRAJ: Watershell Test, non-orthorhombic imaging. CPPTRAJ: Cluster, nosieve CPPTRAJ: Momentum/velocity vector test. CPPTRAJ: Modes analysis, dipole correlation CPPTRAJ: Unwrap orthogonal test All 7 comparisons passed. CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AnalysisRunAvg CPPTRAJ: Analysis Running Average CPPTRAJ: Force vector test. CPPTRAJ: Cluster, sieve5 CPPTRAJ: Atomicfluct test with ADP output CPPTRAJ: OpenDX Grid read test All 2 comparisons passed. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volmap CPPTRAJ: VMD VolMap Algorithm test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SPAM CPPTRAJ: SPAM Test All 14 comparisons passed. CPPTRAJ: Structure Check with PBC ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LIE CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. CPPTRAJ: LIE test CPPTRAJ: Generate matrix with trajectory start/stop/offset All 3 comparisons passed. CPPTRAJ: Closest command test, using mask center CPPTRAJ: Grid with specified center test. CPPTRAJ: Cluster, nosieve savepairdist CPPTRAJ: Modes analysis, pseudo trajectory creation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Density CPPTRAJ: Density along axis tests CPPTRAJ: Generate matrix with action stop/start/offset All 13 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PairDist CPPTRAJ: PairDist Test. CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidOrder CPPTRAJ: Lipid Order Parameter Test. All 15 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_ReadData CPPTRAJ: Closest command test, using mask center and solvent mask All 16 comparisons passed. CPPTRAJ: Read vector data test (no origins, origins) CPPTRAJ: Cluster, nosieve loadpairdist ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_systemVF CPPTRAJ: GIST water-water interaction test All 6 comparisons passed. CPPTRAJ: Grid with box center offset test. CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicCorr CPPTRAJ: Read vector data set (origins, no origins) CPPTRAJ: Atomic Correlation test CPPTRAJ: LCPO test with GAFF atom types CPPTRAJ: Radial test, orthogonal and no imaging CPPTRAJ: Closest command test, solvent mask, water oxygen only All 3 comparisons passed. CPPTRAJ: Read Amber output test CPPTRAJ: Cluster, sieve5 savepairdist ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr CPPTRAJ: AutoCorr test. CPPTRAJ: Grid with mask center offset test. CPPTRAJ: Read CHARMM output test All 9 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Box CPPTRAJ: Multi-frame density along axis test CPPTRAJ: Box Test (Add box info) CPPTRAJ: SPAM Pure Solvent Test CPPTRAJ: Pairdist test, orthogonal imaging. All 1 comparisons passed. CPPTRAJ: 3D data read/write test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomTypeSelect CPPTRAJ: Selection by atom type test. CPPTRAJ: Box test (remove box info) CPPTRAJ: Standard 3D data write test CPPTRAJ: Non-orthogonal grid test. All 1 comparisons passed. All 6 comparisons passed. CPPTRAJ: Box test (Modify box length) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AvgRef ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidSCD CPPTRAJ: RMSD Test with averaged reference coordinates. CPPTRAJ: Basic lipid order parameter test CPPTRAJ: Standard 3D data read test CPPTRAJ: Total system density test CPPTRAJ: Hbond with imaging All 1 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Crank_Stat CPPTRAJ: Box test (auto orthogonal box, no radii) CPPTRAJ: Crankshaft test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateCrd CPPTRAJ: COORDS data set creation and CRDFLUCT test. CPPTRAJ: Standard 3D data read/append test CPPTRAJ: Cluster, sieve5 loadpairdist CPPTRAJ: Hbond, orthogonal imaging All 7 comparisons passed. CPPTRAJ: Box test (auto orthogonal box, VDW radii) CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test All 3 comparisons passed. CPPTRAJ: COORDS data set creation with velocities test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoImage CPPTRAJ: AutoImage test (split DNA duplex) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LoadCrd CPPTRAJ: LoadCrd test. CPPTRAJ: New Lipid Order Parameter Test, DOPC. All 7 comparisons passed. g++ -o a.out main.o NameType.o CpptrajStdio.o CPPTRAJ: Standard 3D data, sparse ******************************************************************************** CPPTRAJ: Randomize (around, overlap) TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MultiVector CPPTRAJ: Multivector test All 23 comparisons passed. CPPTRAJ: LoadTraj test. CPPTRAJ: Grid generation from 'bounds' test. CPPTRAJ: Cluster, nosieve pairwisecache none ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Lifetime CPPTRAJ: Lifetime test. CPPTRAJ: Nonorthogonal grid standard write/read tests. All 1 comparisons passed. ******************************************************************************** CPPTRAJ: LoadTraj from trajin test. TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FFT CPPTRAJ: FFT test. All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Timecorr CPPTRAJ: Timecorr test. CPPTRAJ: Lifetime test with data set caching. CPPTRAJ: LoadCrd append from multiple files test make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' CPPTRAJ: Structure Check with Around '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 13 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CrossCorr CPPTRAJ: TRAJ data set creation and CRDFLUCT test. All 4 comparisons passed. CPPTRAJ: CrossCorr test All 5 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_Multidihedral CPPTRAJ: Multidihedral test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ensemble_MREMD CPPTRAJ: Lifetime average and cumulative average test. CPPTRAJ: M-REMD sort test. All 1 comparisons passed. CPPTRAJ: TRAJ data set creation with velocities test. All 7 comparisons passed. CPPTRAJ: ASP symmetry-corrected RMSD test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotate ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MakeStructure CPPTRAJ: Rotation (and inverse) of coords from matrices CPPTRAJ: Basic makestructure test All 1 comparisons passed. CPPTRAJ: Multidihedral Nucleotide CHI test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Integrate All 12 comparisons passed. CPPTRAJ: GLU symmetry-corrected RMSD test CPPTRAJ: Integration test. CPPTRAJ: Cluster, sieve5 pairwisecache none ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts CPPTRAJ: NativeContacts test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckChiral CPPTRAJ: Check chirality test 1 out of 2 comparisons failed. CPPTRAJ: Multidihedral protein dihedrals test CPPTRAJ: COORDS data set append test CPPTRAJ: Makestructure test with reference. CPPTRAJ: TYR symmetry-corrected RMSD test CPPTRAJ: Rotate with defined axis ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Energy CPPTRAJ: Simple energy tests CPPTRAJ: M-REMD actions test. All 5 comparisons passed. All 1 comparisons passed. CPPTRAJ: Multidihedral cyclic molecule test CPPTRAJ: Longer symmetry-corrected RMSD test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LESsplit CPPTRAJ: LES split/average test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PermuteDihedrals CPPTRAJ: COORDS test storing frame metadata CPPTRAJ: PermuteDihedrals interval -120, phi psi CPPTRAJ: Cluster, random All 3 comparisons passed. 1 out of 6 comparisons failed. All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CCP4 CPPTRAJ: CCP4 read/write and DX conversion test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihCovar CPPTRAJ: Dihedral Covariance Matrix Test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CurveFit CPPTRAJ: Curve fitting test. CPPTRAJ: M-REMD ensemble outtraj test. CPPTRAJ: PermuteDihedrals, random rotations CPPTRAJ: AutoImage test, use anchor mask All 8 comparisons passed. CPPTRAJ: Curve fitting multi-exponential tests. All 2 comparisons passed. CPPTRAJ: TRAJ test storing frame metadata ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetAverage All 28 comparisons passed. CPPTRAJ: Data set averaging and averaging over all sets test. CPPTRAJ: M-REMD no sort, running average test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VectorMath CPPTRAJ: Vector dot/cross product test All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). All 4 comparisons passed. CPPTRAJ: NativeContacts test, save non-native contacts, residue time series ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander SANDER energy tests (long) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. SKIP: SANDER energy tests (long) All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Temperature ******************************************************************************** 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: Temperature test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Spline 1 out of 2 comparisons failed. CPPTRAJ: Randomize (around) CPPTRAJ: Spline test CPPTRAJ: M-REMD, generate RMS data All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_KDE CPPTRAJ: KDE test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Wavelet CPPTRAJ: Wavelet analysis test CPPTRAJ: Temperature with SHAKE on hydrogens. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CIF CPPTRAJ: CIF read test CPPTRAJ: Curve fitting, custom output range. All 1 comparisons passed. CPPTRAJ: M-REMD, meltcurve analysis All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PDB CPPTRAJ: PDB format read/write test CPPTRAJ: Test kinetic energy calculation CPPTRAJ: Temperature with SHAKE on all atoms. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Align CPPTRAJ: Align Tests. CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). 1 out of 6 comparisons failed. All 17 comparisons passed. CPPTRAJ: NativeContacts test, orthorhombic imaging. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multicurve CPPTRAJ: Multicurve test CPPTRAJ: Test total energy calculation ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelocityAutoCorr CPPTRAJ: Temperature calc with extra points. CPPTRAJ: Velocity autocorrelation test CPPTRAJ: Generate offset traj from PDB CPPTRAJ: Test partial energy calculation All 2 comparisons passed. CPPTRAJ: Align, unit cell rotation/imaging test. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelFrc CPPTRAJ: Test combining coordinates, velocities, and forces. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RotateDihedral CPPTRAJ: Wavelet WAFEX test CPPTRAJ: Rotate dihedral to target value. All 4 comparisons passed. CPPTRAJ: Generate offset traj from CIF ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet CPPTRAJ: Clustering, One DataSet CPPTRAJ: Test using velocities as coordinates. CPPTRAJ: PQR file write with various radii All 3 comparisons passed. All 6 comparisons passed. CPPTRAJ: Rotate dihedral by increment ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetCmd All 8 comparisons passed. CPPTRAJ: Data Set commands test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remap CPPTRAJ: Remap Test CPPTRAJ: Test writing velocities (MDVEL) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CompareTop CPPTRAJ: Compare topology test CPPTRAJ: Clustering, Two DataSets All 5 comparisons passed. All 1 comparisons passed. CPPTRAJ: Rotate dihedral in TRAJ data set CPPTRAJ: Test using forces as coordinates. CPPTRAJ: PDB filter alternate atom location IDs test All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Filter ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CombineCrd CPPTRAJ: Basic filter test CPPTRAJ: Combine COORDS test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TopInfo All 1 comparisons passed. CPPTRAJ: Topology info print test. CPPTRAJ: Clustering, dihedral DataSet All 3 comparisons passed. All 10 comparisons passed. CPPTRAJ: Test writing forces (MDFRC) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTrr All 17 comparisons passed. CPPTRAJ: TRR force/velocity read -> NetCDF write test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ewald CPPTRAJ: Direct sum test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TI CPPTRAJ: TI analysis test. CPPTRAJ: Combine COORDS test with box info. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds CPPTRAJ: Fix imaged bonds test (Ortho.) CPPTRAJ: Clustering, two dihedral DataSets All 3 comparisons passed. CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Distance CPPTRAJ: Distance tests CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. CPPTRAJ: Pairdist test, nonorthogonal imaging. All 5 comparisons passed. CPPTRAJ: Clustering, dihedral DataSet, K-means CPPTRAJ: Adding PDB info to topology ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volume CPPTRAJ: Volume tests CPPTRAJ: Data filter test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SetVelocity CPPTRAJ: Set Velocity test CPPTRAJ: Orthogonal imaged distance CPPTRAJ: Fix imaged bonds test (Non-ortho.) All 10 comparisons passed. CPPTRAJ: Clustering, two dihedral DataSets, K-means CPPTRAJ: Split coords and recombine test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remlog CPPTRAJ: Replica log read/analyze test. CPPTRAJ: Scale velocity test CPPTRAJ: Filter matrix test. All 8 comparisons passed. All 1 comparisons passed. CPPTRAJ: Non-orthogonal imaged distance All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AreaPerMol ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN CPPTRAJ: Area per molecule test CPPTRAJ: DBSCAN test 1 out of 3 comparisons failed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DistBasedMask CPPTRAJ: Distance-based atom mask tests (atom, residue) All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Calc CPPTRAJ: Calc test CPPTRAJ: Topology info with reference coords test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CalcState CPPTRAJ: TRR force/velocity read -> TRR write test All 5 comparisons passed. CPPTRAJ: Calcstate test All 3 comparisons passed. All 7 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Change All 1 comparisons passed. CPPTRAJ: DBSCAN automatic parameter determination test. CPPTRAJ: Change atom and residue name tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateReservoir CPPTRAJ: Calc test with data sets ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixAtomOrder CPPTRAJ: Create RREMD NetCDF reservoir test CPPTRAJ: Read specific columns test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LowestCurve CPPTRAJ: Out of order molecules test CPPTRAJ: LowestCurve test All 12 comparisons passed. CPPTRAJ: Distance-based atom mask tests (molecule) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MinImage CPPTRAJ: CRD => TRR CPPTRAJ: Minimum Image test. CPPTRAJ: Change chain ID test All 4 comparisons passed. CPPTRAJ: DBSCAN kdist map test CPPTRAJ: Write non-square matrix All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Regress CPPTRAJ: Linear regression test. CPPTRAJ: Test math functions CPPTRAJ: KDE with Kullback-Leibler divergence test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rst CPPTRAJ: Generate restraints (rst) test CPPTRAJ: Change chain ID of COORDS set test All 4 comparisons passed. CPPTRAJ: DBSCAN with sieve ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pairwise All 1 comparisons passed. All 1 comparisons passed. CPPTRAJ: Pairwise tests All 4 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ParmBox All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Solvent CPPTRAJ: Parmbox test CPPTRAJ: Test solvent command with closest ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Translate CPPTRAJ: Translate test CPPTRAJ: Read non-square matrix ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReplicateCell All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ScaleDihedralK CPPTRAJ: Replicate cell test CPPTRAJ: Scale dihedral force constant test All 1 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans CPPTRAJ: Cpptraj Kmeans ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PhiPsi ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Control All 1 comparisons passed. CPPTRAJ: Phipsi test CPPTRAJ: Loop tests All 1 comparisons passed. All 1 comparisons passed. CPPTRAJ: Randomize (overlap) CPPTRAJ: Read square matrix ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_InfraredSpec CPPTRAJ: Scale dihedral force constant with 'useall' CPPTRAJ: Infrared spectrum calculation test All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cphstats CPPTRAJ: Pairwise test, partial system CPPTRAJ: Explicit pH REMD ensemble data read / sort ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CmdLine CPPTRAJ: Command line trajectory args test, part 1 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XYZformat CPPTRAJ: XYZ format write All 15 comparisons passed. All 2 comparisons passed. All 1 comparisons passed. All 4 comparisons passed. All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CatCrd ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hausdorff ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XtalSymm ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Time CPPTRAJ: Concatenate COORDS data set test CPPTRAJ: XtalSymm Reference CPPTRAJ: Simple Hausdorff distance test. CPPTRAJ: Add time to restart test CPPTRAJ: TRR => CRD ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SplitCoords CPPTRAJ: Test set command CPPTRAJ: SplitCoords test CPPTRAJ: Watershell Test, orthorhombic imaging. All 1 comparisons passed. CPPTRAJ: Command line test trajectory args test, part 2 All 1 comparisons passed. CPPTRAJ: Atom XYZ format read, test 1 CPPTRAJ: Hausdorff distance of 2D rms output test. All 2 comparisons passed. CPPTRAJ: Remove time from restart test CPPTRAJ: Constant pH stats test CPPTRAJ: Cpptraj Kmeans random ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihedralRMS TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diagmatrix ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Slope CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) CPPTRAJ: MW covariance matrix thermo analysis test CPPTRAJ: Finite difference test. All 10 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Emin CPPTRAJ: Basic energy minimization test. CPPTRAJ: Test reading comma-separated list of strings All 1 comparisons passed. CPPTRAJ: Atom XYZ format read, test 2 CPPTRAJ: Add time to trajectory test All 1 comparisons passed. CPPTRAJ: Sorted implicit constant pH stats test CPPTRAJ: Command line wildcard test, part 1 All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau CPPTRAJ: Evalulate plateau test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Graft CPPTRAJ: Dihedral RMSD test (to previous) CPPTRAJ: Graft test CPPTRAJ: Energy minimization with angle term test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Flatten CPPTRAJ: Flatten test. CPPTRAJ: Atom XYZ format read, test 3 CPPTRAJ: Randomize (no restrictions) CPPTRAJ: Command line wildcard test, part 2 CPPTRAJ: Test nested loops and variables in loops All 6 comparisons passed. CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats All 1 comparisons passed. CPPTRAJ: Dihedral RMS fluctuation test. CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. All 1 comparisons passed. CPPTRAJ: Hausdorff distance of 2D rms output test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_SymmRMSD ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Random CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs All 2 comparisons passed. All 2 comparisons passed. CPPTRAJ: Test loop over data set blocks All 5 comparisons passed. CPPTRAJ: Atom XYZ format read, test 4 CPPTRAJ: Energy minimization with nonbond term test. CPPTRAJ: Modify time info test. CPPTRAJ: PCG32 RNG test. CPPTRAJ: Unsorted pH read/write test CPPTRAJ: CRD(1-5) => TRR All 4 comparisons passed. CPPTRAJ: Atom XYZ format read, test 5 CPPTRAJ: Test Stdlib RNG All 16 comparisons passed. CPPTRAJ: Test for filename wildcards and oversets CPPTRAJ: Test Mersenne Twister RNG CPPTRAJ: Atom XYZ format read, test 6 All 5 comparisons passed. All 4 comparisons passed. All 13 comparisons passed. All 6 comparisons passed. All 3 comparisons passed. CPPTRAJ: Ewald test (NaCl crystal) CPPTRAJ: CRD(6-10) => TRR CPPTRAJ: Ewald test (trunc. oct) OpenMM basic energy minimization tests requires OpenMM. Cpptraj was compiled without OpenMM support. Skipped test: OpenMM basic energy minimization tests All 4 comparisons passed. 1 comparisons skipped. CPPTRAJ: XtalSymm Reimaging by Atom All 5 comparisons passed. g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites CPPTRAJ: Cluster command test, coordinate writes. CPPTRAJ: TRR (appended) => CRD CPPTRAJ: Watershell Test, no imaging. CPPTRAJ: Cluster command test, coordinate writes using info file. make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' Unit test passed. make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ: GMX: CRD with offset All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Dpeaks CPPTRAJ: Density peaks clustering test All 3 comparisons passed. All 3 comparisons passed. CPPTRAJ: Ewald test (partial system, trunc. oct) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Nreps CPPTRAJ: Clustering with specified # reps CPPTRAJ: Pairdist test, 2 masks. CPPTRAJ: GMX: TRR with offset All 4 comparisons passed. All 2 comparisons passed. All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc CPPTRAJ: XTC read test Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: Ewald test (trunc. oct), 10 frames Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: Ewald test (ortho), 10 frames All 4 comparisons passed. 2 comparisons skipped. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LibPME CPPTRAJ: Particle mesh Ewald test (NaCl crystal) CPPTRAJ: Particle mesh Ewald test (trunc. oct) CPPTRAJ: CRD => XTC CPPTRAJ: XTC => CRD CPPTRAJ: GIST test, orthogonal cell All 5 comparisons passed. CPPTRAJ: CRD(1-5) => XTC CPPTRAJ: Particle mesh Ewald test (ortho) CPPTRAJ: CRD(6-10) => XTC CPPTRAJ: XTC (appended) => CRD CPPTRAJ: Particle mesh Ewald test (ortho, with mask) CPPTRAJ: GMX: CRD with offset CPPTRAJ: PME test (partial system, trunc. oct) 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. 3 out of 4 comparisons failed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LJ_PME CPPTRAJ: LJ PME test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTNG CPPTRAJ: TNG read test CPPTRAJ: LJ PME kappa sweep test, 0.25 CPPTRAJ: LJ PME kappa sweep test, 0.35 CPPTRAJ: TNG read test (with offset) CPPTRAJ: LJ PME kappa sweep test, 0.45 CPPTRAJ: LJ PME kappa sweep test, 0.5 CPPTRAJ: XtalSymm Reimaging by Molecule CPPTRAJ: LJ with switch function test All 6 comparisons passed. All 5 comparisons passed. All 5 comparisons passed. CPPTRAJ: GIST test, nonorthogonal cell 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. make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' /usr/bin/make -C test summary make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' -rwxr-xr-x 1 pbuilder1 pbuilder1 174677108 Feb 27 09:30 ../bin/cpptraj ===================== TEST SUMMARY ====================== 840 out of 855 comparisons OK (8 failed, 0 warnings, 7 skipped). 475 out of 475 program executions completed. 164 out of 173 tests completed with no issues. 2 tests skipped. ========================================================= make[2]: *** [Makefile:662: summary] Error 8 make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[1]: *** [debian/rules:17: override_dh_auto_test] Error 2 make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' make: *** [debian/rules:10: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/112505 and its subdirectories