Wed Sep 24 15:59:59 UTC 2025 I: starting to build cpptraj/forky/arm64 on jenkins on '2025-09-24 15:59' Wed Sep 24 15:59:59 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_7/98331/console.log Wed Sep 24 15:59:59 UTC 2025 I: Downloading source for forky/cpptraj=5.1.0+dfsg-5 --2025-09-24 15:59:59-- http://deb.debian.org/debian/pool/main/c/cpptraj/cpptraj_5.1.0%2bdfsg-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1814 (1.8K) [text/prs.lines.tag] Saving to: ‘cpptraj_5.1.0+dfsg-5.dsc’ 0K . 100% 197M=0s 2025-09-24 15:59:59 (197 MB/s) - ‘cpptraj_5.1.0+dfsg-5.dsc’ saved [1814/1814] Wed Sep 24 15:59:59 UTC 2025 I: cpptraj_5.1.0+dfsg-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: cpptraj Binary: cpptraj Architecture: any Version: 5.1.0+dfsg-5 Maintainer: Debichem Team Uploaders: Andrius Merkys , Homepage: https://github.com/Amber-MD/cpptraj Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/debichem-team/cpptraj Vcs-Git: https://salsa.debian.org/debichem-team/cpptraj.git Testsuite: autopkgtest Testsuite-Triggers: netcdf-bin Build-Depends: debhelper-compat (= 13), gfortran, libarpack2-dev, libbz2-dev, libfftw3-dev, libnetcdf-dev, libopenmm-dev [amd64 arm64 armhf mips64el ppc64el riscv64], libreadline-dev, netcdf-bin Package-List: cpptraj deb science optional arch=any Checksums-Sha1: b326e493769758a5e5e29173898e049c6a60e9a2 28363024 cpptraj_5.1.0+dfsg.orig.tar.xz e9dc2e6320baf83a1225663e91801c50e40a9147 6432 cpptraj_5.1.0+dfsg-5.debian.tar.xz Checksums-Sha256: 89e279bbb5d35db4d2599fa98322bb8c4b876ce6117f8896e75520a3da1182f3 28363024 cpptraj_5.1.0+dfsg.orig.tar.xz afa4e2f53d68cad0fb8b9e16765447cfea6ea2ce80c193584290ef0cc06b897c 6432 cpptraj_5.1.0+dfsg-5.debian.tar.xz Files: bf932a3aed87ad43645613135c712505 28363024 cpptraj_5.1.0+dfsg.orig.tar.xz 15d8033b48593c90d52a78d14c2123b8 6432 cpptraj_5.1.0+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEE1Uw7+v+wQt44LaXXQc5/C58bizIFAmjQbVMACgkQQc5/C58b izIz6gf/WjR+5nSzltiyJHX/bbX+3K2yXDw6fApYK81iLll8tXfZh5VkYIDj70bY CQwvwis0EotREZxbGsxUYoDtDYH6HXcTXg5jwtxg+gR1E38k/mCpMbLvSYdyuP7s fRg5TFoghH590QUSA0OnjH+UyVPIIToH4AjfwO7EI+k9XiSMUOoe0OBxxGbYwFnv 72vtG5coGLqEvBlCFuMooe83HghLLzjYbRw+dks3BqePkkIa+HfxOKZ2BhhYk53I BBmfKKaaRhH8Liiy/kWmuqfTYqrS/yZHHzvCkScV2ijRFsgHg73I4I2DlbtRKzDi 1mTZCm//jdxLt2xisTu+501kNNcqow== =AqHB -----END PGP SIGNATURE----- Wed Sep 24 15:59:59 UTC 2025 I: Checking whether the package is not for us Wed Sep 24 15:59:59 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Wed Sep 24 15:59:59 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Wed Sep 24 16:05:05 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 24 04:00:01 -12 2025 I: pbuilder-time-stamp: 1758729601 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [cpptraj_5.1.0+dfsg-5.dsc] I: copying [./cpptraj_5.1.0+dfsg.orig.tar.xz] I: copying [./cpptraj_5.1.0+dfsg-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./cpptraj_5.1.0+dfsg-5.dsc: no acceptable signature found dpkg-source: info: extracting cpptraj in cpptraj-5.1.0+dfsg dpkg-source: info: unpacking cpptraj_5.1.0+dfsg.orig.tar.xz dpkg-source: info: unpacking cpptraj_5.1.0+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-system-libraries.patch dpkg-source: info: applying skip-failing-test.patch dpkg-source: info: applying gcc-15.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/576532/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='b2f7fbda0348405789bdda377934f20c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='576532' 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.S1PB3lNE/pbuilderrc_jmvC --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.S1PB3lNE/b1 --logfile b1/build.log cpptraj_5.1.0+dfsg-5.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/576532/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), gfortran, libarpack2-dev, libbz2-dev, libfftw3-dev, libnetcdf-dev, libopenmm-dev, libreadline-dev, netcdf-bin dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20020 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on libarpack2-dev; however: Package libarpack2-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on libnetcdf-dev; however: Package libnetcdf-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmm-dev; however: Package libopenmm-dev is not installed. pbuilder-satisfydepends-dummy depends on libreadline-dev; however: Package libreadline-dev is not installed. pbuilder-satisfydepends-dummy depends on netcdf-bin; however: Package netcdf-bin is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran{a} gfortran-15{a} gfortran-15-aarch64-linux-gnu{a} gfortran-aarch64-linux-gnu{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarpack2-dev{a} libarpack2t64{a} libblas-dev{a} libblas3{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libffi8{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-single3{a} libfile-stripnondeterminism-perl{a} libgfortran-15-dev{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-310{a} libhdf5-cpp-310{a} libhdf5-dev{a} libhdf5-fortran-310{a} libhdf5-hl-310{a} libhdf5-hl-cpp-310{a} libhdf5-hl-fortran-310{a} libidn2-0{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnetcdf-dev{a} libnetcdf22{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libopenmm-dev{a} libopenmm8.1{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} libreadline-dev{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsz2{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2-16{a} libxml2-dev{a} libzstd-dev{a} m4{a} man-db{a} netcdf-bin{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 131 newly installed, 0 to remove and 0 not upgraded. Need to get 124 MB of archives. After unpacking 549 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 readline-common all 8.3-3 [74.8 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.1-3 [98.1 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.20-1 [316 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 automake all 1:1.17-4 [862 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 comerr-dev arm64 2.1-1.47.2-3+b3 [56.9 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.26 [91.8 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-5 [540 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 22 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 25 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.193-3 [189 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.16-2 [100 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.5+dfsg-0.2 [582 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 30 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 31 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian forky/main arm64 debhelper all 13.26 [939 kB] Get: 33 http://deb.debian.org/debian forky/main arm64 libgfortran5 arm64 15.2.0-4 [371 kB] Get: 34 http://deb.debian.org/debian forky/main arm64 libgfortran-15-dev arm64 15.2.0-4 [411 kB] Get: 35 http://deb.debian.org/debian forky/main arm64 gfortran-15-aarch64-linux-gnu arm64 15.2.0-4 [76.9 MB] Get: 36 http://deb.debian.org/debian forky/main arm64 gfortran-15 arm64 15.2.0-4 [17.9 kB] Get: 37 http://deb.debian.org/debian forky/main arm64 gfortran-aarch64-linux-gnu arm64 4:15.2.0-4 [1280 B] Get: 38 http://deb.debian.org/debian forky/main arm64 gfortran arm64 4:15.2.0-4 [1428 B] Get: 39 http://deb.debian.org/debian forky/main arm64 hdf5-helpers arm64 1.14.5+repack-4 [26.7 kB] Get: 40 http://deb.debian.org/debian forky/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 41 http://deb.debian.org/debian forky/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 42 http://deb.debian.org/debian forky/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 43 http://deb.debian.org/debian forky/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 44 http://deb.debian.org/debian forky/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 45 http://deb.debian.org/debian forky/main arm64 libgssrpc4t64 arm64 1.21.3-5 [57.2 kB] Get: 46 http://deb.debian.org/debian forky/main arm64 libkadm5clnt-mit12 arm64 1.21.3-5 [41.1 kB] Get: 47 http://deb.debian.org/debian forky/main arm64 libkdb5-10t64 arm64 1.21.3-5 [41.3 kB] Get: 48 http://deb.debian.org/debian forky/main arm64 libkadm5srv-mit12 arm64 1.21.3-5 [53.0 kB] Get: 49 http://deb.debian.org/debian forky/main arm64 krb5-multidev arm64 1.21.3-5 [126 kB] Get: 50 http://deb.debian.org/debian forky/main arm64 libaec0 arm64 1.1.4-2 [22.6 kB] Get: 51 http://deb.debian.org/debian forky/main arm64 libsz2 arm64 1.1.4-2 [8072 B] Get: 52 http://deb.debian.org/debian forky/main arm64 libaec-dev arm64 1.1.4-2 [20.3 kB] Get: 53 http://deb.debian.org/debian forky/main arm64 libblas3 arm64 3.12.1-7 [135 kB] Get: 54 http://deb.debian.org/debian forky/main arm64 liblapack3 arm64 3.12.1-7 [1846 kB] Get: 55 http://deb.debian.org/debian forky/main arm64 libarpack2t64 arm64 3.9.1-6 [84.2 kB] Get: 56 http://deb.debian.org/debian forky/main arm64 libblas-dev arm64 3.12.1-7 [145 kB] Get: 57 http://deb.debian.org/debian forky/main arm64 liblapack-dev arm64 3.12.1-7 [3829 kB] Get: 58 http://deb.debian.org/debian forky/main arm64 libarpack2-dev arm64 3.9.1-6 [102 kB] Get: 59 http://deb.debian.org/debian forky/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 60 http://deb.debian.org/debian forky/main arm64 libbrotli-dev arm64 1.1.0-2+b7 [308 kB] Get: 61 http://deb.debian.org/debian forky/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 62 http://deb.debian.org/debian forky/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get: 63 http://deb.debian.org/debian forky/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 64 http://deb.debian.org/debian forky/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 65 http://deb.debian.org/debian forky/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 66 http://deb.debian.org/debian forky/main arm64 libgnutls30t64 arm64 3.8.9-3 [1375 kB] Get: 67 http://deb.debian.org/debian forky/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 68 http://deb.debian.org/debian forky/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 69 http://deb.debian.org/debian forky/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 70 http://deb.debian.org/debian forky/main arm64 libnghttp2-14 arm64 1.64.0-1.1+b1 [71.7 kB] Get: 71 http://deb.debian.org/debian forky/main arm64 libnghttp3-9 arm64 1.11.0-1 [66.7 kB] Get: 72 http://deb.debian.org/debian forky/main arm64 libngtcp2-16 arm64 1.15.1-1 [122 kB] Get: 73 http://deb.debian.org/debian forky/main arm64 libngtcp2-crypto-gnutls8 arm64 1.15.1-1 [18.6 kB] Get: 74 http://deb.debian.org/debian forky/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 75 http://deb.debian.org/debian forky/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3 [56.3 kB] Get: 76 http://deb.debian.org/debian forky/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 77 http://deb.debian.org/debian forky/main arm64 libcurl3t64-gnutls arm64 8.16.0-1 [382 kB] Get: 78 http://deb.debian.org/debian forky/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 79 http://deb.debian.org/debian forky/main arm64 libunbound8 arm64 1.23.1-1 [561 kB] Get: 80 http://deb.debian.org/debian forky/main arm64 libgnutls-dane0t64 arm64 3.8.9-3 [453 kB] Get: 81 http://deb.debian.org/debian forky/main arm64 libgnutls-openssl27t64 arm64 3.8.9-3 [453 kB] Get: 82 http://deb.debian.org/debian forky/main arm64 libidn2-dev arm64 2.3.8-4 [102 kB] Get: 83 http://deb.debian.org/debian forky/main arm64 libp11-kit-dev arm64 0.25.5-3 [208 kB] Get: 84 http://deb.debian.org/debian forky/main arm64 libtasn1-6-dev arm64 4.20.0-2 [96.7 kB] Get: 85 http://deb.debian.org/debian forky/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-5 [329 kB] Get: 86 http://deb.debian.org/debian forky/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-5 [621 kB] Get: 87 http://deb.debian.org/debian forky/main arm64 nettle-dev arm64 3.10.1-1 [1325 kB] Get: 88 http://deb.debian.org/debian forky/main arm64 libgnutls28-dev arm64 3.8.9-3 [1416 kB] Get: 89 http://deb.debian.org/debian forky/main arm64 libkrb5-dev arm64 1.21.3-5 [16.1 kB] Get: 90 http://deb.debian.org/debian forky/main arm64 libldap-dev arm64 2.6.10+dfsg-1 [305 kB] Get: 91 http://deb.debian.org/debian forky/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 92 http://deb.debian.org/debian forky/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 93 http://deb.debian.org/debian forky/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 94 http://deb.debian.org/debian forky/main arm64 libnghttp2-dev arm64 1.64.0-1.1+b1 [112 kB] Get: 95 http://deb.debian.org/debian forky/main arm64 libnghttp3-dev arm64 1.11.0-1 [94.6 kB] Get: 96 http://deb.debian.org/debian forky/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.15.1-1 [24.5 kB] Get: 97 http://deb.debian.org/debian forky/main arm64 libngtcp2-dev arm64 1.15.1-1 [179 kB] Get: 98 http://deb.debian.org/debian forky/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 99 http://deb.debian.org/debian forky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 100 http://deb.debian.org/debian forky/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-3 [173 kB] Get: 101 http://deb.debian.org/debian forky/main arm64 libssl-dev arm64 3.5.3-1 [3377 kB] Get: 102 http://deb.debian.org/debian forky/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 103 http://deb.debian.org/debian forky/main arm64 libzstd-dev arm64 1.5.7+dfsg-1.1 [335 kB] Get: 104 http://deb.debian.org/debian forky/main arm64 libcurl4-gnutls-dev arm64 8.16.0-1 [525 kB] Get: 105 http://deb.debian.org/debian forky/main arm64 libcurl4t64 arm64 8.16.0-1 [388 kB] Get: 106 http://deb.debian.org/debian forky/main arm64 libfftw3-double3 arm64 3.3.10-2+b1 [337 kB] Get: 107 http://deb.debian.org/debian forky/main arm64 libfftw3-long3 arm64 3.3.10-2+b1 [546 kB] Get: 108 http://deb.debian.org/debian forky/main arm64 libfftw3-single3 arm64 3.3.10-2+b1 [517 kB] Get: 109 http://deb.debian.org/debian forky/main arm64 libfftw3-bin arm64 3.3.10-2+b1 [44.3 kB] Get: 110 http://deb.debian.org/debian forky/main arm64 libfftw3-dev arm64 3.3.10-2+b1 [1280 kB] Get: 111 http://deb.debian.org/debian forky/main arm64 libhdf5-310 arm64 1.14.5+repack-4 [1177 kB] Get: 112 http://deb.debian.org/debian forky/main arm64 libhdf5-cpp-310 arm64 1.14.5+repack-4 [129 kB] Get: 113 http://deb.debian.org/debian forky/main arm64 libhdf5-fortran-310 arm64 1.14.5+repack-4 [114 kB] Get: 114 http://deb.debian.org/debian forky/main arm64 libhdf5-hl-310 arm64 1.14.5+repack-4 [68.4 kB] Get: 115 http://deb.debian.org/debian forky/main arm64 libhdf5-hl-fortran-310 arm64 1.14.5+repack-4 [44.5 kB] Get: 116 http://deb.debian.org/debian forky/main arm64 libhdf5-hl-cpp-310 arm64 1.14.5+repack-4 [24.9 kB] Get: 117 http://deb.debian.org/debian forky/main arm64 libjpeg62-turbo arm64 1:2.1.5-4 [173 kB] Get: 118 http://deb.debian.org/debian forky/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-4 [293 kB] Get: 119 http://deb.debian.org/debian forky/main arm64 libjpeg-dev arm64 1:2.1.5-4 [72.2 kB] Get: 120 http://deb.debian.org/debian forky/main arm64 libhdf5-dev arm64 1.14.5+repack-4 [3219 kB] Get: 121 http://deb.debian.org/debian forky/main arm64 liblzma-dev arm64 5.8.1-1.1 [344 kB] Get: 122 http://deb.debian.org/debian forky/main arm64 libncurses6 arm64 6.5+20250216-2 [96.1 kB] Get: 123 http://deb.debian.org/debian forky/main arm64 libncurses-dev arm64 6.5+20250216-2 [340 kB] Get: 124 http://deb.debian.org/debian forky/main arm64 libnetcdf22 arm64 1:4.9.3-1+b1 [480 kB] Get: 125 http://deb.debian.org/debian forky/main arm64 libxml2-dev arm64 2.14.5+dfsg-0.2 [709 kB] Get: 126 http://deb.debian.org/debian forky/main arm64 libnetcdf-dev arm64 1:4.9.3-1+b1 [116 kB] Get: 127 http://deb.debian.org/debian forky/main arm64 libopenmm8.1 arm64 8.1.2+dfsg-11 [921 kB] Get: 128 http://deb.debian.org/debian forky/main arm64 libopenmm-dev arm64 8.1.2+dfsg-11 [331 kB] Get: 129 http://deb.debian.org/debian forky/main arm64 libreadline8t64 arm64 8.3-3 [169 kB] Get: 130 http://deb.debian.org/debian forky/main arm64 libreadline-dev arm64 8.3-3 [163 kB] Get: 131 http://deb.debian.org/debian forky/main arm64 netcdf-bin arm64 1:4.9.3-1+b1 [245 kB] Fetched 124 MB in 1s (129 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 ... 20020 files and directories currently installed.) Preparing to unpack .../000-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../003-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.23.1-2+b1_arm64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../006-libuchardet0_0.0.8-2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../007-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../008-bsdextrautils_2.41.1-3_arm64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../009-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../010-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../011-m4_1.4.20-1_arm64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../012-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../013-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../014-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../015-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../016-libcom-err2_1.47.2-3+b3_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2-3+b3) ... Selecting previously unselected package comerr-dev:arm64. Preparing to unpack .../017-comerr-dev_2.1-1.47.2-3+b3_arm64.deb ... Unpacking comerr-dev:arm64 (2.1-1.47.2-3+b3) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../018-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../019-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../020-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../021-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../022-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../023-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../024-libelf1t64_0.193-3_arm64.deb ... Unpacking libelf1t64:arm64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../025-dwz_0.16-2_arm64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../026-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2-16:arm64. Preparing to unpack .../027-libxml2-16_2.14.5+dfsg-0.2_arm64.deb ... Unpacking libxml2-16:arm64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../028-gettext_0.23.1-2+b1_arm64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../029-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../030-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../031-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../032-libgfortran5_15.2.0-4_arm64.deb ... Unpacking libgfortran5:arm64 (15.2.0-4) ... Selecting previously unselected package libgfortran-15-dev:arm64. Preparing to unpack .../033-libgfortran-15-dev_15.2.0-4_arm64.deb ... Unpacking libgfortran-15-dev:arm64 (15.2.0-4) ... Selecting previously unselected package gfortran-15-aarch64-linux-gnu. Preparing to unpack .../034-gfortran-15-aarch64-linux-gnu_15.2.0-4_arm64.deb ... Unpacking gfortran-15-aarch64-linux-gnu (15.2.0-4) ... Selecting previously unselected package gfortran-15. Preparing to unpack .../035-gfortran-15_15.2.0-4_arm64.deb ... Unpacking gfortran-15 (15.2.0-4) ... Selecting previously unselected package gfortran-aarch64-linux-gnu. Preparing to unpack .../036-gfortran-aarch64-linux-gnu_4%3a15.2.0-4_arm64.deb ... Unpacking gfortran-aarch64-linux-gnu (4:15.2.0-4) ... Selecting previously unselected package gfortran. Preparing to unpack .../037-gfortran_4%3a15.2.0-4_arm64.deb ... Unpacking gfortran (4:15.2.0-4) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../038-hdf5-helpers_1.14.5+repack-4_arm64.deb ... Unpacking hdf5-helpers (1.14.5+repack-4) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../039-libkrb5support0_1.21.3-5_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-5) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../040-libk5crypto3_1.21.3-5_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../041-libkeyutils1_1.6.3-6_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../042-libkrb5-3_1.21.3-5_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../043-libgssapi-krb5-2_1.21.3-5_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-5) ... Selecting previously unselected package libgssrpc4t64:arm64. Preparing to unpack .../044-libgssrpc4t64_1.21.3-5_arm64.deb ... Unpacking libgssrpc4t64:arm64 (1.21.3-5) ... Selecting previously unselected package libkadm5clnt-mit12:arm64. Preparing to unpack .../045-libkadm5clnt-mit12_1.21.3-5_arm64.deb ... Unpacking libkadm5clnt-mit12:arm64 (1.21.3-5) ... Selecting previously unselected package libkdb5-10t64:arm64. Preparing to unpack .../046-libkdb5-10t64_1.21.3-5_arm64.deb ... Unpacking libkdb5-10t64:arm64 (1.21.3-5) ... Selecting previously unselected package libkadm5srv-mit12:arm64. Preparing to unpack .../047-libkadm5srv-mit12_1.21.3-5_arm64.deb ... Unpacking libkadm5srv-mit12:arm64 (1.21.3-5) ... Selecting previously unselected package krb5-multidev:arm64. Preparing to unpack .../048-krb5-multidev_1.21.3-5_arm64.deb ... Unpacking krb5-multidev:arm64 (1.21.3-5) ... Selecting previously unselected package libaec0:arm64. Preparing to unpack .../049-libaec0_1.1.4-2_arm64.deb ... Unpacking libaec0:arm64 (1.1.4-2) ... Selecting previously unselected package libsz2:arm64. Preparing to unpack .../050-libsz2_1.1.4-2_arm64.deb ... Unpacking libsz2:arm64 (1.1.4-2) ... Selecting previously unselected package libaec-dev:arm64. Preparing to unpack .../051-libaec-dev_1.1.4-2_arm64.deb ... Unpacking libaec-dev:arm64 (1.1.4-2) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../052-libblas3_3.12.1-7_arm64.deb ... Unpacking libblas3:arm64 (3.12.1-7) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../053-liblapack3_3.12.1-7_arm64.deb ... Unpacking liblapack3:arm64 (3.12.1-7) ... Selecting previously unselected package libarpack2t64:arm64. Preparing to unpack .../054-libarpack2t64_3.9.1-6_arm64.deb ... Unpacking libarpack2t64:arm64 (3.9.1-6) ... Selecting previously unselected package libblas-dev:arm64. Preparing to unpack .../055-libblas-dev_3.12.1-7_arm64.deb ... Unpacking libblas-dev:arm64 (3.12.1-7) ... Selecting previously unselected package liblapack-dev:arm64. Preparing to unpack .../056-liblapack-dev_3.12.1-7_arm64.deb ... Unpacking liblapack-dev:arm64 (3.12.1-7) ... Selecting previously unselected package libarpack2-dev:arm64. Preparing to unpack .../057-libarpack2-dev_3.9.1-6_arm64.deb ... Unpacking libarpack2-dev:arm64 (3.9.1-6) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../058-libbrotli1_1.1.0-2+b7_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b7) ... Selecting previously unselected package libbrotli-dev:arm64. Preparing to unpack .../059-libbrotli-dev_1.1.0-2+b7_arm64.deb ... Unpacking libbrotli-dev:arm64 (1.1.0-2+b7) ... Selecting previously unselected package libbz2-dev:arm64. Preparing to unpack .../060-libbz2-dev_1.0.8-6_arm64.deb ... Unpacking libbz2-dev:arm64 (1.0.8-6) ... Selecting previously unselected package libidn2-0:arm64. Preparing to unpack .../061-libidn2-0_2.3.8-4_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.8-4) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../062-libffi8_3.5.2-2_arm64.deb ... Unpacking libffi8:arm64 (3.5.2-2) ... Selecting previously unselected package libp11-kit0:arm64. Preparing to unpack .../063-libp11-kit0_0.25.5-3_arm64.deb ... Unpacking libp11-kit0:arm64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:arm64. Preparing to unpack .../064-libtasn1-6_4.20.0-2_arm64.deb ... Unpacking libtasn1-6:arm64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:arm64. Preparing to unpack .../065-libgnutls30t64_3.8.9-3_arm64.deb ... Unpacking libgnutls30t64:arm64 (3.8.9-3) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../066-libsasl2-modules-db_2.1.28+dfsg1-9_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../067-libsasl2-2_2.1.28+dfsg1-9_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:arm64. Preparing to unpack .../068-libldap2_2.6.10+dfsg-1_arm64.deb ... Unpacking libldap2:arm64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../069-libnghttp2-14_1.64.0-1.1+b1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1.1+b1) ... Selecting previously unselected package libnghttp3-9:arm64. Preparing to unpack .../070-libnghttp3-9_1.11.0-1_arm64.deb ... Unpacking libnghttp3-9:arm64 (1.11.0-1) ... Selecting previously unselected package libngtcp2-16:arm64. Preparing to unpack .../071-libngtcp2-16_1.15.1-1_arm64.deb ... Unpacking libngtcp2-16:arm64 (1.15.1-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:arm64. Preparing to unpack .../072-libngtcp2-crypto-gnutls8_1.15.1-1_arm64.deb ... Unpacking libngtcp2-crypto-gnutls8:arm64 (1.15.1-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../073-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../074-librtmp1_2.4+20151223.gitfa8646d.1-3_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-3) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../075-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:arm64. Preparing to unpack .../076-libcurl3t64-gnutls_8.16.0-1_arm64.deb ... Unpacking libcurl3t64-gnutls:arm64 (8.16.0-1) ... Selecting previously unselected package libevent-2.1-7t64:arm64. Preparing to unpack .../077-libevent-2.1-7t64_2.1.12-stable-10+b1_arm64.deb ... Unpacking libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... 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Selecting previously unselected package libldap-dev:arm64. Preparing to unpack .../089-libldap-dev_2.6.10+dfsg-1_arm64.deb ... Unpacking libldap-dev:arm64 (2.6.10+dfsg-1) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../090-libpkgconf3_1.8.1-4_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../091-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../092-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Selecting previously unselected package libnghttp2-dev:arm64. Preparing to unpack .../093-libnghttp2-dev_1.64.0-1.1+b1_arm64.deb ... Unpacking libnghttp2-dev:arm64 (1.64.0-1.1+b1) ... Selecting previously unselected package libnghttp3-dev:arm64. Preparing to unpack .../094-libnghttp3-dev_1.11.0-1_arm64.deb ... Unpacking libnghttp3-dev:arm64 (1.11.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls-dev:arm64. Preparing to unpack .../095-libngtcp2-crypto-gnutls-dev_1.15.1-1_arm64.deb ... Unpacking libngtcp2-crypto-gnutls-dev:arm64 (1.15.1-1) ... Selecting previously unselected package libngtcp2-dev:arm64. Preparing to unpack .../096-libngtcp2-dev_1.15.1-1_arm64.deb ... Unpacking libngtcp2-dev:arm64 (1.15.1-1) ... Selecting previously unselected package libpsl-dev:arm64. Preparing to unpack .../097-libpsl-dev_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl-dev:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../098-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package librtmp-dev:arm64. Preparing to unpack .../099-librtmp-dev_2.4+20151223.gitfa8646d.1-3_arm64.deb ... Unpacking librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-3) ... Selecting previously unselected package libssl-dev:arm64. Preparing to unpack .../100-libssl-dev_3.5.3-1_arm64.deb ... Unpacking libssl-dev:arm64 (3.5.3-1) ... Selecting previously unselected package libssh2-1-dev:arm64. Preparing to unpack .../101-libssh2-1-dev_1.11.1-1_arm64.deb ... Unpacking libssh2-1-dev:arm64 (1.11.1-1) ... Selecting previously unselected package libzstd-dev:arm64. Preparing to unpack .../102-libzstd-dev_1.5.7+dfsg-1.1_arm64.deb ... Unpacking libzstd-dev:arm64 (1.5.7+dfsg-1.1) ... Selecting previously unselected package libcurl4-gnutls-dev:arm64. Preparing to unpack .../103-libcurl4-gnutls-dev_8.16.0-1_arm64.deb ... Unpacking libcurl4-gnutls-dev:arm64 (8.16.0-1) ... Selecting previously unselected package libcurl4t64:arm64. Preparing to unpack .../104-libcurl4t64_8.16.0-1_arm64.deb ... Unpacking libcurl4t64:arm64 (8.16.0-1) ... Selecting previously unselected package libfftw3-double3:arm64. Preparing to unpack .../105-libfftw3-double3_3.3.10-2+b1_arm64.deb ... Unpacking libfftw3-double3:arm64 (3.3.10-2+b1) ... Selecting previously unselected package libfftw3-long3:arm64. Preparing to unpack .../106-libfftw3-long3_3.3.10-2+b1_arm64.deb ... Unpacking libfftw3-long3:arm64 (3.3.10-2+b1) ... Selecting previously unselected package libfftw3-single3:arm64. Preparing to unpack .../107-libfftw3-single3_3.3.10-2+b1_arm64.deb ... Unpacking libfftw3-single3:arm64 (3.3.10-2+b1) ... Selecting previously unselected package libfftw3-bin. Preparing to unpack .../108-libfftw3-bin_3.3.10-2+b1_arm64.deb ... Unpacking libfftw3-bin (3.3.10-2+b1) ... Selecting previously unselected package libfftw3-dev:arm64. Preparing to unpack .../109-libfftw3-dev_3.3.10-2+b1_arm64.deb ... Unpacking libfftw3-dev:arm64 (3.3.10-2+b1) ... Selecting previously unselected package libhdf5-310:arm64. Preparing to unpack .../110-libhdf5-310_1.14.5+repack-4_arm64.deb ... Unpacking libhdf5-310:arm64 (1.14.5+repack-4) ... Selecting previously unselected package libhdf5-cpp-310:arm64. 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Preparing to unpack .../116-libjpeg62-turbo_1%3a2.1.5-4_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-4) ... Selecting previously unselected package libjpeg62-turbo-dev:arm64. Preparing to unpack .../117-libjpeg62-turbo-dev_1%3a2.1.5-4_arm64.deb ... Unpacking libjpeg62-turbo-dev:arm64 (1:2.1.5-4) ... Selecting previously unselected package libjpeg-dev:arm64. Preparing to unpack .../118-libjpeg-dev_1%3a2.1.5-4_arm64.deb ... Unpacking libjpeg-dev:arm64 (1:2.1.5-4) ... Selecting previously unselected package libhdf5-dev. Preparing to unpack .../119-libhdf5-dev_1.14.5+repack-4_arm64.deb ... Unpacking libhdf5-dev (1.14.5+repack-4) ... Selecting previously unselected package liblzma-dev:arm64. Preparing to unpack .../120-liblzma-dev_5.8.1-1.1_arm64.deb ... Unpacking liblzma-dev:arm64 (5.8.1-1.1) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../121-libncurses6_6.5+20250216-2_arm64.deb ... Unpacking libncurses6:arm64 (6.5+20250216-2) ... Selecting previously unselected package libncurses-dev:arm64. Preparing to unpack .../122-libncurses-dev_6.5+20250216-2_arm64.deb ... Unpacking libncurses-dev:arm64 (6.5+20250216-2) ... Selecting previously unselected package libnetcdf22:arm64. Preparing to unpack .../123-libnetcdf22_1%3a4.9.3-1+b1_arm64.deb ... Unpacking libnetcdf22:arm64 (1:4.9.3-1+b1) ... Selecting previously unselected package libxml2-dev:arm64. Preparing to unpack .../124-libxml2-dev_2.14.5+dfsg-0.2_arm64.deb ... Unpacking libxml2-dev:arm64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package libnetcdf-dev. Preparing to unpack .../125-libnetcdf-dev_1%3a4.9.3-1+b1_arm64.deb ... Unpacking libnetcdf-dev (1:4.9.3-1+b1) ... Selecting previously unselected package libopenmm8.1. Preparing to unpack .../126-libopenmm8.1_8.1.2+dfsg-11_arm64.deb ... Unpacking libopenmm8.1 (8.1.2+dfsg-11) ... Selecting previously unselected package libopenmm-dev. Preparing to unpack .../127-libopenmm-dev_8.1.2+dfsg-11_arm64.deb ... Unpacking libopenmm-dev (8.1.2+dfsg-11) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../128-libreadline8t64_8.3-3_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.3-3) ... Selecting previously unselected package libreadline-dev:arm64. Preparing to unpack .../129-libreadline-dev_8.3-3_arm64.deb ... Unpacking libreadline-dev:arm64 (8.3-3) ... Selecting previously unselected package netcdf-bin. Preparing to unpack .../130-netcdf-bin_1%3a4.9.3-1+b1_arm64.deb ... Unpacking netcdf-bin (1:4.9.3-1+b1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libkeyutils1:arm64 (1.6.3-6) ... Setting up libfftw3-single3:arm64 (3.3.10-2+b1) ... Setting up libzstd-dev:arm64 (1.5.7+dfsg-1.1) ... Setting up bsdextrautils (2.41.1-3) ... Setting up hdf5-helpers (1.14.5+repack-4) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:arm64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libbrotli1:arm64 (1.1.0-2+b7) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up libnghttp2-14:arm64 (1.64.0-1.1+b1) ... Setting up libfftw3-long3:arm64 (3.3.10-2+b1) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Setting up libcom-err2:arm64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up libaec0:arm64 (1.1.4-2) ... Setting up libelf1t64:arm64 (0.193-3) ... Setting up libkrb5support0:arm64 (1.21.3-5) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-9) ... Setting up autotools-dev (20240727.1) ... Setting up libblas3:arm64 (3.12.1-7) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libunbound8:arm64 (1.23.1-1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-5) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-4) ... Setting up libjpeg62-turbo-dev:arm64 (1:2.1.5-4) ... Setting up libncurses6:arm64 (6.5+20250216-2) ... Setting up comerr-dev:arm64 (2.1-1.47.2-3+b3) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up libssl-dev:arm64 (3.5.3-1) ... Setting up autopoint (0.23.1-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:arm64 (1.21.3-5) ... Setting up libfftw3-double3:arm64 (3.3.10-2+b1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:arm64 (15.2.0-4) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:arm64 (1.11.0-1) ... Setting up libnghttp3-dev:arm64 (1.11.0-1) ... Setting up liblzma-dev:arm64 (5.8.1-1.1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:arm64 (0.0.8-2) ... Setting up libtasn1-6:arm64 (4.20.0-2) ... Setting up libngtcp2-16:arm64 (1.15.1-1) ... Setting up libkrb5-3:arm64 (1.21.3-5) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up libtasn1-6-dev:arm64 (4.20.0-2) ... Setting up libopenmm8.1 (8.1.2+dfsg-11) ... Setting up readline-common (8.3-3) ... Setting up libldap2:arm64 (2.6.10+dfsg-1) ... Setting up libbrotli-dev:arm64 (1.1.0-2+b7) ... Setting up libblas-dev:arm64 (3.12.1-7) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up libsz2:arm64 (1.1.4-2) ... Setting up libbz2-dev:arm64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up liblapack3:arm64 (3.12.1-7) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libncurses-dev:arm64 (6.5+20250216-2) ... Setting up gettext (0.23.1-2+b1) ... Setting up libarpack2t64:arm64 (3.9.1-6) ... Setting up libgmp-dev:arm64 (2:6.3.0+dfsg-5) ... Setting up nettle-dev:arm64 (3.10.1-1) ... Setting up libtool (2.5.4-5) ... Setting up libfftw3-bin (3.3.10-2+b1) ... Setting up libaec-dev:arm64 (1.1.4-2) ... Setting up libjpeg-dev:arm64 (1:2.1.5-4) ... Setting up libidn2-0:arm64 (2.3.8-4) ... Setting up libngtcp2-dev:arm64 (1.15.1-1) ... Setting up libgfortran-15-dev:arm64 (15.2.0-4) ... Setting up libopenmm-dev (8.1.2+dfsg-11) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libxml2-dev:arm64 (2.14.5+dfsg-0.2) ... Setting up gfortran-15-aarch64-linux-gnu (15.2.0-4) ... Setting up libldap-dev:arm64 (2.6.10+dfsg-1) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up liblapack-dev:arm64 (3.12.1-7) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ... Setting up libssh2-1-dev:arm64 (1.11.1-1) ... Setting up libidn2-dev:arm64 (2.3.8-4) ... Setting up libreadline8t64:arm64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up gfortran-aarch64-linux-gnu (4:15.2.0-4) ... Setting up libfftw3-dev:arm64 (3.3.10-2+b1) ... Setting up libp11-kit-dev:arm64 (0.25.5-3) ... Setting up gfortran-15 (15.2.0-4) ... Setting up libgnutls30t64:arm64 (3.8.9-3) ... Setting up libgnutls-openssl27t64:arm64 (3.8.9-3) ... Setting up libnghttp2-dev:arm64 (1.64.0-1.1+b1) ... Setting up libarpack2-dev:arm64 (3.9.1-6) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up libreadline-dev:arm64 (8.3-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran (4:15.2.0-4) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libpsl-dev:arm64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:arm64 (3.8.9-3) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libgssrpc4t64:arm64 (1.21.3-5) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.15.1-1) ... Setting up libkadm5clnt-mit12:arm64 (1.21.3-5) ... Setting up libgnutls28-dev:arm64 (3.8.9-3) ... Setting up libcurl4t64:arm64 (8.16.0-1) ... Setting up libkdb5-10t64:arm64 (1.21.3-5) ... Setting up libcurl3t64-gnutls:arm64 (8.16.0-1) ... Setting up debhelper (13.26) ... Setting up libngtcp2-crypto-gnutls-dev:arm64 (1.15.1-1) ... Setting up librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libhdf5-310:arm64 (1.14.5+repack-4) ... Setting up libkadm5srv-mit12:arm64 (1.21.3-5) ... Setting up libhdf5-fortran-310:arm64 (1.14.5+repack-4) ... Setting up krb5-multidev:arm64 (1.21.3-5) ... Setting up libhdf5-cpp-310:arm64 (1.14.5+repack-4) ... Setting up libhdf5-hl-310:arm64 (1.14.5+repack-4) ... Setting up libnetcdf22:arm64 (1:4.9.3-1+b1) ... Setting up netcdf-bin (1:4.9.3-1+b1) ... Setting up libkrb5-dev:arm64 (1.21.3-5) ... Setting up libhdf5-hl-cpp-310:arm64 (1.14.5+repack-4) ... Setting up libhdf5-hl-fortran-310:arm64 (1.14.5+repack-4) ... Setting up libcurl4-gnutls-dev:arm64 (8.16.0-1) ... Setting up libhdf5-dev (1.14.5+repack-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libnetcdf-dev (1:4.9.3-1+b1) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: 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-5_source.changes dpkg-buildpackage: info: source package cpptraj dpkg-buildpackage: info: source version 5.1.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Santiago Vila dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' touch config.h external.config.h dh_auto_clean make -j12 clean make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' /bin/rm -f SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o cpptraj *.LIBCPPTRAJ.o libcpptraj # cd readline && make clean cd xdrfile && make clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' /bin/rm -f *.o libxdrfile.a a.out test.trr test.xtc test.xdr make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' # cd arpack && make clean cd cuda_kernels && make clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/cuda_kernels' /bin/rm -f *.o libcpptraj_cuda.a make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/cuda_kernels' cd tng && make clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' /bin/rm -f *.o libtng_io.a tng_io_testing.o a.out tng_example_out.tng tng_test.tng make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' cd test && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' Cleaning all test directories: make test.complete test.libcpptraj OPT=clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' cd unitTests && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' Cleaning unit tests. make test.complete OPT=clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' rm -rf bin make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' ./configure gnu --with-arpack=/usr/lib/aarch64-linux-gnu --with-fftw3=/usr/lib/aarch64-linux-gnu --with-readline=/usr/lib/aarch64-linux-gnu --with-openmm=/usr/lib/aarch64-linux-gnu arpack specified: /usr/lib/aarch64-linux-gnu fftw3 specified: /usr/lib/aarch64-linux-gnu readline specified: /usr/lib/aarch64-linux-gnu openmm specified: /usr/lib/aarch64-linux-gnu Testing C++ compiler: OK Testing C compiler: OK Testing basic C++11 support: OK Testing system headers for C++11 support: OK Warning: Compilation of sanderlib requires AMBERHOME to be set Warning: if --with-sanderlib not specified. Checking BZLIB: OK Checking ZLIB: OK Checking NetCDF: OK Checking LAPACK/BLAS: OK Checking ARPACK: OK Checking FFTW3: OK Checking Readline: OK Checking OpenMM: OK vmdplugin disabled due to nonfree source. Configuration summary: Build type: Serial Options: netcdf bzlib tng zlib arpack lapack blas fftw3 readline xdrfile openmm Target platform: Linux, 64-bit. gnu compilers in use. C++11 support enabled. PME support enabled. Compiler optimizations are on. Cleaning source directory. -------------------------------------------------------------------------------- An environment resource file for CPPTRAJ has been created: /build/reproducible-path/cpptraj-5.1.0+dfsg/cpptraj.sh You may 'source' this file to set up your environment for CPPTRAJ. -------------------------------------------------------------------------------- CPPTRAJ configuration complete. make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make install make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' CXX SpaceGroup.cpp CXX ActionFrameCounter.cpp CXX ActionList.cpp CXX ActionTopWriter.cpp CXX Action_Align.cpp CXX Action_Angle.cpp CXX Action_AreaPerMol.cpp CXX Action_AtomMap.cpp CXX Action_AtomicCorr.cpp CXX Action_AtomicFluct.cpp CXX Action_AutoImage.cpp CXX Action_Average.cpp CXX Action_Bounds.cpp CXX Action_Center.cpp CXX Action_Box.cpp CXX Action_Channel.cpp CXX Action_CheckChirality.cpp CXX Action_CheckStructure.cpp CXX Action_Closest.cpp CXX Action_ClusterDihedral.cpp CXX Action_Contacts.cpp CXX Action_CreateCrd.cpp CXX Action_CreateReservoir.cpp CXX Action_DNAionTracker.cpp CXX Action_DSSP.cpp CXX Action_Density.cpp CXX Action_Diffusion.cpp CXX Action_Dihedral.cpp CXX Action_DihedralRMS.cpp CXX Action_Dipole.cpp CXX Action_Distance.cpp CXX Action_DistRmsd.cpp CXX Action_Energy.cpp In file included from Ewald_ParticleMesh.h:5, from Action_Energy.cpp:4: helpme_standalone.h:2324: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2324 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:2344: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2344 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3015: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3015 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3121: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3121 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3248: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3248 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3702: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3702 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3740: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3740 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3803: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3803 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3841: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3841 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4045: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4045 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4053: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4053 | #pragma omp for helpme_standalone.h:4098: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4098 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4146: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4146 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4173: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4173 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4225: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4225 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4229: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4229 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4276: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4276 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4389: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4389 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4420: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4420 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4504: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4504 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4511: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4511 | #pragma omp for CXX Action_FilterByData.cpp CXX Action_FixAtomOrder.cpp CXX Action_FixImagedBonds.cpp CXX Action_GIST.cpp CXX Action_Grid.cpp CXX Action_GridFreeEnergy.cpp CXX Action_HydrogenBond.cpp CXX Action_Image.cpp CXX Action_InfraredSpectrum.cpp CXX Action_Jcoupling.cpp CXX Action_LESsplit.cpp CXX Action_LIE.cpp CXX Action_LipidOrder.cpp CXX Action_MakeStructure.cpp CXX Action_Mask.cpp CXX Action_Matrix.cpp CXX Action_MinImage.cpp In file included from Matrix_3x3.h:3, from Box.h:3, from Frame.h:5, from Topology.h:10, from DataSet_Coords.h:4, from DataSet_Coords_REF.h:3, from ReferenceFrame.h:3, from DataSetList.h:4, from DataFile.h:4, from DataFileList.h:3, from ActionState.h:3, from Action.h:5, from Action_GIST.h:3, from Action_GIST.cpp:3: In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:814:31: Vec3.h:76:23: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:814:31: Vec3.h:76:40: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:814:31: Vec3.h:76:57: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:815:31: Vec3.h:76:23: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:815:31: Vec3.h:76:40: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:815:31: Vec3.h:76:57: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ CXX Action_Molsurf.cpp CXX Action_MultiDihedral.cpp CXX Action_MultiVector.cpp CXX Action_NAstruct.cpp CXX Action_NativeContacts.cpp CXX Action_NMRrst.cpp CXX Action_OrderParameter.cpp CXX Action_Outtraj.cpp CXX Action_PairDist.cpp CXX Action_Pairwise.cpp CXX Action_Principal.cpp CXX Action_Projection.cpp CXX Action_Pucker.cpp CXX Action_Radgyr.cpp CXX Action_Radial.cpp CXX Action_RandomizeIons.cpp CXX Action_Remap.cpp CXX Action_ReplicateCell.cpp CXX Action_Rmsd.cpp CXX Action_Rotate.cpp CXX Action_RunningAvg.cpp CXX Action_STFC_Diffusion.cpp CXX Action_Scale.cpp CXX Action_SetVelocity.cpp CXX Action_Spam.cpp CXX Action_Strip.cpp CXX Action_Surf.cpp CXX Action_SymmetricRmsd.cpp CXX Action_Temperature.cpp CXX Action_Time.cpp CXX Action_Translate.cpp CXX Action_Unstrip.cpp CXX Action_Unwrap.cpp CXX Action_Vector.cpp CXX Action_VelocityAutoCorr.cpp CXX Action_Volmap.cpp CXX Action_Volume.cpp CXX Action_Watershell.cpp CXX Action_XtalSymm.cpp CXX AnalysisList.cpp CXX Analysis_AmdBias.cpp CXX Analysis_AutoCorr.cpp CXX Analysis_Average.cpp CXX Analysis_Clustering.cpp CXX Analysis_Corr.cpp CXX Analysis_ConstantPHStats.cpp CXX Analysis_CrankShaft.cpp CXX Analysis_CrdFluct.cpp CXX Analysis_CrossCorr.cpp CXX Analysis_CurveFit.cpp CXX Analysis_Divergence.cpp CXX Analysis_EvalPlateau.cpp CXX Analysis_FFT.cpp CXX Analysis_HausdorffDistance.cpp CXX Analysis_Hist.cpp CXX Analysis_Integrate.cpp CXX Analysis_IRED.cpp CXX Analysis_KDE.cpp CXX Analysis_Lifetime.cpp CXX Analysis_LowestCurve.cpp CXX Analysis_Matrix.cpp In file included from /usr/include/c++/15/vector:68, from ArgList.h:3, from Action.h:4, from Action_XtalSymm.h:3, from Action_XtalSymm.cpp:1: In member function 'void std::vector<_Tp, _Alloc>::assign(size_type, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]', inlined from 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)' at Action_XtalSymm.cpp:57:12: /usr/include/c++/15/bits/stl_vector.h:876:23: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 876 | { _M_fill_assign(__n, __val); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/15/vector:74: /usr/include/c++/15/bits/vector.tcc: In member function 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)': /usr/include/c++/15/bits/vector.tcc:270:5: note: by argument 3 of type 'const std::vector::value_type&' {aka 'const Vec3&'} to 'void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]' declared here 270 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ Action_XtalSymm.cpp:57:33: note: '' declared here 57 | T_.assign( nCopyTotal, Vec3()); | ^ In member function 'void std::vector<_Tp, _Alloc>::assign(size_type, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]', inlined from 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)' at Action_XtalSymm.cpp:58:15: /usr/include/c++/15/bits/stl_vector.h:876:23: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 876 | { _M_fill_assign(__n, __val); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/15/bits/vector.tcc: In member function 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)': /usr/include/c++/15/bits/vector.tcc:270:5: note: by argument 3 of type 'const std::vector::value_type&' {aka 'const Vec3&'} to 'void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]' declared here 270 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ Action_XtalSymm.cpp:58:33: note: '' declared here 58 | RefT_.assign(nCopyTotal, Vec3()); | ^ CXX Analysis_MeltCurve.cpp CXX Analysis_Modes.cpp CXX Analysis_Multicurve.cpp CXX Analysis_MultiHist.cpp CXX Analysis_Overlap.cpp CXX Analysis_PhiPsi.cpp CXX Analysis_Regression.cpp CXX Analysis_RemLog.cpp CXX Analysis_Rms2d.cpp CXX Analysis_RmsAvgCorr.cpp CXX Analysis_Rotdif.cpp CXX Analysis_RunningAvg.cpp CXX Analysis_Slope.cpp CXX Analysis_Spline.cpp CXX Analysis_State.cpp CXX Analysis_Statistics.cpp CXX Analysis_TI.cpp CXX Analysis_Timecorr.cpp CXX Analysis_VectorMath.cpp CXX Analysis_Wavelet.cpp CXX ArgList.cpp CXX Array1D.cpp CXX AssociatedData.cpp CXX Atom.cpp CXX AtomMap.cpp CXX AtomMask.cpp CXX AxisType.cpp CXX BondSearch.cpp CXX Box.cpp CXX BoxArgs.cpp CXX BufferedFrame.cpp CXX BufferedLine.cpp CXX ByteRoutines.cpp CXX CharMask.cpp CXX CharmmParamFile.cpp CXX CIFfile.cpp CXX ClusterDist.cpp CXX ClusterList.cpp CXX ClusterMap.cpp CXX ClusterMatrix.cpp CXX ClusterNode.cpp CXX ClusterSieve.cpp CXX Cluster_DBSCAN.cpp CXX Cluster_DPeaks.cpp CXX Cluster_HierAgglo.cpp CXX Cluster_Kmeans.cpp CXX Cluster_ReadInfo.cpp CXX Cmd.cpp CXX CmdInput.cpp CXX CmdList.cpp CXX CompactFrameArray.cpp CXX ComplexArray.cpp CXX Constraints.cpp CXX ControlBlock_For.cpp CXX CoordinateInfo.cpp CXX Corr.cpp CXX Cph.cpp CXX CpptrajFile.cpp CXX CpptrajState.cpp CXX CpptrajStdio.cpp CXX CurveFit.cpp CXX DataFile.cpp CXX DataFileList.cpp CXX DataFilter.cpp CXX DataIO.cpp CXX DataIO_CCP4.cpp CXX DataIO_CharmmFastRep.cpp CXX DataIO_CharmmOutput.cpp CXX DataIO_CharmmRepLog.cpp CXX DataIO_CharmmRtfPrm.cpp CXX DataIO_Cmatrix.cpp CXX DataIO_Cpout.cpp CXX DataIO_Evecs.cpp CXX DataIO_Gnuplot.cpp CXX DataIO_Grace.cpp CXX DataIO_OpenDx.cpp CXX DataIO_Peaks.cpp CXX DataIO_Mdout.cpp CXX DataIO_NC_Cmatrix.cpp CXX DataIO_RemLog.cpp CXX DataIO_Std.cpp CXX DataIO_VecTraj.cpp CXX DataIO_Xplor.cpp CXX DataIO_XVG.cpp CXX DataSet.cpp CXX DataSetList.cpp CXX DataSet_1D.cpp CXX DataSet_3D.cpp CXX DataSet_Cmatrix.cpp CXX DataSet_Cmatrix_DISK.cpp CXX DataSet_Cmatrix_MEM.cpp CXX DataSet_Cmatrix_NOMEM.cpp CXX DataSet_Coords.cpp CXX DataSet_Coords_CRD.cpp CXX DataSet_Coords_REF.cpp CXX DataSet_Coords_TRJ.cpp CXX DataSet_GridDbl.cpp CXX DataSet_GridFlt.cpp CXX DataSet_Mat3x3.cpp CXX DataSet_MatrixDbl.cpp CXX DataSet_MatrixFlt.cpp CXX DataSet_Mesh.cpp CXX DataSet_Modes.cpp CXX DataSet_Parameters.cpp CXX DataSet_pH.cpp CXX DataSet_PHREMD_Explicit.cpp CXX DataSet_PHREMD_Implicit.cpp CXX DataSet_RemLog.cpp CXX DataSet_Topology.cpp CXX DataSet_Vector.cpp CXX DataSet_Vector_Scalar.cpp CXX DataSet_double.cpp CXX DataSet_float.cpp CXX DataSet_integer_disk.cpp CXX DataSet_integer_mem.cpp CXX DataSet_string.cpp CXX DataSet_StringVar.cpp CXX DataSet_Tensor.cpp CXX DataSet_unsignedInt.cpp CXX Deprecated.cpp CXX DihedralSearch.cpp CXX DistRoutines.cpp CXX Energy.cpp CXX EnergyArray.cpp CXX EnsembleIn.cpp CXX EnsembleIn_Multi.cpp CXX EnsembleIn_Single.cpp CXX EnsembleNavigator.cpp CXX EnsembleOut.cpp CXX EnsembleOut_Multi.cpp CXX EnsembleOut_Single.cpp CXX EnsembleOutList.cpp CXX Ewald.cpp CXX Ewald_ParticleMesh.cpp CXX Ewald_Regular.cpp In file included from Ewald_ParticleMesh.h:5, from Ewald_ParticleMesh.cpp:4: helpme_standalone.h:2324: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2324 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:2344: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2344 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3015: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3015 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3121: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3121 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3248: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3248 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3702: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3702 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3740: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3740 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3803: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3803 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3841: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3841 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4045: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4045 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4053: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4053 | #pragma omp for helpme_standalone.h:4098: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4098 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4146: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4146 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4173: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4173 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4225: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4225 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4229: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4229 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4276: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4276 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4389: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4389 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4420: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4420 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4504: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4504 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4511: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4511 | #pragma omp for CXX ExclusionArray.cpp helpme_standalone.h: In instantiation of 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]': helpme_standalone.h:3899:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3899 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:1011:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 1011 | for (int val = 0; val < nRows_; ++val) eigenPairs.push_back({eigenValues[val][0], unsortedEigenVectors[val]}); | ~~~~^~~~~~~~ helpme_standalone.h:1014:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 1014 | for (int val = 0; val < nRows_; ++val) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::PMEInstance >::sanityChecks(int, const RealMat&, const RealMat&, int) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5019:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5019 | sanityChecks(parameterAngMom, parameters, coordinates); | ^~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3199:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3199 | if (parameters.nCols() != (nCartesian(parameterAngMom) - cartesianOffset)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::PMEInstance >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5020:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5020 | filterAtomsAndBuildSplineCache(parameterAngMom, coordinates); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3747:45: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3747 | for (size_t row = threadID; row < gridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~ helpme_standalone.h:3754:37: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3754 | for (int atom = 0; atom < nAtoms; ++atom) { | ~~~~~^~~~~~~~ helpme_standalone.h:3762:61: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3762 | if (cGridIterator.size() && thisAtomsThread == threadID) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~ helpme_standalone.h:3751:25: warning: unused variable 'gridIteratorC' [-Wunused-variable] 3751 | const auto &gridIteratorC = threadedGridIteratorC_[threadID]; | ^~~~~~~~~~~~~ helpme_standalone.h:3795:55: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3795 | for (int atom = splineCache_.size(); atom < newSize; ++atom) | ~~~~~^~~~~~~~~ helpme_standalone.h:3811:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3811 | for (size_t cRow = threadID; cRow < gridDimensionC_; cRow += nThreads_) { | ~~~~~^~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'Real* helpme::PMEInstance >::spreadParameters(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5021:25: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5021 | auto realGrid = spreadParameters(parameterAngMom, parameters); | ^~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3709:45: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3709 | for (size_t row = threadID; row < myGridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'helpme::PMEInstance >::Complex* helpme::PMEInstance >::forwardTransform(Real*) [with Real = double; typename std::enable_if::value, int>::type = 0; Complex = std::complex]': helpme_standalone.h:5024:32: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5024 | auto gridAddress = forwardTransform(realGrid); | ^~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:4005:28: warning: variable 'realCBA' set but not used [-Wunused-but-set-variable] 4005 | Real *__restrict__ realCBA; | ^~~~~~~ CXX Exec_AddMissingRes.cpp helpme_standalone.h: In instantiation of 'void helpme::Matrix::assertSymmetric(const Real&) const [with Real = double]': helpme_standalone.h:1001:9: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 1001 | assertSymmetric(); | ^~~~~~~~~~~~~~~ helpme_standalone.h:3899:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3899 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:797:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 797 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::JacobiCyclicDiagonalization(Real*, Real*, const Real*, int) [with Real = double]': helpme_standalone.h:1007:42: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 1007 | JacobiCyclicDiagonalization(eigenValues[0], unsortedEigenVectors[0], cbegin(), nRows_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3899:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3899 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:214:20: warning: variable 'cos_2phi' set but not used [-Wunused-but-set-variable] 214 | Real sin_2phi, cos_2phi, cot_2phi; | ^~~~~~~~ helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::applyOperation(const std::function&) const [with Real = double]': helpme_standalone.h:786:26: required from 'helpme::Matrix helpme::Matrix::inverse() const [with Real = double]' 786 | return this->applyOperation([](Real& element) { element = 1 / element; }); | ~~~~~~^~~~~~~~~~~~~~ helpme_standalone.h:3911:44: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3911 | recVecs_ = boxVecs_.inverse(); | ~~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:825:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 825 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::BSpline::update(short int, Real, short int, short int) [with Real = double]': helpme_standalone.h:3830:47: required from 'void helpme::PMEInstance >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 3830 | atomSplines.aSpline.update(aStartingGridPoint, gridDimensionA_ * aCoord - aStartingGridPoint, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3831 | splineOrder_, splineDerivativeLevel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:5020:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5020 | filterAtomsAndBuildSplineCache(parameterAngMom, coordinates); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:2209:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 2209 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:2209:72: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2209 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::multiply(const helpme::Matrix&) const [with Real = double]': helpme_standalone.h:878:64: required from 'helpme::Matrix helpme::Matrix::operator*(const helpme::Matrix&) const [with Real = double]' 878 | Matrix operator*(const Matrix& other) const { return this->multiply(other); } | ~~~~~~^~~~~~~~ helpme_standalone.h:830:22: required from 'helpme::Matrix helpme::Matrix::applyOperation(const std::function&) const [with Real = double]' 830 | return evecs * evecsT; | ~~~~~~^~~~~~~~ helpme_standalone.h:786:26: required from 'helpme::Matrix helpme::Matrix::inverse() const [with Real = double]' 786 | return this->applyOperation([](Real& element) { element = 1 / element; }); | ~~~~~~^~~~~~~~~~~~~~ helpme_standalone.h:3911:44: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3911 | recVecs_ = boxVecs_.inverse(); | ~~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:861:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 861 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h:863:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 863 | for (int col = 0; col < other.nCols_; ++col) { | ~~~~^~~~~~~~~~~~~~ helpme_standalone.h:864:41: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 864 | for (int link = 0; link < nCols_; ++link) { | ~~~~~^~~~~~~~ CXX Exec_Analyze.cpp CXX Exec_Calc.cpp CXX Exec_CatCrd.cpp CXX Exec_Change.cpp CXX Exec_ClusterMap.cpp CXX Exec_CombineCoords.cpp CXX Exec_Commands.cpp CXX Exec_CompareTop.cpp CXX Exec_CrdAction.cpp CXX Exec_CrdOut.cpp CXX Exec_CreateSet.cpp CXX Exec_DataFile.cpp CXX Exec_DataFilter.cpp CXX Exec_DataSetCmd.cpp CXX Exec_Emin.cpp CXX Exec_Flatten.cpp CXX Exec_GenerateAmberRst.cpp CXX Exec_Graft.cpp CXX Exec_Help.cpp CXX Exec_LoadCrd.cpp CXX Exec_LoadTraj.cpp helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3471:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3471 | fftHelperA_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3471:31: note: '' declared here 3471 | fftHelperA_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3472:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3472 | fftHelperB_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3472:31: note: '' declared here 3472 | fftHelperB_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3473:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3473 | fftHelperC_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3473:31: note: '' declared here 3473 | fftHelperC_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3504:43: helpme_standalone.h:520:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] 520 | class Matrix { | ^~~~~~ helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3504:45: note: '' declared here 3504 | compressionCoefficientsA_ = RealMat(); | ^~~~~~~~~ In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3505:43: helpme_standalone.h:520:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] 520 | class Matrix { | ^~~~~~ helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3505:45: note: '' declared here 3505 | compressionCoefficientsB_ = RealMat(); | ^~~~~~~~~ In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3506:43: helpme_standalone.h:520:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] 520 | class Matrix { | ^~~~~~ helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3506:45: note: '' declared here 3506 | compressionCoefficientsC_ = RealMat(); | ^~~~~~~~~ CXX Exec_ParallelAnalysis.cpp CXX Exec_ParmBox.cpp CXX Exec_ParmSolvent.cpp CXX Exec_ParmStrip.cpp CXX Exec_ParmWrite.cpp CXX Exec_PermuteDihedrals.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:5032:16: warning: 'energy' may be used uninitialized [-Wmaybe-uninitialized] 5032 | return energy; | ^~~~~~ helpme_standalone.h:5022:14: note: 'energy' was declared here 5022 | Real energy; | ^~~~~~ CXX Exec_Precision.cpp CXX Exec_PrepareForLeap.cpp CXX Exec_PrintData.cpp CXX Exec_Random.cpp CXX Exec_ReadData.cpp CXX Exec_ReadEnsembleData.cpp CXX Exec_ReadInput.cpp CXX Exec_RotateDihedral.cpp CXX Exec_RunAnalysis.cpp CXX Exec_ScaleDihedralK.cpp CXX Exec_Set.cpp CXX Exec_SequenceAlign.cpp CXX Exec_Show.cpp CXX Exec_SortEnsembleData.cpp CXX Exec_SplitCoords.cpp CXX Exec_System.cpp CXX Exec_Top.cpp CXX Exec_Traj.cpp CXX Exec_UpdateParameters.cpp CXX Exec_ViewRst.cpp CXX File_TempName.cpp CXX FileIO_Bzip2.cpp CXX FileIO_Gzip.cpp CXX FileIO_Mpi.cpp CXX FileIO_MpiShared.cpp CXX FileIO_Std.cpp CXX FileName.cpp CXX FileType.cpp CXX FileTypes.cpp CXX ForLoop.cpp CXX ForLoop_dataSetBlocks.cpp CXX ForLoop_integer.cpp CXX ForLoop_list.cpp CXX ForLoop_mask.cpp CXX ForLoop_overSets.cpp CXX Frame.cpp CXX GridAction.cpp CXX HistBin.cpp CXX Hungarian.cpp CXX ImageRoutines.cpp CXX Image_List_Mask.cpp CXX Image_List_Pair.cpp CXX Image_List_Unit.cpp CXX InputTrajCommon.cpp CXX KDE.cpp CXX MapAtom.cpp CXX MaskArray.cpp CXX MaskToken.cpp CXX Matrix_3x3.cpp CXX MdOpts.cpp CXX MetaData.cpp CXX Minimize_SteepestDescent.cpp CXX Mol.cpp CXX Mol2File.cpp CXX NameType.cpp CXX NC_Cmatrix.cpp CXX NC_Routines.cpp CXX NetcdfFile.cpp CXX OMM_helpers.cpp CXX OutputTrajCommon.cpp CXX ParameterSet.cpp CXX PDBfile.cpp CXX PairList.cpp CXX Parallel.cpp CXX ParallelNetcdf.cpp CXX ParmFile.cpp CXX Parm_Amber.cpp CXX Parm_CharmmPsf.cpp CXX Parm_CIF.cpp CXX Parm_Gromacs.cpp CXX Parm_Mol2.cpp CXX Parm_PDB.cpp CXX Parm_SDF.cpp CXX Parm_Tinker.cpp CXX PotentialFunction.cpp CXX PotentialTerm.cpp CXX PotentialTerm_Angle.cpp CXX PotentialTerm_Bond.cpp CXX PotentialTerm_Dihedral.cpp CXX PotentialTerm_LJ_Coulomb.cpp CXX PotentialTerm_OpenMM.cpp CXX ProgressBar.cpp CXX ProgressTimer.cpp CXX PubFFT.cpp CXX ExternalFxn.cpp CXX Random.cpp CXX Range.cpp CXX RNG.cpp CXX RNG_Marsaglia.cpp CXX RNG_MersenneTwister.cpp CXX RNG_PCG32.cpp CXX RNG_Stdlib.cpp CXX RNG_Xoshiro128pp.cpp CXX RPNcalc.cpp CXX ReferenceAction.cpp CXX RemdReservoirNC.cpp CXX Residue.cpp CXX SDFfile.cpp CXX SimplexMin.cpp CXX Spline.cpp CXX SplineFxnTable.cpp CXX StringRoutines.cpp CXX StructureCheck.cpp CXX StructureMapper.cpp CXX SymmetricRmsdCalc.cpp CXX TextFormat.cpp CXX Timer.cpp CXX TinkerFile.cpp CXX TopInfo.cpp CXX Topology.cpp CXX TorsionRoutines.cpp CXX Traj_AmberCoord.cpp CXX Traj_AmberNetcdf.cpp CXX Traj_AmberRestart.cpp CXX Traj_AmberRestartNC.cpp CXX Traj_Binpos.cpp CXX Traj_CharmmCor.cpp CXX Traj_CharmmDcd.cpp CXX Traj_CharmmRestart.cpp CXX Traj_CIF.cpp CXX Traj_Conflib.cpp CXX Traj_DTR.cpp CXX Traj_GmxDump.cpp CXX Traj_GmxTng.cpp CXX Traj_GmxTrX.cpp CXX Traj_GmxXtc.cpp CXX Traj_Gro.cpp CXX Traj_Mol2File.cpp CXX Traj_NcEnsemble.cpp CXX Traj_PDBfile.cpp CXX Traj_SDF.cpp CXX Traj_SQM.cpp CXX Traj_Tinker.cpp CXX Traj_XYZ.cpp CXX TrajectoryFile.cpp CXX TrajectoryIO.cpp CXX TrajFrameCounter.cpp CXX TrajinList.cpp CXX Trajin_Multi.cpp CXX Trajin_Single.cpp CXX TrajIOarray.cpp CXX Trajout_Single.cpp CXX TrajoutList.cpp CXX Vec3.cpp CXX ViewRst.cpp CXX xoshiro128plusplus.cpp xoshiro128plusplus.cpp: In function 'void jump()': xoshiro128plusplus.cpp:60:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 60 | for(int i = 0; i < sizeof JUMP / sizeof *JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ xoshiro128plusplus.cpp: In function 'void long_jump()': xoshiro128plusplus.cpp:90:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 90 | for(int i = 0; i < sizeof LONG_JUMP / sizeof *LONG_JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CXX Action_Esander.cpp CXX Command.cpp CXX Cpptraj.cpp CXX Energy_Sander.cpp CXX ReadLine.cpp CXX main.cpp CC molsurf.c Skipping bundled READLINE build cd xdrfile && make all make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' CC xdrfile.c Skipping bundled ARPACK build cd tng && make all make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' CC md5.c CC xdr_seek.c CC tng_io.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 /bin/rm -f libxdrfile.a CC xtc2.c ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' CC widemuldiv.c CC huffmem.c CC vals16.c CC bwt.c CC mtf.c CC rle.c CC lz77.c CC dict.c CC huffman.c CC merge_sort.c tng_io.c: In function 'tng_gen_data_block_add': tng_io.c:12600:9: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tng_io.c:12600:47: note: length computed here 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ /bin/rm -f libtng_io.a ar cqs libtng_io.a md5.o tng_io.o tng_compress.o coder.o warnmalloc.o fixpoint.o xtc3.o bwlzh.o xtc2.o widemuldiv.o huffmem.o vals16.o bwt.o mtf.o rle.o lz77.o dict.o huffman.o merge_sort.o make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o -L/usr/lib/aarch64-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/aarch64-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/aarch64-linux-gnu/lib -lfftw3 -L/usr/lib/aarch64-linux-gnu/lib -lOpenMM -lnetcdf -lbz2 tng/libtng_io.a -lz xdrfile/libxdrfile.a -Wl,-z,relro mv cpptraj "/build/reproducible-path/cpptraj-5.1.0+dfsg/bin" make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_auto_test -- check unittest make -j12 test "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 check unittest make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' make[2]: Nothing to be done for 'test'. cd test && make test.complete summary cd unitTests && make test.complete summary make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList CPPTRAJ: NameType class unit test. make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' g++ -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp CPPTRAJ: ArgList class unit test. g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o NameType.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/NameType.cpp make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp g++ -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o ArgList.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/ArgList.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o StringRoutines.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/StringRoutines.cpp -rwxr-xr-x 1 pbuilder1 pbuilder1 181912848 Sep 24 16:04 ../bin/cpptraj -rwxr-xr-x 1 pbuilder1 pbuilder1 181912848 Sep 24 16:04 ../bin/cpptraj make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Strip CPPTRAJ: One frame strip command test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_General ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj CPPTRAJ: Broken Traj: Running good trajectory. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RemdTraj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_trajout_framerange CPPTRAJ: CRD Replica Trajectory Run with offset CPPTRAJ: General tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TrajinOffset CPPTRAJ: Trajout Frame Range [Amber Restart] CPPTRAJ: Normal trajectory read with offsets. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD CPPTRAJ: Per-Residue RMSD Test. CPPTRAJ: Gzipped trajectory read with offsets CPPTRAJ: CRD Replica Trajectory Run CPPTRAJ: Broken Traj: Running broken trajectory. CPPTRAJ: Per-Residue RMSD Test with averaging CPPTRAJ: NetCDF Replica Trajectory Run test CPPTRAJ: Bzip2ed trajectory read with offsets CPPTRAJ: Trajout Frame Range [Amber Coordinates] CPPTRAJ: Unstrip (Lig/Rec/Complex) command test All 6 comparisons passed. CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj CPPTRAJ: Per-Residue RMSD Test with residue centering. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DSSP CPPTRAJ: Secstruct (DSSP) command test. CPPTRAJ: Start argument offset CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj All 4 comparisons passed. CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Center CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. CPPTRAJ: Center command test. CPPTRAJ: Multi frame strip command test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hbond CPPTRAJ: Solute Hbond test CPPTRAJ: Compressed broken trajectory test CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NCrestart CPPTRAJ: NetCDF Restart Test - TXT->NetCDF CPPTRAJ: Strip topology with PDB info CPPTRAJ: Secstruct (DSSP) command with changing number of residues. CPPTRAJ: Center origin command test. CPPTRAJ: NetCDF Restart Test - NetCDF->TXT CPPTRAJ: CRD Replica Trajectory Run with remdout All 2 comparisons passed. All 11 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Image CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF CPPTRAJ: Orthorhombic imaged distance test. CPPTRAJ: Center origin mass command test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf CPPTRAJ: Surface calculation test All 8 comparisons passed. CPPTRAJ: Secstruct (DSSP): SS assign output test CPPTRAJ: Solute Hbond test with disk caching ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radgyr CPPTRAJ: Radius of gyration command test CPPTRAJ: Non-orthorhombic imaged distance test. CPPTRAJ: Center reference command test. CPPTRAJ: FtuFabI Assignment test All 2 comparisons passed. CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt CPPTRAJ: Solute-solvent hbond test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mask All 15 comparisons passed. CPPTRAJ: Center point test. CPPTRAJ: Mask single frame test CPPTRAJ: Orthorhombic coordinate imaging test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Parallel CPPTRAJ: Parallel tests. All 2 comparisons passed. All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diffusion CPPTRAJ: Diffusion test, no imaging. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Jcoupling CPPTRAJ: Mask longer command test. All 10 comparisons passed. CPPTRAJ: J-Coupling single frame test CPPTRAJ: Nonorthorhombic coordinate imaging test CPPTRAJ: Hbond, no intramolecular hydrogen bonds test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj CPPTRAJ: RMSD Test with outtraj. CPPTRAJ: Parallel test with trajectory offset All 5 comparisons passed. J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. Skipped test: J-Coupling extended test All 1 comparisons passed. 1 comparisons skipped. CPPTRAJ: Diffusion test, old syntax. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm CPPTRAJ: CHARMM PSF/DCD test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotdif ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj CPPTRAJ: Convert mdcrd -> NetCDF CPPTRAJ: Rotational diffusion calculation test CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar CPPTRAJ: Hbond, specified solute masks CPPTRAJ: CHARMM DCD Write, step 1. All 7 comparisons passed. CPPTRAJ: CHARMM DCD Write, step 2. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Runavg CPPTRAJ: Coordinate Running Average test. All 4 comparisons passed. CPPTRAJ: Diffusion test, new syntax. CPPTRAJ: Hbond, no angle cutoff test CPPTRAJ: Convert NetCDF -> mdcrd CPPTRAJ: CHAMBER topology read/strip test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RMSD CPPTRAJ: Basic RMSD tests CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM CPPTRAJ: Hbond, Bridge nointramol test CPPTRAJ: Coordinate Running Average Traj Write CPPTRAJ: Diffusion test, nonorthogonal box CPPTRAJ: Read CHARMM restart CPPTRAJ: STFC Diffusion Test All 2 comparisons passed. CPPTRAJ: CHARMM PSF write ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_2DRMS All 6 comparisons passed. CPPTRAJ: 2D RMSD Test. CPPTRAJ: Partial Surface calculation test CPPTRAJ: CHARMM COORdinates test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mol2 CPPTRAJ: RMS coordinate rotation/rotation matrices test All 1 comparisons passed. CPPTRAJ: Mol2 Parm/Traj Read/Write Test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct CPPTRAJ: NAstruct command test. All 6 comparisons passed. CPPTRAJ: STFC Diffusion Test with individual distances CPPTRAJ: 2D RMSD Test, mass-weighted. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CharmmParams CPPTRAJ: Test updating topology with Charmm parameters (single residue) CPPTRAJ: Outtraj Test with maxmin. CPPTRAJ: PDB => Mol2 CPPTRAJ: RMS fit with no coordinates modification test. CPPTRAJ: STFC Diffusion Test with COM CPPTRAJ: 2D RMSD Test with reference trajectory CPPTRAJ: Amber Top/Rst => Mol2 All 2 comparisons passed. CPPTRAJ: STFC Diffusion Test with second mask ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Average CPPTRAJ: 2D DME Test. CPPTRAJ: NAstruct command test, single strand Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. Skipped test: Amber Top/Rst => Mol2, SYBYL atom types All 4 comparisons passed. 1 comparisons skipped. CPPTRAJ: Average Test. All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pucker CPPTRAJ: Pucker command test CPPTRAJ: 2D RMSD with reference mask test. CPPTRAJ: RMS fit to previous test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomMap All 11 comparisons passed. CPPTRAJ: AtomMap Test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct_8OG CPPTRAJ: NA test (8OG) All 2 comparisons passed. CPPTRAJ: 2D RMSD test, no fitting. CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Datafile CPPTRAJ: Data file output precision test CPPTRAJ: RMS: imaging after unit cell rotation CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. All 6 comparisons passed. All 3 comparisons passed. g++ -o a.out main.o NameType.o CpptrajStdio.o CPPTRAJ: AtomMap with 'rmsfit' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial CPPTRAJ: Radial test, non-orthogonal imaging ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist All 3 comparisons passed. CPPTRAJ: LCPO test with GAFF atom types CPPTRAJ: 1D/2D Histogram Analysis test CPPTRAJ: Standard -> Grace Data All 12 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest CPPTRAJ: Closest command test using first solvent atom. CPPTRAJ: Grace -> Standard Data CPPTRAJ: Atom map charmm->amber atom order ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DRMSD CPPTRAJ: Distance RMSD test All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster All 16 comparisons passed. CPPTRAJ: Cluster command test, in-memory pairwise distances. CPPTRAJ: X column format/precision test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_IRED CPPTRAJ: IRED vector/matrix test CPPTRAJ: Atom map charmm->amber atom order, by residue CPPTRAJ: Hbond with imaging All 9 comparisons passed. make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' All 1 comparisons passed. 'ZN' 'HA2' 'HA' 'HA' 'CT11' Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeName' Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeString' Unit test passed. CPPTRAJ: Data file group by name test CPPTRAJ: 3D histogram test. CPPTRAJ: Cluster command test, read pairwise distances. CPPTRAJ: Hbond, orthogonal imaging ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Molsurf CPPTRAJ: Molsurf test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Corr ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons CPPTRAJ: Correlation test CPPTRAJ: Closest command test using all solvent atoms. CPPTRAJ: randomizeions test (original algorithm) All 7 comparisons passed. CPPTRAJ: Data file group by aspect test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckStructure CPPTRAJ: Structure Check All 2 comparisons passed. CPPTRAJ: Cluster command test, read NetCDF pairwise distances. All 23 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RmsAvgCorr CPPTRAJ: RmsAvgCorr Reference ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Contacts CPPTRAJ: Contacts test. All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Principal CPPTRAJ: Cluster command test, write ASCII pairwise distances. CPPTRAJ: Structure Check with Around and Skip CPPTRAJ: Principal Test CPPTRAJ: RmsAvgCorr First All 3 comparisons passed. CPPTRAJ: Cluster command test, read ASCII pairwise distances. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ClusterDihedral CPPTRAJ: clusterdihedral test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Vector CPPTRAJ: Basic vector tests All 9 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve CPPTRAJ: Cluster, nosieve All 4 comparisons passed. CPPTRAJ: Radial test, orthogonal and no imaging ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Matrix CPPTRAJ: Structure Check with PBC CPPTRAJ: Matrix Tests CPPTRAJ: Cluster, sieve5 All 1 comparisons passed. CPPTRAJ: Test vector center with magnitude All 9 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Grid CPPTRAJ: Dipole test CPPTRAJ: Momentum/velocity vector test. CPPTRAJ: Closest command test, using mask center CPPTRAJ: Cluster, nosieve savepairdist CPPTRAJ: Grid test CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. CPPTRAJ: Force vector test. CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. CPPTRAJ: Closest command test, using mask center and solvent mask All 3 comparisons passed. CPPTRAJ: Randomize (around, overlap) CPPTRAJ: OpenDX Grid read test CPPTRAJ: Cluster, nosieve loadpairdist ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Unwrap CPPTRAJ: Unwrap non-orthogonal test All 14 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_Project CPPTRAJ: Grid with specified center test. CPPTRAJ: Projection CPPTRAJ: Closest command test, solvent mask, water oxygen only CPPTRAJ: Cluster, sieve5 savepairdist CPPTRAJ: Atomicfluct test with ADP output All 1 comparisons passed. CPPTRAJ: Unwrap orthogonal test CPPTRAJ: Grid with box center offset test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes CPPTRAJ: Modes analysis, RMS fluctuations CPPTRAJ: Generate matrix with trajectory start/stop/offset CPPTRAJ: Grid with mask center offset test. CPPTRAJ: Generate matrix with action stop/start/offset All 2 comparisons passed. CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. CPPTRAJ: Modes analysis, displacements ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Watershell All 15 comparisons passed. CPPTRAJ: Watershell Test, non-orthorhombic imaging. CPPTRAJ: Non-orthogonal grid test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AnalysisRunAvg CPPTRAJ: Cluster, sieve5 loadpairdist CPPTRAJ: Analysis Running Average All 13 comparisons passed. CPPTRAJ: Modes analysis, dipole correlation ******************************************************************************** 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 2 comparisons passed. CPPTRAJ: Cluster, nosieve pairwisecache none ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LIE CPPTRAJ: LIE test CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test CPPTRAJ: Modes analysis, pseudo trajectory creation test VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. Skipped test: VMD VolMap Algorithm longer tests All 2 comparisons passed. 1 comparisons skipped. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Density CPPTRAJ: Density along axis tests CPPTRAJ: Grid generation from 'bounds' test. CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test All 6 comparisons passed. All 13 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidOrder CPPTRAJ: Lipid Order Parameter Test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PairDist ******************************************************************************** CPPTRAJ: PairDist Test. TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReadData CPPTRAJ: Read vector data test (no origins, origins) CPPTRAJ: Randomize (around) CPPTRAJ: Structure Check with Around CPPTRAJ: Read vector data set (origins, no origins) CPPTRAJ: Cluster, sieve5 pairwisecache none CPPTRAJ: Multi-frame density along axis test CPPTRAJ: Read Amber output test CPPTRAJ: Pairdist test, orthogonal imaging. CPPTRAJ: Read CHARMM output test CPPTRAJ: Cluster, random CPPTRAJ: 3D data read/write test All 8 comparisons passed. All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST CPPTRAJ: GIST water-water interaction test CPPTRAJ: Standard 3D data write test CPPTRAJ: Total system density test All 28 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidSCD ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve CPPTRAJ: Basic lipid order parameter test CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). CPPTRAJ: Standard 3D data read test All 1 comparisons passed. All 7 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_systemVF CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicCorr CPPTRAJ: Atomic Correlation test CPPTRAJ: New Lipid Order Parameter Test, DOPC. CPPTRAJ: Standard 3D data read/append test All 4 comparisons passed. CPPTRAJ: Standard 3D data, sparse ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet All 8 comparisons passed. CPPTRAJ: Clustering, One DataSet ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr CPPTRAJ: AutoCorr test. All 4 comparisons passed. CPPTRAJ: Nonorthogonal grid standard write/read tests. All 1 comparisons passed. All 1 comparisons passed. CPPTRAJ: Clustering, Two DataSets ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Box CPPTRAJ: Box Test (Add box info) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomTypeSelect CPPTRAJ: Selection by atom type test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AvgRef CPPTRAJ: RMSD Test with averaged reference coordinates. CPPTRAJ: Box test (remove box info) All 1 comparisons passed. CPPTRAJ: Clustering, dihedral DataSet All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Crank_Stat CPPTRAJ: Crankshaft test CPPTRAJ: Randomize (overlap) CPPTRAJ: Box test (Modify box length) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateCrd CPPTRAJ: COORDS data set creation and CRDFLUCT test. CPPTRAJ: Clustering, two dihedral DataSets All 3 comparisons passed. CPPTRAJ: Box test (auto orthogonal box, no radii) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoImage CPPTRAJ: AutoImage test (split DNA duplex) CPPTRAJ: Clustering, dihedral DataSet, K-means CPPTRAJ: COORDS data set creation with velocities test CPPTRAJ: Box test (auto orthogonal box, VDW radii) CPPTRAJ: Clustering, two dihedral DataSets, K-means All 7 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LoadCrd CPPTRAJ: LoadCrd test. All 8 comparisons passed. CPPTRAJ: Randomize (no restrictions) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o CPPTRAJ: DBSCAN test CPPTRAJ: Pairdist test, nonorthogonal imaging. CPPTRAJ: LoadTraj test. CPPTRAJ: DBSCAN automatic parameter determination test. CPPTRAJ: LoadTraj from trajin test. CPPTRAJ: TRAJ data set creation and CRDFLUCT test. All 5 comparisons passed. CPPTRAJ: AutoImage test, use anchor mask ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MultiVector CPPTRAJ: DBSCAN kdist map test CPPTRAJ: Multivector test CPPTRAJ: LoadCrd append from multiple files test CPPTRAJ: TRAJ data set creation with velocities test. All 4 comparisons passed. All 1 comparisons passed. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Lifetime CPPTRAJ: DBSCAN with sieve ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FFT TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Timecorr CPPTRAJ: Lifetime test. CPPTRAJ: Timecorr test. CPPTRAJ: FFT test. 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' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CrossCorr CPPTRAJ: CrossCorr test CPPTRAJ: COORDS data set append test All 4 comparisons passed. CPPTRAJ: Lifetime test with data set caching. CPPTRAJ: COORDS test storing frame metadata ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans CPPTRAJ: Cpptraj Kmeans All 1 comparisons passed. All 5 comparisons passed. All 7 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ensemble_MREMD ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SymmRmsd ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multidihedral CPPTRAJ: SymmRmsd CPPTRAJ: Multidihedral test CPPTRAJ: M-REMD sort test. CPPTRAJ: Read specific columns test. CPPTRAJ: ASP symmetry-corrected RMSD test CPPTRAJ: Write non-square matrix CPPTRAJ: Lifetime average and cumulative average test. CPPTRAJ: TRAJ test storing frame metadata CPPTRAJ: Multidihedral Nucleotide CHI test CPPTRAJ: Cpptraj Kmeans random CPPTRAJ: Read non-square matrix CPPTRAJ: GLU symmetry-corrected RMSD test All 12 comparisons passed. CPPTRAJ: M-REMD actions test. CPPTRAJ: Multidihedral protein dihedrals test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MakeStructure CPPTRAJ: Basic makestructure test CPPTRAJ: Read square matrix CPPTRAJ: TYR symmetry-corrected RMSD test All 8 comparisons passed. CPPTRAJ: Watershell Test, orthorhombic imaging. CPPTRAJ: Multidihedral cyclic molecule test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotate All 6 comparisons passed. CPPTRAJ: Rotation (and inverse) of coords from matrices All 15 comparisons passed. CPPTRAJ: Longer symmetry-corrected RMSD test. CPPTRAJ: M-REMD ensemble outtraj test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_SymmRMSD CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) CPPTRAJ: Makestructure test with reference. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Integrate CPPTRAJ: Integration test. All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts All 2 comparisons passed. All 8 comparisons passed. All 5 comparisons passed. CPPTRAJ: NativeContacts test. CPPTRAJ: Rotate with defined axis All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckChiral CPPTRAJ: Check chirality test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Energy CPPTRAJ: M-REMD no sort, running average test CPPTRAJ: Simple energy tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PermuteDihedrals CPPTRAJ: PermuteDihedrals interval -120, phi psi ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LESsplit CPPTRAJ: LES split/average test All 3 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CCP4 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihCovar CPPTRAJ: Dihedral Covariance Matrix Test CPPTRAJ: CCP4 read/write and DX conversion test. CPPTRAJ: M-REMD, generate RMS data CPPTRAJ: PermuteDihedrals, random rotations All 2 comparisons passed. CPPTRAJ: M-REMD, meltcurve analysis CPPTRAJ: Test kinetic energy calculation All 4 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CurveFit ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetAverage CPPTRAJ: Curve fitting test. CPPTRAJ: Data set averaging and averaging over all sets test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VectorMath CPPTRAJ: Vector dot/cross product test All 17 comparisons passed. CPPTRAJ: NativeContacts test, save non-native contacts, residue time series All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander SANDER energy tests (long) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. SKIP: SANDER energy tests (long) CPPTRAJ: Test total energy calculation CPPTRAJ: Watershell Test, no imaging. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites CPPTRAJ: Cluster command test, coordinate writes. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander_Short Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. SKIP: Energy via sander API short tests (GB/PME) All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Temperature CPPTRAJ: Temperature test. CPPTRAJ: Curve fitting multi-exponential tests. ******************************************************************************** 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_Spline CPPTRAJ: Test partial energy calculation CPPTRAJ: Spline test CPPTRAJ: Temperature with SHAKE on hydrogens. All 1 comparisons passed. CPPTRAJ: NativeContacts test, orthorhombic imaging. All 6 comparisons passed. CPPTRAJ: Cluster command test, coordinate writes using info file. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Wavelet CPPTRAJ: Wavelet analysis test CPPTRAJ: Pairdist test, 2 masks. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CIF CPPTRAJ: Curve fitting, custom output range. CPPTRAJ: CIF read test CPPTRAJ: Temperature with SHAKE on all atoms. All 2 comparisons passed. All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PDB All 4 comparisons passed. CPPTRAJ: PDB format read/write test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multicurve CPPTRAJ: Multicurve test CPPTRAJ: Temperature calc with extra points. CPPTRAJ: KDE with Kullback-Leibler divergence test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Align CPPTRAJ: Align Tests. All 1 comparisons passed. CPPTRAJ: Wavelet WAFEX test CPPTRAJ: Generate offset traj from PDB All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelocityAutoCorr CPPTRAJ: Velocity autocorrelation test All 3 comparisons passed. CPPTRAJ: Align, unit cell rotation/imaging test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelFrc CPPTRAJ: Test combining coordinates, velocities, and forces. All 8 comparisons passed. All 17 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RotateDihedral CPPTRAJ: Rotate dihedral to target value. CPPTRAJ: Generate offset traj from CIF CPPTRAJ: Test using velocities as coordinates. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Dpeaks CPPTRAJ: Density peaks clustering test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetCmd All 5 comparisons passed. CPPTRAJ: Data Set commands test CPPTRAJ: PQR file write with various radii ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remap CPPTRAJ: Test writing velocities (MDVEL) CPPTRAJ: Remap Test CPPTRAJ: Rotate dihedral by increment All 3 comparisons passed. All 3 comparisons passed. All 2 comparisons passed. All 1 comparisons passed. All 3 comparisons passed. CPPTRAJ: Test using forces as coordinates. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CompareTop CPPTRAJ: Compare topology test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Filter CPPTRAJ: Basic filter test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CombineCrd CPPTRAJ: PDB filter alternate atom location IDs test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Nreps CPPTRAJ: Rotate dihedral in TRAJ data set CPPTRAJ: Combine COORDS test. CPPTRAJ: Clustering with specified # reps All 10 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TopInfo CPPTRAJ: Topology info print test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTrr CPPTRAJ: TRR force/velocity read -> NetCDF write test All 3 comparisons passed. All 1 comparisons passed. CPPTRAJ: Test writing forces (MDFRC) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TI CPPTRAJ: TI analysis test. CPPTRAJ: Combine COORDS test with box info. ******************************************************************************** CPPTRAJ: GIST test, orthogonal cell TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ewald CPPTRAJ: Direct sum test CPPTRAJ: Adding PDB info to topology CPPTRAJ: Data filter test. CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. All 5 comparisons passed. CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. All 2 comparisons passed. All 10 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds CPPTRAJ: Fix imaged bonds test (Ortho.) CPPTRAJ: Filter matrix test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Distance CPPTRAJ: Distance tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volume CPPTRAJ: Volume tests CPPTRAJ: Split coords and recombine test. CPPTRAJ: TRR force/velocity read -> TRR write test All 5 comparisons passed. All 1 comparisons passed. CPPTRAJ: Orthogonal imaged distance ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SetVelocity All 5 comparisons passed. CPPTRAJ: Set Velocity test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remlog CPPTRAJ: Replica log read/analyze test. CPPTRAJ: Fix imaged bonds test (Non-ortho.) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AreaPerMol CPPTRAJ: Area per molecule test CPPTRAJ: CRD => TRR CPPTRAJ: Topology info with reference coords test CPPTRAJ: Non-orthogonal imaged distance CPPTRAJ: Scale velocity test All 12 comparisons passed. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DistBasedMask All 7 comparisons passed. CPPTRAJ: Distance-based atom mask tests (atom, residue) 1 out of 3 comparisons failed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Calc CPPTRAJ: Calc test ******************************************************************************** ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateReservoir TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CalcState TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Change CPPTRAJ: Change atom and residue name tests CPPTRAJ: Calcstate test CPPTRAJ: Create RREMD NetCDF reservoir test CPPTRAJ: TRR => CRD CPPTRAJ: Calc test with data sets CPPTRAJ: Change chain ID test All 6 comparisons passed. CPPTRAJ: Distance-based atom mask tests (molecule) All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixAtomOrder CPPTRAJ: Change chain ID of COORDS set test CPPTRAJ: Test math functions CPPTRAJ: Out of order molecules test All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LowestCurve CPPTRAJ: LowestCurve test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MinImage All 4 comparisons passed. CPPTRAJ: Minimum Image test. All 3 comparisons passed. All 4 comparisons passed. CPPTRAJ: Ewald test (NaCl crystal) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Regress All 2 comparisons passed. CPPTRAJ: Linear regression test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rst ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pairwise CPPTRAJ: Pairwise tests CPPTRAJ: Generate restraints (rst) test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ParmBox CPPTRAJ: Parmbox test CPPTRAJ: Ewald test (trunc. oct) All 1 comparisons passed. CPPTRAJ: CRD(1-5) => TRR All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Solvent All 1 comparisons passed. CPPTRAJ: Test solvent command with closest All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Translate CPPTRAJ: Translate test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReplicateCell ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ScaleDihedralK CPPTRAJ: Replicate cell test CPPTRAJ: Scale dihedral force constant test All 6 comparisons passed. CPPTRAJ: CRD(6-10) => TRR ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PhiPsi CPPTRAJ: Pairwise test, partial system CPPTRAJ: Phipsi test All 1 comparisons passed. All 1 comparisons passed. All 1 comparisons passed. All 1 comparisons passed. CPPTRAJ: Scale dihedral force constant with 'useall' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Control ******************************************************************************** CPPTRAJ: Loop tests TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_InfraredSpec CPPTRAJ: Infrared spectrum calculation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cphstats ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CmdLine CPPTRAJ: Command line trajectory args test, part 1 CPPTRAJ: Explicit pH REMD ensemble data read / sort All 10 comparisons passed. All 1 comparisons passed. All 2 comparisons passed. CPPTRAJ: TRR (appended) => CRD ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hausdorff CPPTRAJ: Simple Hausdorff distance test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XYZformat CPPTRAJ: XYZ format write CPPTRAJ: Command line test trajectory args test, part 2 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CatCrd CPPTRAJ: Concatenate COORDS data set test All 2 comparisons passed. CPPTRAJ: Test set command CPPTRAJ: Hausdorff distance of 2D rms output test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XtalSymm CPPTRAJ: XtalSymm Reference CPPTRAJ: Constant pH stats test CPPTRAJ: Command line wildcard test, part 1 CPPTRAJ: Atom XYZ format read, test 1 All 1 comparisons passed. CPPTRAJ: Command line wildcard test, part 2 CPPTRAJ: Test reading comma-separated list of strings ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Time CPPTRAJ: Add time to restart test CPPTRAJ: GMX: CRD with offset CPPTRAJ: Sorted implicit constant pH stats test CPPTRAJ: Atom XYZ format read, test 2 All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SplitCoords CPPTRAJ: SplitCoords test CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats CPPTRAJ: Remove time from restart test CPPTRAJ: Atom XYZ format read, test 3 CPPTRAJ: Test nested loops and variables in loops CPPTRAJ: Hausdorff distance of 2D rms output test. CPPTRAJ: Add time to trajectory test CPPTRAJ: Atom XYZ format read, test 4 All 1 comparisons passed. CPPTRAJ: Test loop over data set blocks CPPTRAJ: Unsorted pH read/write test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihedralRMS CPPTRAJ: GMX: TRR with offset CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) All 16 comparisons passed. CPPTRAJ: Atom XYZ format read, test 5 CPPTRAJ: Test for filename wildcards and oversets CPPTRAJ: Ewald test (partial system, trunc. oct) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Slope CPPTRAJ: Finite difference test. CPPTRAJ: Modify time info test. CPPTRAJ: Atom XYZ format read, test 6 CPPTRAJ: Dihedral RMSD test (to previous) All 4 comparisons passed. All 13 comparisons passed. All 1 comparisons passed. All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diagmatrix All 3 comparisons passed. CPPTRAJ: MW covariance matrix thermo analysis test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Emin CPPTRAJ: Basic energy minimization test. CPPTRAJ: Dihedral RMS fluctuation test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Graft CPPTRAJ: Evalulate plateau test CPPTRAJ: Graft test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc All 6 comparisons passed. CPPTRAJ: XTC read test All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Flatten CPPTRAJ: Energy minimization with angle term test. CPPTRAJ: Flatten test. All 5 comparisons passed. CPPTRAJ: XtalSymm Reimaging by Atom All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Random CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs All 2 comparisons passed. All 1 comparisons passed. Ewald test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: Ewald test (trunc. oct), 10 frames Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: Ewald test (ortho), 10 frames All 4 comparisons passed. 2 comparisons skipped. CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LibPME CPPTRAJ: Particle mesh Ewald test (NaCl crystal) CPPTRAJ: PCG32 RNG test. All 5 comparisons passed. CPPTRAJ: Energy minimization with nonbond term test. CPPTRAJ: CRD => XTC CPPTRAJ: Test Stdlib RNG CPPTRAJ: Particle mesh Ewald test (trunc. oct) CPPTRAJ: Test Mersenne Twister RNG All 4 comparisons passed. CPPTRAJ: XTC => CRD CPPTRAJ: OpenMM basic energy minimization tests (bonds) CPPTRAJ: CRD(1-5) => XTC CPPTRAJ: OpenMM basic energy minimization tests (angles) CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) CPPTRAJ: CRD(6-10) => XTC CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) CPPTRAJ: XTC (appended) => CRD CPPTRAJ: Particle mesh Ewald test (ortho) CPPTRAJ: GMX: CRD with offset CPPTRAJ: GMX: XTC with offset CPPTRAJ: Particle mesh Ewald test (ortho, with mask) All 4 comparisons passed. CPPTRAJ: PME test (partial system, trunc. oct) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTNG CPPTRAJ: TNG read test CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) PME test (trunc. oct), 10 frames is a long test and long tests disabled. Use 'long' to run. Skipped test: PME test (trunc. oct), 10 frames All 5 comparisons passed. 1 comparisons skipped. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LJ_PME CPPTRAJ: LJ PME test. CPPTRAJ: LJ PME kappa sweep test, 0.25 CPPTRAJ: TNG read test (with offset) CPPTRAJ: LJ PME kappa sweep test, 0.35 CPPTRAJ: GIST test, nonorthogonal cell CPPTRAJ: LJ PME kappa sweep test, 0.45 CPPTRAJ: LJ PME kappa sweep test, 0.5 All 6 comparisons passed. CPPTRAJ: LJ with switch function test All 5 comparisons passed. CPPTRAJ: XtalSymm Reimaging by Molecule All 9 comparisons passed. 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. ../MasterTest.sh: line 495: 609802 Segmentation fault $cpptraj_cmd >> $CPPTRAJ_OUTPUT Error: cpptraj exited with status 139 CPPTRAJ: SPAM Pure Solvent Test 1 out of 2 executions exited with an error. 2 out of 5 comparisons failed. make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' /usr/bin/make -C test summary make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' -rwxr-xr-x 1 pbuilder1 pbuilder1 181912848 Sep 24 16:04 ../bin/cpptraj ===================== TEST SUMMARY ====================== 850 out of 859 comparisons OK (3 failed, 0 warnings, 6 skipped). 479 out of 480 program executions completed. 168 out of 173 tests completed with no issues. 2 tests skipped. ========================================================= make[2]: *** [Makefile:662: summary] Error 4 make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[1]: *** [debian/rules:17: override_dh_auto_test] Error 2 make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' make: *** [debian/rules:10: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/576532 and its subdirectories Wed Sep 24 16:05:06 UTC 2025 W: No second build log, what happened?