Running as unit: rb-build-amd64_19-64290.service ==================================================================================== Wed Aug 6 22:26:42 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_19) on jenkins, called using "ionos1-amd64 ionos15-amd64" as arguments. Wed Aug 6 22:26:42 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-Lg1EwLIc" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Aug 6 22:26:42 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Wed Aug 6 22:26:42 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-jls0ty' Wed Aug 6 22:26:43 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Wed Aug 6 22:26:43 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-HKRtXM' ok, let's check if cpptraj is building anywhere yet… ok, cpptraj is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of cpptraj in unstable on amd64 on jenkins now. 1st build will be done on ionos1-amd64.debian.net. 2nd build will be done on ionos15-amd64.debian.net. ============================================================================= Wed Aug 6 22:26:56 UTC 2025 I: starting to build cpptraj/unstable/amd64 on jenkins on '2025-08-06 22:26' Wed Aug 6 22:26:56 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_19/64290/console.log 1754519216 amd64 unstable cpptraj Wed Aug 6 22:26:56 UTC 2025 I: Downloading source for unstable/cpptraj=5.1.0+dfsg-4 --2025-08-06 22:26:56-- http://deb.debian.org/debian/pool/main/c/cpptraj/cpptraj_5.1.0%2bdfsg-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2184 (2.1K) [text/prs.lines.tag] Saving to: ‘cpptraj_5.1.0+dfsg-4.dsc’ 0K .. 100% 266M=0s 2025-08-06 22:26:56 (266 MB/s) - ‘cpptraj_5.1.0+dfsg-4.dsc’ saved [2184/2184] --2025-08-06 22:26:56-- http://deb.debian.org/debian/pool/main/c/cpptraj/cpptraj_5.1.0%2bdfsg-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2184 (2.1K) [text/prs.lines.tag] Saving to: ‘cpptraj_5.1.0+dfsg-4.dsc’ 0K .. 100% 266M=0s 2025-08-06 22:26:56 (266 MB/s) - ‘cpptraj_5.1.0+dfsg-4.dsc’ saved [2184/2184] Wed Aug 6 22:26:56 UTC 2025 I: cpptraj_5.1.0+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: cpptraj Binary: cpptraj Architecture: any Version: 5.1.0+dfsg-4 Maintainer: Debichem Team Uploaders: Andrius Merkys , Homepage: https://github.com/Amber-MD/cpptraj Standards-Version: 4.6.1 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 01a62f884bc2739ce8f799c62b3e260f8205b82c 6084 cpptraj_5.1.0+dfsg-4.debian.tar.xz Checksums-Sha256: 89e279bbb5d35db4d2599fa98322bb8c4b876ce6117f8896e75520a3da1182f3 28363024 cpptraj_5.1.0+dfsg.orig.tar.xz 0e96d529626c3f73247201aa16e7b8c8afba853694be1a331a3ae73a5fe4bf3c 6084 cpptraj_5.1.0+dfsg-4.debian.tar.xz Files: bf932a3aed87ad43645613135c712505 28363024 cpptraj_5.1.0+dfsg.orig.tar.xz 6e26922e03d8c1c199dfd28f36581cba 6084 cpptraj_5.1.0+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmZCJuQSHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKHhmEP/igOOwHV5yAXVBSlVNtYT+DL2jzFwcLP /LYplbd5pvvDm9Aw8+6fAj7aDwFLhCQJg9/MR+Xu90VQ7ymrdWRRnqX0RcwggbPs JGGG0RRU0NrZnbyxTKD1Z/H6w1NkenykJpnoOrkBlFMZJc9kCAdWnLwKFSxcg2Xl SX11O3s7QwLrjlqcCF2gXy3eWGjKJHLiW0WN+O+j3PNYd5QcnrfvtFvV4lUoTv6q 9UFvejofK1hkx1ysw/P/V2DlAawOzX0BVzRBU9xCwXAXFv0lu5JJWdD66NWaCb0N ja6vW2eZTvs5Ble8s1AoF0EevpTh6PICJ75e6T/PIS2AH/DbBmCo6ATEbpnALd3Z pj4D1HTrBlaRw60ZlyqKK4iqKd35KmSJRDT1Fa2YilCBInJDd1fZQHgEVPj2WF7S DsyS59VonzRUmCznTxKPFybDCmUdVveN6jpxWpcYjYg+cO/L5rPXERwU28jDpCuK QWZz+AK0tzQLm05TFV4Qg7QJFgn/mIOPYF1HQgsGtJ/V0RNSBd+/NeKWGF1qSX7y +eERIOK+8DrYjOebe24bRUs/lR1Vx+HTxpAQw47+VZBvogGbyDfp1AiElZvb0Ia4 pQ5omJd6jxqbHFP0HdxVwMZYDPFJlkYN5O1sHQTFq+3wYzEhmvIzE0tV9fqCOBKw gP/0H6lIFBch =XQSu -----END PGP SIGNATURE----- Wed Aug 6 22:26:56 UTC 2025 I: Checking whether the package is not for us Wed Aug 6 22:26:56 UTC 2025 I: Starting 1st build on remote node ionos1-amd64.debian.net. Wed Aug 6 22:26:56 UTC 2025 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Wed Aug 6 22:26:56 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Wed Aug 6 22:26:56 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-q1EVmt' ==================================================================================== Wed Aug 6 22:26:58 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "1 cpptraj unstable /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4 5.1.0+dfsg-4" as arguments. Wed Aug 6 22:26:58 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-cjdqPoqN" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Aug 6 22:26:58 UTC 2025 I: Downloading source for unstable/cpptraj=5.1.0+dfsg-4 Reading package lists... NOTICE: 'cpptraj' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/cpptraj.git Please use: git clone https://salsa.debian.org/debichem-team/cpptraj.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 28.4 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main cpptraj 5.1.0+dfsg-4 (dsc) [2184 B] Get:2 http://deb.debian.org/debian unstable/main cpptraj 5.1.0+dfsg-4 (tar) [28.4 MB] Get:3 http://deb.debian.org/debian unstable/main cpptraj 5.1.0+dfsg-4 (diff) [6084 B] Fetched 28.4 MB in 0s (128 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'cpptraj' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/cpptraj.git Please use: git clone https://salsa.debian.org/debichem-team/cpptraj.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 28.4 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main cpptraj 5.1.0+dfsg-4 (dsc) [2184 B] Get:2 http://deb.debian.org/debian unstable/main cpptraj 5.1.0+dfsg-4 (tar) [28.4 MB] Get:3 http://deb.debian.org/debian unstable/main cpptraj 5.1.0+dfsg-4 (diff) [6084 B] Fetched 28.4 MB in 0s (128 MB/s) Download complete and in download only mode ============================================================================= Building cpptraj in unstable on amd64 on ionos1-amd64 now. Date: Wed Aug 6 22:26:58 UTC 2025 Date UTC: Wed Aug 6 22:26:58 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Aug 6 10:26:58 -12 2025 I: pbuilder-time-stamp: 1754519218 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [cpptraj_5.1.0+dfsg-4.dsc] I: copying [./cpptraj_5.1.0+dfsg.orig.tar.xz] I: copying [./cpptraj_5.1.0+dfsg-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./cpptraj_5.1.0+dfsg-4.dsc: 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-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-system-libraries.patch dpkg-source: info: applying skip-failing-test.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2415790/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='bce42d0f097543b7a362b6996b6ac080' 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='2415790' 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.dE0NwvQ4/pbuilderrc_rHzM --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/b1 --logfile b1/build.log cpptraj_5.1.0+dfsg-4.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2415790/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), gfortran, libarpack2-dev, libbz2-dev, libfftw3-dev, libnetcdf-dev, libopenmm-dev, libreadline-dev, netcdf-bin dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19850 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on libarpack2-dev; however: Package libarpack2-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on libnetcdf-dev; however: Package libnetcdf-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmm-dev; however: Package libopenmm-dev is not installed. pbuilder-satisfydepends-dummy depends on libreadline-dev; however: Package libreadline-dev is not installed. pbuilder-satisfydepends-dummy depends on netcdf-bin; however: Package netcdf-bin is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran{a} gfortran-14{a} gfortran-14-x86-64-linux-gnu{a} gfortran-x86-64-linux-gnu{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarpack2-dev{a} libarpack2t64{a} libblas-dev{a} libblas3{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libffi8{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-quad3{a} libfftw3-single3{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-310{a} libhdf5-cpp-310{a} libhdf5-dev{a} libhdf5-fortran-310{a} libhdf5-hl-310{a} libhdf5-hl-cpp-310{a} libhdf5-hl-fortran-310{a} libidn2-0{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-dev{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnetcdf-dev{a} libnetcdf22{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libopenmm-dev{a} libopenmm8.1{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} libreadline-dev{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsz2{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2{a} libxml2-dev{a} libzstd-dev{a} m4{a} man-db{a} netcdf-bin{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 131 newly installed, 0 to remove and 0 not upgraded. Need to get 64.2 MB of archives. After unpacking 249 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b3 [56.7 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 25 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libgfortran-14-dev amd64 14.2.0-19 [880 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-19 [11.7 MB] Get: 36 http://deb.debian.org/debian unstable/main amd64 gfortran-14 amd64 14.2.0-19 [14.5 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1 [1284 B] Get: 38 http://deb.debian.org/debian unstable/main amd64 gfortran amd64 4:14.2.0-1 [1436 B] Get: 39 http://deb.debian.org/debian unstable/main amd64 hdf5-helpers amd64 1.14.5+repack-3 [26.6 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 43 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 52 http://deb.debian.org/debian unstable/main amd64 libaec-dev amd64 1.1.3-1+b1 [21.5 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-5 [159 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-5 [2448 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libarpack2t64 amd64 3.9.1-6 [104 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-5 [170 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.1-5 [4991 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libarpack2-dev amd64 3.9.1-6 [120 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.14.1-2 [384 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-2 [598 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-3 [455 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-3 [455 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-2 [103 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-3 [1406 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.10+dfsg-1 [312 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1 [116 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.5.1-1 [2954 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.14.1-2 [503 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.14.1-2 [391 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libfftw3-double3 amd64 3.3.10-2+b1 [781 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libfftw3-long3 amd64 3.3.10-2+b1 [347 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libfftw3-quad3 amd64 3.3.10-2+b1 [618 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libfftw3-single3 amd64 3.3.10-2+b1 [809 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libfftw3-bin amd64 3.3.10-2+b1 [51.3 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libfftw3-dev amd64 3.3.10-2+b1 [2118 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libhdf5-cpp-310 amd64 1.14.5+repack-3 [133 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libhdf5-fortran-310 amd64 1.14.5+repack-3 [111 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [69.3 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-fortran-310 amd64 1.14.5+repack-3 [43.9 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-cpp-310 amd64 1.14.5+repack-3 [24.4 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-4 [292 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-4 [72.2 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libhdf5-dev amd64 1.14.5+repack-3 [3165 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5+20250216-2 [353 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libnetcdf22 amd64 1:4.9.3-1 [517 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-2.1 [794 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libnetcdf-dev amd64 1:4.9.3-1 [116 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-11 [1059 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libopenmm-dev amd64 8.1.2+dfsg-11 [346 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libreadline-dev amd64 8.2-6 [153 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 netcdf-bin amd64 1:4.9.3-1 [260 kB] Fetched 64.2 MB in 1s (51.0 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 ... 19850 files and directories currently installed.) Preparing to unpack .../000-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../003-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.23.1-2_amd64.deb ... Unpacking gettext-base (0.23.1-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../006-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../007-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../008-bsdextrautils_2.41-5_amd64.deb ... Unpacking bsdextrautils (2.41-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../009-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../010-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../011-m4_1.4.19-8_amd64.deb ... Unpacking m4 (1.4.19-8) ... 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:amd64. Preparing to unpack .../016-libcom-err2_1.47.2-3+b3_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b3) ... Selecting previously unselected package comerr-dev:amd64. Preparing to unpack .../017-comerr-dev_2.1-1.47.2-3+b3_amd64.deb ... Unpacking comerr-dev:amd64 (2.1-1.47.2-3+b3) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../018-libdebhelper-perl_13.24.2_all.deb ... Unpacking libdebhelper-perl (13.24.2) ... Selecting previously unselected package libtool. Preparing to unpack .../019-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../020-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../021-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../022-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../023-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../024-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../025-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../026-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../027-libxml2_2.12.7+dfsg+really2.9.14-2.1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Selecting previously unselected package gettext. Preparing to unpack .../028-gettext_0.23.1-2_amd64.deb ... Unpacking gettext (0.23.1-2) ... 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_13.24.2_all.deb ... Unpacking debhelper (13.24.2) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../032-libgfortran5_14.2.0-19_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-19) ... Selecting previously unselected package libgfortran-14-dev:amd64. Preparing to unpack .../033-libgfortran-14-dev_14.2.0-19_amd64.deb ... Unpacking libgfortran-14-dev:amd64 (14.2.0-19) ... Selecting previously unselected package gfortran-14-x86-64-linux-gnu. Preparing to unpack .../034-gfortran-14-x86-64-linux-gnu_14.2.0-19_amd64.deb ... Unpacking gfortran-14-x86-64-linux-gnu (14.2.0-19) ... Selecting previously unselected package gfortran-14. Preparing to unpack .../035-gfortran-14_14.2.0-19_amd64.deb ... Unpacking gfortran-14 (14.2.0-19) ... Selecting previously unselected package gfortran-x86-64-linux-gnu. Preparing to unpack .../036-gfortran-x86-64-linux-gnu_4%3a14.2.0-1_amd64.deb ... Unpacking gfortran-x86-64-linux-gnu (4:14.2.0-1) ... Selecting previously unselected package gfortran. Preparing to unpack .../037-gfortran_4%3a14.2.0-1_amd64.deb ... Unpacking gfortran (4:14.2.0-1) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../038-hdf5-helpers_1.14.5+repack-3_amd64.deb ... Unpacking hdf5-helpers (1.14.5+repack-3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../039-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../040-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../041-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../042-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../043-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package libgssrpc4t64:amd64. Preparing to unpack .../044-libgssrpc4t64_1.21.3-5_amd64.deb ... Unpacking libgssrpc4t64:amd64 (1.21.3-5) ... Selecting previously unselected package libkadm5clnt-mit12:amd64. Preparing to unpack .../045-libkadm5clnt-mit12_1.21.3-5_amd64.deb ... Unpacking libkadm5clnt-mit12:amd64 (1.21.3-5) ... Selecting previously unselected package libkdb5-10t64:amd64. Preparing to unpack .../046-libkdb5-10t64_1.21.3-5_amd64.deb ... Unpacking libkdb5-10t64:amd64 (1.21.3-5) ... Selecting previously unselected package libkadm5srv-mit12:amd64. Preparing to unpack .../047-libkadm5srv-mit12_1.21.3-5_amd64.deb ... Unpacking libkadm5srv-mit12:amd64 (1.21.3-5) ... Selecting previously unselected package krb5-multidev:amd64. Preparing to unpack .../048-krb5-multidev_1.21.3-5_amd64.deb ... Unpacking krb5-multidev:amd64 (1.21.3-5) ... Selecting previously unselected package libaec0:amd64. Preparing to unpack .../049-libaec0_1.1.3-1+b1_amd64.deb ... Unpacking libaec0:amd64 (1.1.3-1+b1) ... Selecting previously unselected package libsz2:amd64. Preparing to unpack .../050-libsz2_1.1.3-1+b1_amd64.deb ... Unpacking libsz2:amd64 (1.1.3-1+b1) ... Selecting previously unselected package libaec-dev:amd64. Preparing to unpack .../051-libaec-dev_1.1.3-1+b1_amd64.deb ... Unpacking libaec-dev:amd64 (1.1.3-1+b1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../052-libblas3_3.12.1-5_amd64.deb ... Unpacking libblas3:amd64 (3.12.1-5) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../053-liblapack3_3.12.1-5_amd64.deb ... Unpacking liblapack3:amd64 (3.12.1-5) ... Selecting previously unselected package libarpack2t64:amd64. Preparing to unpack .../054-libarpack2t64_3.9.1-6_amd64.deb ... Unpacking libarpack2t64:amd64 (3.9.1-6) ... Selecting previously unselected package libblas-dev:amd64. Preparing to unpack .../055-libblas-dev_3.12.1-5_amd64.deb ... 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Selecting previously unselected package libngtcp2-crypto-gnutls-dev:amd64. Preparing to unpack .../095-libngtcp2-crypto-gnutls-dev_1.11.0-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls-dev:amd64 (1.11.0-1) ... Selecting previously unselected package libngtcp2-dev:amd64. Preparing to unpack .../096-libngtcp2-dev_1.11.0-1_amd64.deb ... Unpacking libngtcp2-dev:amd64 (1.11.0-1) ... Selecting previously unselected package libpsl-dev:amd64. Preparing to unpack .../097-libpsl-dev_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl-dev:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../098-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package librtmp-dev:amd64. Preparing to unpack .../099-librtmp-dev_2.4+20151223.gitfa8646d.1-2+b5_amd64.deb ... Unpacking librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... 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Setting up libaec0:amd64 (1.1.3-1+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-5) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libunbound8:amd64 (1.22.0-2) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-3) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-4) ... Setting up libjpeg62-turbo-dev:amd64 (1:2.1.5-4) ... Setting up libncurses6:amd64 (6.5+20250216-2) ... Setting up libfftw3-quad3:amd64 (3.3.10-2+b1) ... Setting up comerr-dev:amd64 (2.1-1.47.2-3+b3) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up libssl-dev:amd64 (3.5.1-1) ... Setting up autopoint (0.23.1-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libfftw3-double3:amd64 (3.3.10-2+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up libgfortran5:amd64 (14.2.0-19) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.8.0-1) ... Setting up libnghttp3-dev:amd64 (1.8.0-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up libngtcp2-16:amd64 (1.11.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libtasn1-6-dev:amd64 (4.20.0-2) ... Setting up libopenmm8.1 (8.1.2+dfsg-11) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b7) ... Setting up libblas-dev:amd64 (3.12.1-5) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libsz2:amd64 (1.1.3-1+b1) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:amd64 (14.2.0-19) ... Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up liblapack3:amd64 (3.12.1-5) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libncurses-dev:amd64 (6.5+20250216-2) ... Setting up gettext (0.23.1-2) ... Setting up libarpack2t64:amd64 (3.9.1-6) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up nettle-dev:amd64 (3.10.1-1) ... Setting up libtool (2.5.4-4) ... Setting up libfftw3-bin (3.3.10-2+b1) ... Setting up libaec-dev:amd64 (1.1.3-1+b1) ... Setting up libjpeg-dev:amd64 (1:2.1.5-4) ... Setting up libidn2-0:amd64 (2.3.8-2) ... Setting up libngtcp2-dev:amd64 (1.11.0-1) ... Setting up libopenmm-dev (8.1.2+dfsg-11) ... Setting up gfortran-14-x86-64-linux-gnu (14.2.0-19) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libxml2-dev:amd64 (2.12.7+dfsg+really2.9.14-2.1) ... Setting up libldap-dev:amd64 (2.6.10+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up liblapack-dev:amd64 (3.12.1-5) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libidn2-dev:amd64 (2.3.8-2) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up gfortran-14 (14.2.0-19) ... Setting up libfftw3-dev:amd64 (3.3.10-2+b1) ... Setting up libp11-kit-dev:amd64 (0.25.5-3) ... Setting up libgnutls30t64:amd64 (3.8.9-3) ... Setting up libgnutls-openssl27t64:amd64 (3.8.9-3) ... Setting up libnghttp2-dev:amd64 (1.64.0-1.1) ... Setting up libarpack2-dev:amd64 (3.9.1-6) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libreadline-dev:amd64 (8.2-6) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran-x86-64-linux-gnu (4:14.2.0-1) ... Setting up gfortran (4:14.2.0-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.9-3) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libgssrpc4t64:amd64 (1.21.3-5) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-5) ... Setting up libgnutls28-dev:amd64 (3.8.9-3) ... Setting up libcurl4t64:amd64 (8.14.1-2) ... Setting up libkdb5-10t64:amd64 (1.21.3-5) ... Setting up libcurl3t64-gnutls:amd64 (8.14.1-2) ... Setting up debhelper (13.24.2) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.11.0-1) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libhdf5-310:amd64 (1.14.5+repack-3) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-5) ... Setting up libhdf5-fortran-310:amd64 (1.14.5+repack-3) ... Setting up krb5-multidev:amd64 (1.21.3-5) ... Setting up libhdf5-cpp-310:amd64 (1.14.5+repack-3) ... Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3) ... Setting up libnetcdf22:amd64 (1:4.9.3-1) ... Setting up netcdf-bin (1:4.9.3-1) ... Setting up libkrb5-dev:amd64 (1.21.3-5) ... Setting up libhdf5-hl-cpp-310:amd64 (1.14.5+repack-3) ... Setting up libhdf5-hl-fortran-310:amd64 (1.14.5+repack-3) ... Setting up libcurl4-gnutls-dev:amd64 (8.14.1-2) ... Setting up libhdf5-dev (1.14.5+repack-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libnetcdf-dev (1:4.9.3-1) ... Processing triggers for libc-bin (2.41-12) ... 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-4_source.changes dpkg-buildpackage: info: source package cpptraj dpkg-buildpackage: info: source version 5.1.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' touch config.h external.config.h dh_auto_clean make -j40 clean make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' /bin/rm -f SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o cpptraj *.LIBCPPTRAJ.o libcpptraj # cd readline && make clean cd xdrfile && make clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' /bin/rm -f *.o libxdrfile.a a.out test.trr test.xtc test.xdr make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' # cd arpack && make clean cd cuda_kernels && make clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/cuda_kernels' /bin/rm -f *.o libcpptraj_cuda.a make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/cuda_kernels' cd tng && make clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' /bin/rm -f *.o libtng_io.a tng_io_testing.o a.out tng_example_out.tng tng_test.tng make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' cd test && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' Cleaning all test directories: make test.complete test.libcpptraj OPT=clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' cd unitTests && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' Cleaning unit tests. make test.complete OPT=clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' rm -rf bin make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' ./configure gnu --with-arpack=/usr/lib/x86_64-linux-gnu --with-fftw3=/usr/lib/x86_64-linux-gnu --with-readline=/usr/lib/x86_64-linux-gnu --with-openmm=/usr/lib/x86_64-linux-gnu arpack specified: /usr/lib/x86_64-linux-gnu fftw3 specified: /usr/lib/x86_64-linux-gnu readline specified: /usr/lib/x86_64-linux-gnu openmm specified: /usr/lib/x86_64-linux-gnu Testing C++ compiler: OK Testing C compiler: OK Testing basic C++11 support: OK Testing system headers for C++11 support: OK Warning: Compilation of sanderlib requires AMBERHOME to be set Warning: if --with-sanderlib not specified. Checking BZLIB: OK Checking ZLIB: OK Checking NetCDF: OK Checking LAPACK/BLAS: OK Checking ARPACK: OK Checking FFTW3: OK Checking Readline: OK Checking OpenMM: OK vmdplugin disabled due to nonfree source. Configuration summary: Build type: Serial Options: netcdf bzlib tng zlib arpack lapack blas fftw3 readline xdrfile openmm Target platform: Linux, 64-bit. gnu compilers in use. C++11 support enabled. PME support enabled. Compiler optimizations are on. Cleaning source directory. -------------------------------------------------------------------------------- An environment resource file for CPPTRAJ has been created: /build/reproducible-path/cpptraj-5.1.0+dfsg/cpptraj.sh You may 'source' this file to set up your environment for CPPTRAJ. -------------------------------------------------------------------------------- CPPTRAJ configuration complete. make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_auto_build make -j40 make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make install make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' CXX SpaceGroup.cpp CXX ActionFrameCounter.cpp CXX ActionList.cpp CXX ActionTopWriter.cpp CXX Action_Align.cpp CXX Action_Angle.cpp CXX Action_AreaPerMol.cpp CXX Action_AtomMap.cpp CXX Action_AtomicCorr.cpp CXX Action_AtomicFluct.cpp CXX Action_AutoImage.cpp CXX Action_Average.cpp CXX Action_Bounds.cpp CXX Action_Box.cpp CXX Action_Center.cpp CXX Action_Channel.cpp CXX Action_CheckChirality.cpp CXX Action_CheckStructure.cpp CXX Action_Closest.cpp CXX Action_ClusterDihedral.cpp CXX Action_Contacts.cpp CXX Action_CreateCrd.cpp CXX Action_CreateReservoir.cpp CXX Action_DNAionTracker.cpp CXX Action_DSSP.cpp CXX Action_Density.cpp CXX Action_Diffusion.cpp CXX Action_Dihedral.cpp CXX Action_DihedralRMS.cpp CXX Action_Dipole.cpp CXX Action_Distance.cpp CXX Action_DistRmsd.cpp CXX Action_Energy.cpp CXX Action_FilterByData.cpp CXX Action_FixAtomOrder.cpp CXX Action_FixImagedBonds.cpp CXX Action_GIST.cpp CXX Action_Grid.cpp CXX Action_GridFreeEnergy.cpp CXX Action_HydrogenBond.cpp In file included from Ewald_ParticleMesh.h:5, from Action_Energy.cpp:4: helpme_standalone.h:2323: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2323 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:2343: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2343 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3014: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3014 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3120: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3120 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3247: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3247 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3701: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3701 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3739: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3739 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3802: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3802 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3840: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3840 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4044: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4044 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4052: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4052 | #pragma omp for helpme_standalone.h:4097: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4097 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4145: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4145 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4172: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4172 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4224: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4224 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4228: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4228 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4275: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4275 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4388: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4388 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4419: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4503: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4503 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4510: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4510 | #pragma omp for CXX Action_Image.cpp CXX Action_InfraredSpectrum.cpp CXX Action_Jcoupling.cpp CXX Action_LESsplit.cpp CXX Action_LIE.cpp CXX Action_LipidOrder.cpp CXX Action_MakeStructure.cpp CXX Action_Mask.cpp CXX Action_Matrix.cpp CXX Action_MinImage.cpp CXX Action_Molsurf.cpp CXX Action_MultiDihedral.cpp CXX Action_MultiVector.cpp CXX Action_NAstruct.cpp CXX Action_NativeContacts.cpp CXX Action_NMRrst.cpp 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 In file included from Matrix_3x3.h:3, from Box.h:3, from Frame.h:5, from Topology.h:10, from DataSet_Coords.h:4, from DataSet_Coords_REF.h:3, from ReferenceFrame.h:3, from DataSetList.h:4, from DataFile.h:4, from DataFileList.h:3, from ActionState.h:3, from Action.h:5, from Action_GIST.h:3, from Action_GIST.cpp:3: In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:814:31: Vec3.h:76:57: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:814:31: Vec3.h:76:23: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:814:31: Vec3.h:76:40: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:814:31: Vec3.h:76:23: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:815:31: Vec3.h:76:57: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:815:31: Vec3.h:76:23: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ CXX Action_ReplicateCell.cpp CXX Action_Rmsd.cpp CXX Action_Rotate.cpp CXX Action_RunningAvg.cpp CXX Action_STFC_Diffusion.cpp CXX Action_Scale.cpp CXX Action_SetVelocity.cpp CXX Action_Spam.cpp CXX Action_Strip.cpp CXX Action_Surf.cpp CXX Action_SymmetricRmsd.cpp CXX Action_Temperature.cpp CXX Action_Time.cpp CXX Action_Translate.cpp CXX Action_Unstrip.cpp CXX Action_Unwrap.cpp CXX Action_Vector.cpp CXX Action_VelocityAutoCorr.cpp CXX Action_Volmap.cpp CXX Action_Volume.cpp CXX Action_Watershell.cpp CXX Action_XtalSymm.cpp CXX AnalysisList.cpp CXX Analysis_AmdBias.cpp CXX Analysis_AutoCorr.cpp CXX Analysis_Average.cpp CXX Analysis_Clustering.cpp CXX Analysis_Corr.cpp CXX Analysis_ConstantPHStats.cpp CXX Analysis_CrankShaft.cpp CXX Analysis_CrdFluct.cpp CXX Analysis_CrossCorr.cpp CXX Analysis_CurveFit.cpp CXX Analysis_Divergence.cpp CXX Analysis_EvalPlateau.cpp CXX Analysis_FFT.cpp CXX Analysis_HausdorffDistance.cpp CXX Analysis_Hist.cpp CXX Analysis_Integrate.cpp CXX Analysis_IRED.cpp CXX Analysis_KDE.cpp CXX Analysis_Lifetime.cpp CXX Analysis_LowestCurve.cpp CXX Analysis_Matrix.cpp CXX Analysis_MeltCurve.cpp CXX Analysis_Modes.cpp CXX Analysis_Multicurve.cpp CXX Analysis_MultiHist.cpp CXX Analysis_Overlap.cpp CXX Analysis_PhiPsi.cpp CXX Analysis_Regression.cpp CXX Analysis_RemLog.cpp CXX Analysis_Rms2d.cpp CXX Analysis_RmsAvgCorr.cpp CXX Analysis_Rotdif.cpp CXX Analysis_RunningAvg.cpp CXX Analysis_Slope.cpp CXX Analysis_Spline.cpp CXX Analysis_State.cpp CXX Analysis_Statistics.cpp CXX Analysis_TI.cpp CXX Analysis_Timecorr.cpp CXX Analysis_VectorMath.cpp CXX Analysis_Wavelet.cpp CXX ArgList.cpp CXX Array1D.cpp 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 In file included from /usr/include/c++/14/vector:66, from ArgList.h:3, from Action.h:4, from Action_XtalSymm.h:3, from Action_XtalSymm.cpp:1: In member function 'void std::vector<_Tp, _Alloc>::assign(size_type, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]', inlined from 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)' at Action_XtalSymm.cpp:57:12: /usr/include/c++/14/bits/stl_vector.h:809:23: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 809 | { _M_fill_assign(__n, __val); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:72: /usr/include/c++/14/bits/vector.tcc: In member function 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)': /usr/include/c++/14/bits/vector.tcc:270:5: note: by argument 3 of type 'const std::vector::value_type&' {aka 'const Vec3&'} to 'void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]' declared here 270 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ Action_XtalSymm.cpp:57:33: note: '' declared here 57 | T_.assign( nCopyTotal, Vec3()); | ^ In member function 'void std::vector<_Tp, _Alloc>::assign(size_type, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]', inlined from 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)' at Action_XtalSymm.cpp:58:15: /usr/include/c++/14/bits/stl_vector.h:809:23: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 809 | { _M_fill_assign(__n, __val); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/14/bits/vector.tcc: In member function 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)': /usr/include/c++/14/bits/vector.tcc:270:5: note: by argument 3 of type 'const std::vector::value_type&' {aka 'const Vec3&'} to 'void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]' declared here 270 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ Action_XtalSymm.cpp:58:33: note: '' declared here 58 | RefT_.assign(nCopyTotal, Vec3()); | ^ CXX DataIO_VecTraj.cpp CXX DataIO_Xplor.cpp CXX DataIO_XVG.cpp CXX DataSet.cpp CXX DataSetList.cpp CXX DataSet_1D.cpp CXX DataSet_3D.cpp CXX DataSet_Cmatrix.cpp CXX DataSet_Cmatrix_DISK.cpp CXX DataSet_Cmatrix_MEM.cpp CXX DataSet_Cmatrix_NOMEM.cpp CXX DataSet_Coords.cpp CXX DataSet_Coords_CRD.cpp CXX DataSet_Coords_REF.cpp CXX DataSet_Coords_TRJ.cpp CXX DataSet_GridDbl.cpp CXX DataSet_GridFlt.cpp CXX DataSet_Mat3x3.cpp CXX DataSet_MatrixDbl.cpp CXX DataSet_MatrixFlt.cpp CXX DataSet_Mesh.cpp CXX DataSet_Modes.cpp CXX DataSet_Parameters.cpp CXX DataSet_pH.cpp CXX DataSet_PHREMD_Explicit.cpp CXX DataSet_PHREMD_Implicit.cpp CXX DataSet_RemLog.cpp CXX DataSet_Topology.cpp CXX DataSet_Vector.cpp CXX DataSet_Vector_Scalar.cpp CXX DataSet_double.cpp CXX DataSet_float.cpp CXX DataSet_integer_disk.cpp CXX DataSet_integer_mem.cpp CXX DataSet_string.cpp CXX DataSet_StringVar.cpp CXX DataSet_Tensor.cpp CXX DataSet_unsignedInt.cpp CXX Deprecated.cpp CXX DihedralSearch.cpp CXX DistRoutines.cpp CXX Energy.cpp CXX EnergyArray.cpp CXX EnsembleIn.cpp CXX EnsembleIn_Multi.cpp CXX EnsembleIn_Single.cpp CXX EnsembleNavigator.cpp CXX EnsembleOut.cpp CXX EnsembleOut_Multi.cpp CXX EnsembleOut_Single.cpp CXX EnsembleOutList.cpp CXX Ewald.cpp CXX Ewald_ParticleMesh.cpp CXX Ewald_Regular.cpp CXX ExclusionArray.cpp CXX Exec_AddMissingRes.cpp CXX Exec_Analyze.cpp CXX Exec_Calc.cpp CXX Exec_CatCrd.cpp CXX Exec_Change.cpp In file included from Ewald_ParticleMesh.h:5, from Ewald_ParticleMesh.cpp:4: helpme_standalone.h:2323: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2323 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:2343: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2343 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3014: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3014 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3120: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3120 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3247: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3247 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3701: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3701 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3739: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3739 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3802: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3802 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3840: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3840 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4044: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4044 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4052: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4052 | #pragma omp for helpme_standalone.h:4097: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4097 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4145: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4145 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4172: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4172 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4224: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4224 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4228: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4228 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4275: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4275 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4388: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4388 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4419: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4503: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4503 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4510: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4510 | #pragma omp for CXX Exec_ClusterMap.cpp CXX Exec_CombineCoords.cpp CXX Exec_Commands.cpp CXX Exec_CompareTop.cpp CXX Exec_CrdAction.cpp CXX Exec_CrdOut.cpp CXX Exec_CreateSet.cpp CXX Exec_DataFile.cpp CXX Exec_DataFilter.cpp CXX Exec_DataSetCmd.cpp CXX Exec_Emin.cpp CXX Exec_Flatten.cpp CXX Exec_GenerateAmberRst.cpp CXX Exec_Graft.cpp CXX Exec_Help.cpp CXX Exec_LoadCrd.cpp helpme_standalone.h: In instantiation of 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]': helpme_standalone.h:3898:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3898 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:1010:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 1010 | for (int val = 0; val < nRows_; ++val) eigenPairs.push_back({eigenValues[val][0], unsortedEigenVectors[val]}); | ~~~~^~~~~~~~ helpme_standalone.h:1013:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 1013 | for (int val = 0; val < nRows_; ++val) { | ~~~~^~~~~~~~ CXX Exec_LoadTraj.cpp helpme_standalone.h: In instantiation of 'void helpme::PMEInstance >::sanityChecks(int, const RealMat&, const RealMat&, int) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5018:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5018 | sanityChecks(parameterAngMom, parameters, coordinates); | ^~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3198:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3198 | if (parameters.nCols() != (nCartesian(parameterAngMom) - cartesianOffset)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::PMEInstance >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5019:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5019 | filterAtomsAndBuildSplineCache(parameterAngMom, coordinates); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3746:45: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3746 | for (size_t row = threadID; row < gridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~ helpme_standalone.h:3753:37: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3753 | for (int atom = 0; atom < nAtoms; ++atom) { | ~~~~~^~~~~~~~ helpme_standalone.h:3761:61: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3761 | if (cGridIterator.size() && thisAtomsThread == threadID) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~ helpme_standalone.h:3750:25: warning: unused variable 'gridIteratorC' [-Wunused-variable] 3750 | const auto &gridIteratorC = threadedGridIteratorC_[threadID]; | ^~~~~~~~~~~~~ helpme_standalone.h:3794:55: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3794 | for (int atom = splineCache_.size(); atom < newSize; ++atom) | ~~~~~^~~~~~~~~ helpme_standalone.h:3810:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3810 | for (size_t cRow = threadID; cRow < gridDimensionC_; cRow += nThreads_) { | ~~~~~^~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'Real* helpme::PMEInstance >::spreadParameters(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5020:25: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5020 | auto realGrid = spreadParameters(parameterAngMom, parameters); | ^~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3708:45: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3708 | for (size_t row = threadID; row < myGridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'helpme::PMEInstance >::Complex* helpme::PMEInstance >::forwardTransform(Real*) [with Real = double; typename std::enable_if::value, int>::type = 0; Complex = std::complex]': helpme_standalone.h:5023:32: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5023 | auto gridAddress = forwardTransform(realGrid); | ^~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:4004:28: warning: variable 'realCBA' set but not used [-Wunused-but-set-variable] 4004 | Real *__restrict__ realCBA; | ^~~~~~~ CXX Exec_ParallelAnalysis.cpp helpme_standalone.h: In instantiation of 'void helpme::Matrix::assertSymmetric(const Real&) const [with Real = double]': helpme_standalone.h:1000:9: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 1000 | assertSymmetric(); | ^~~~~~~~~~~~~~~ helpme_standalone.h:3898:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3898 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:796:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 796 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::JacobiCyclicDiagonalization(Real*, Real*, const Real*, int) [with Real = double]': helpme_standalone.h:1006:42: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 1006 | JacobiCyclicDiagonalization(eigenValues[0], unsortedEigenVectors[0], cbegin(), nRows_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3898:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3898 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:213:20: warning: variable 'cos_2phi' set but not used [-Wunused-but-set-variable] 213 | Real sin_2phi, cos_2phi, cot_2phi; | ^~~~~~~~ helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::applyOperation(const std::function&) const [with Real = double]': helpme_standalone.h:785:26: required from 'helpme::Matrix helpme::Matrix::inverse() const [with Real = double]' 785 | return this->applyOperation([](Real& element) { element = 1 / element; }); | ~~~~~~^~~~~~~~~~~~~~ helpme_standalone.h:3910:44: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3910 | recVecs_ = boxVecs_.inverse(); | ~~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:824:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 824 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::BSpline::update(short int, Real, short int, short int) [with Real = double]': helpme_standalone.h:3829:47: required from 'void helpme::PMEInstance >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 3829 | atomSplines.aSpline.update(aStartingGridPoint, gridDimensionA_ * aCoord - aStartingGridPoint, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3830 | splineOrder_, splineDerivativeLevel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:5019:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5019 | filterAtomsAndBuildSplineCache(parameterAngMom, coordinates); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:2208:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 2208 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:2208:72: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2208 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~ CXX Exec_ParmBox.cpp helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::multiply(const helpme::Matrix&) const [with Real = double]': helpme_standalone.h:877:64: required from 'helpme::Matrix helpme::Matrix::operator*(const helpme::Matrix&) const [with Real = double]' 877 | Matrix operator*(const Matrix& other) const { return this->multiply(other); } | ~~~~~~^~~~~~~~ helpme_standalone.h:829:22: required from 'helpme::Matrix helpme::Matrix::applyOperation(const std::function&) const [with Real = double]' 829 | return evecs * evecsT; | ~~~~~~^~~~~~~~ helpme_standalone.h:785:26: required from 'helpme::Matrix helpme::Matrix::inverse() const [with Real = double]' 785 | return this->applyOperation([](Real& element) { element = 1 / element; }); | ~~~~~~^~~~~~~~~~~~~~ helpme_standalone.h:3910:44: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3910 | recVecs_ = boxVecs_.inverse(); | ~~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:860:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 860 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h:862:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 862 | for (int col = 0; col < other.nCols_; ++col) { | ~~~~^~~~~~~~~~~~~~ helpme_standalone.h:863:41: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 863 | for (int link = 0; link < nCols_; ++link) { | ~~~~~^~~~~~~~ CXX Exec_ParmSolvent.cpp CXX Exec_ParmStrip.cpp CXX Exec_ParmWrite.cpp CXX Exec_PermuteDihedrals.cpp CXX Exec_Precision.cpp CXX Exec_PrepareForLeap.cpp CXX Exec_PrintData.cpp CXX Exec_Random.cpp CXX Exec_ReadData.cpp CXX Exec_ReadEnsembleData.cpp CXX Exec_ReadInput.cpp CXX Exec_RotateDihedral.cpp CXX Exec_RunAnalysis.cpp CXX Exec_ScaleDihedralK.cpp CXX Exec_Set.cpp CXX Exec_SequenceAlign.cpp CXX Exec_Show.cpp CXX Exec_SortEnsembleData.cpp CXX Exec_SplitCoords.cpp CXX Exec_System.cpp CXX Exec_Top.cpp CXX Exec_Traj.cpp CXX Exec_UpdateParameters.cpp CXX Exec_ViewRst.cpp CXX File_TempName.cpp CXX FileIO_Bzip2.cpp CXX FileIO_Gzip.cpp CXX FileIO_Mpi.cpp CXX FileIO_MpiShared.cpp CXX FileIO_Std.cpp CXX FileName.cpp CXX FileType.cpp CXX FileTypes.cpp CXX ForLoop.cpp CXX ForLoop_dataSetBlocks.cpp CXX ForLoop_integer.cpp CXX ForLoop_list.cpp CXX ForLoop_mask.cpp CXX ForLoop_overSets.cpp CXX Frame.cpp CXX GridAction.cpp CXX HistBin.cpp CXX Hungarian.cpp CXX ImageRoutines.cpp CXX Image_List_Mask.cpp CXX Image_List_Pair.cpp CXX Image_List_Unit.cpp CXX InputTrajCommon.cpp CXX KDE.cpp CXX MapAtom.cpp CXX MaskArray.cpp CXX MaskToken.cpp CXX Matrix_3x3.cpp CXX MdOpts.cpp CXX MetaData.cpp CXX Minimize_SteepestDescent.cpp CXX Mol.cpp CXX Mol2File.cpp CXX NameType.cpp CXX NC_Cmatrix.cpp CXX NC_Routines.cpp CXX NetcdfFile.cpp CXX OMM_helpers.cpp CXX OutputTrajCommon.cpp CXX ParameterSet.cpp CXX PDBfile.cpp CXX PairList.cpp CXX Parallel.cpp CXX ParallelNetcdf.cpp CXX ParmFile.cpp CXX Parm_Amber.cpp CXX Parm_CharmmPsf.cpp CXX Parm_CIF.cpp CXX Parm_Gromacs.cpp CXX Parm_Mol2.cpp CXX Parm_PDB.cpp CXX Parm_SDF.cpp CXX Parm_Tinker.cpp CXX PotentialFunction.cpp CXX PotentialTerm.cpp CXX PotentialTerm_Angle.cpp CXX PotentialTerm_Bond.cpp CXX PotentialTerm_Dihedral.cpp CXX PotentialTerm_LJ_Coulomb.cpp CXX PotentialTerm_OpenMM.cpp CXX ProgressBar.cpp CXX ProgressTimer.cpp CXX PubFFT.cpp CXX ExternalFxn.cpp CXX Random.cpp CXX Range.cpp CXX RNG.cpp CXX RNG_Marsaglia.cpp CXX RNG_MersenneTwister.cpp CXX RNG_PCG32.cpp CXX RNG_Stdlib.cpp CXX RPNcalc.cpp CXX RNG_Xoshiro128pp.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 helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3470:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3470 | fftHelperA_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3470:31: note: '' declared here 3470 | fftHelperA_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3471:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3471 | fftHelperB_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3471:31: note: '' declared here 3471 | fftHelperB_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3472:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3472 | fftHelperC_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3472:31: note: '' declared here 3472 | fftHelperC_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3503:43: helpme_standalone.h:519:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] 519 | class Matrix { | ^~~~~~ helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3503:45: note: '' declared here 3503 | compressionCoefficientsA_ = RealMat(); | ^~~~~~~~~ In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3504:43: helpme_standalone.h:519:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] 519 | class Matrix { | ^~~~~~ helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3504:45: note: '' declared here 3504 | compressionCoefficientsB_ = RealMat(); | ^~~~~~~~~ In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3505:43: helpme_standalone.h:519:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] 519 | class Matrix { | ^~~~~~ helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3505:45: note: '' declared here 3505 | compressionCoefficientsC_ = RealMat(); | ^~~~~~~~~ CXX 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 helpme_standalone.h: In member function 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:5031:16: warning: 'energy' may be used uninitialized [-Wmaybe-uninitialized] 5031 | return energy; | ^~~~~~ helpme_standalone.h:5021:14: note: 'energy' was declared here 5021 | Real energy; | ^~~~~~ CXX TrajinList.cpp CXX Trajin_Multi.cpp CXX Trajin_Single.cpp CXX TrajIOarray.cpp CXX Trajout_Single.cpp CXX TrajoutList.cpp CXX Vec3.cpp CXX ViewRst.cpp CXX xoshiro128plusplus.cpp CXX Action_Esander.cpp xoshiro128plusplus.cpp: In function 'void jump()': xoshiro128plusplus.cpp:60:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 60 | for(int i = 0; i < sizeof JUMP / sizeof *JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ xoshiro128plusplus.cpp: In function 'void long_jump()': xoshiro128plusplus.cpp:90:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 90 | for(int i = 0; i < sizeof LONG_JUMP / sizeof *LONG_JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CXX Command.cpp CXX Cpptraj.cpp CXX Energy_Sander.cpp CXX ReadLine.cpp CXX main.cpp CC molsurf.c Skipping bundled READLINE build cd xdrfile && make all make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' CC xdrfile.c Skipping bundled ARPACK build cd tng && make all make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' CC md5.c CC xdr_seek.c CC xdrfile_trr.c CC xdrfile_xtc.c CC tng_io.c CC tng_compress.c CC coder.c CC warnmalloc.c CC fixpoint.c CC xtc3.c CC bwlzh.c CC xtc2.c CC widemuldiv.c CC huffmem.c CC vals16.c CC bwt.c CC mtf.c CC rle.c CC lz77.c CC dict.c CC huffman.c CC merge_sort.c /bin/rm -f libxdrfile.a ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' tng_io.c: In function 'tng_gen_data_block_add': tng_io.c:12600:9: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tng_io.c:12600:47: note: length computed here 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ /bin/rm -f libtng_io.a ar cqs libtng_io.a md5.o tng_io.o tng_compress.o coder.o warnmalloc.o fixpoint.o xtc3.o bwlzh.o xtc2.o widemuldiv.o huffmem.o vals16.o bwt.o mtf.o rle.o lz77.o dict.o huffman.o merge_sort.o make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o -L/usr/lib/x86_64-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/x86_64-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/x86_64-linux-gnu/lib -lfftw3 -L/usr/lib/x86_64-linux-gnu/lib -lOpenMM -lnetcdf -lbz2 tng/libtng_io.a -lz xdrfile/libxdrfile.a -Wl,-z,relro mv cpptraj "/build/reproducible-path/cpptraj-5.1.0+dfsg/bin" make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_auto_test -- check unittest make -j40 test "TESTSUITEFLAGS=-j40 --verbose" VERBOSE=1 check unittest make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' make[2]: Nothing to be done for 'test'. cd test && make test.complete summary cd unitTests && make test.complete summary make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList CPPTRAJ: NameType class unit test. CPPTRAJ: ArgList class unit test. make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' g++ -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o NameType.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/NameType.cpp make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' g++ -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o ArgList.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/ArgList.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o StringRoutines.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/StringRoutines.cpp -rwxr-xr-x 1 pbuilder1 pbuilder1 186123352 Aug 6 22:29 ../bin/cpptraj -rwxr-xr-x 1 pbuilder1 pbuilder1 186123352 Aug 6 22:29 ../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_TrajinOffset TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Strip ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_General ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RemdTraj TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DSSP ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hbond CPPTRAJ: Normal trajectory read with offsets. CPPTRAJ: Broken Traj: Running good trajectory. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_trajout_framerange CPPTRAJ: One frame strip command test CPPTRAJ: CRD Replica Trajectory Run with offset CPPTRAJ: Secstruct (DSSP) command test. CPPTRAJ: Per-Residue RMSD Test. ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Center TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Image CPPTRAJ: Solute Hbond test ******************************************************************************** CPPTRAJ: General tests TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NCrestart ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radgyr CPPTRAJ: Trajout Frame Range [Amber Restart] ******************************************************************************** CPPTRAJ: Center command test. TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Jcoupling CPPTRAJ: Orthorhombic imaged distance test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diffusion ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf CPPTRAJ: Radius of gyration command test CPPTRAJ: NetCDF Restart Test - TXT->NetCDF TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotdif ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm ******************************************************************************** CPPTRAJ: J-Coupling single frame test TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_2DRMS ******************************************************************************** CPPTRAJ: RMSD Test with outtraj. TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mol2 CPPTRAJ: Surface calculation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Average ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RMSD ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Runavg CPPTRAJ: Diffusion test, no imaging. ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mask TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomMap ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pucker ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Datafile CPPTRAJ: NAstruct command test. ******************************************************************************** CPPTRAJ: Average Test. TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj CPPTRAJ: Mol2 Parm/Traj Read/Write Test. CPPTRAJ: Coordinate Running Average test. CPPTRAJ: 2D RMSD Test. CPPTRAJ: Basic RMSD tests CPPTRAJ: CHARMM PSF/DCD test CPPTRAJ: AtomMap Test CPPTRAJ: Pucker command test CPPTRAJ: Mask single frame test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial CPPTRAJ: Data file output precision test CPPTRAJ: Convert mdcrd -> NetCDF ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist CPPTRAJ: Rotational diffusion calculation test CPPTRAJ: 1D/2D Histogram Analysis test CPPTRAJ: Radial test, non-orthogonal imaging ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest CPPTRAJ: Gzipped trajectory read with offsets CPPTRAJ: Closest command test using first solvent atom. CPPTRAJ: CRD Replica Trajectory Run CPPTRAJ: NetCDF Restart Test - NetCDF->TXT J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DRMSD Skipped test: J-Coupling extended test CPPTRAJ: 2D RMSD Test, mass-weighted. All 1 comparisons passed. 1 comparisons skipped. CPPTRAJ: Distance RMSD test CPPTRAJ: Broken Traj: Running broken trajectory. CPPTRAJ: CHARMM DCD Write, step 1. All 2 comparisons passed. CPPTRAJ: Center origin command test. CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster CPPTRAJ: PDB => Mol2 CPPTRAJ: Non-orthorhombic imaged distance test. All 2 comparisons passed. CPPTRAJ: Cluster command test, in-memory pairwise distances. CPPTRAJ: Coordinate Running Average Traj Write CPPTRAJ: Diffusion test, old syntax. CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. CPPTRAJ: Per-Residue RMSD Test with averaging CPPTRAJ: Standard -> Grace Data ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_IRED All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons CPPTRAJ: Mask longer command test. CPPTRAJ: IRED vector/matrix test CPPTRAJ: randomizeions test (original algorithm) CPPTRAJ: Trajout Frame Range [Amber Coordinates] CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF CPPTRAJ: AtomMap with 'rmsfit' CPPTRAJ: Bzip2ed trajectory read with offsets ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Molsurf CPPTRAJ: Solute Hbond test with disk caching CPPTRAJ: NetCDF Replica Trajectory Run test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Corr CPPTRAJ: CHARMM DCD Write, step 2. CPPTRAJ: Molsurf test CPPTRAJ: Unstrip (Lig/Rec/Complex) command test CPPTRAJ: Correlation test CPPTRAJ: 2D RMSD Test with reference trajectory CPPTRAJ: Amber Top/Rst => Mol2 All 2 comparisons passed. CPPTRAJ: NAstruct command test, single strand CPPTRAJ: 3D histogram test. CPPTRAJ: Center origin mass command test. CPPTRAJ: Orthorhombic coordinate imaging test CPPTRAJ: Grace -> Standard Data CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckStructure CPPTRAJ: Structure Check All 6 comparisons passed. CPPTRAJ: Secstruct (DSSP) command with changing number of residues. CPPTRAJ: Atom map charmm->amber atom order CPPTRAJ: RMS coordinate rotation/rotation matrices test CPPTRAJ: Convert NetCDF -> mdcrd CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj CPPTRAJ: Per-Residue RMSD Test with residue centering. CPPTRAJ: CHAMBER topology read/strip test. CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt All 1 comparisons passed. 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: Cluster command test, read pairwise distances. CPPTRAJ: 2D DME Test. All 5 comparisons passed. CPPTRAJ: Start argument offset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RmsAvgCorr CPPTRAJ: RmsAvgCorr Reference CPPTRAJ: Solute-solvent hbond test All 11 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Contacts ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Principal CPPTRAJ: Contacts test. CPPTRAJ: Closest command test using all solvent atoms. All 7 comparisons passed. CPPTRAJ: Principal Test All 3 comparisons passed. All 2 comparisons passed. CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj CPPTRAJ: Diffusion test, new syntax. CPPTRAJ: Read CHARMM restart ******************************************************************************** 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_NAstruct_8OG ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Vector ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Matrix CPPTRAJ: NA test (8OG) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct CPPTRAJ: Basic vector tests CPPTRAJ: Matrix Tests CPPTRAJ: X column format/precision test. CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. CPPTRAJ: Center reference command test. All 4 comparisons passed. CPPTRAJ: Structure Check with Around and Skip CPPTRAJ: Nonorthorhombic coordinate imaging test CPPTRAJ: 2D RMSD with reference mask test. CPPTRAJ: Secstruct (DSSP): SS assign output test CPPTRAJ: Atom map charmm->amber atom order, by residue All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Grid All 3 comparisons passed. CPPTRAJ: RmsAvgCorr First CPPTRAJ: Dipole test CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj CPPTRAJ: RMS fit with no coordinates modification test. CPPTRAJ: CHARMM PSF write ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Project CPPTRAJ: Cluster command test, read NetCDF pairwise distances. All 3 comparisons passed. CPPTRAJ: Projection CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Unwrap CPPTRAJ: Hbond, no intramolecular hydrogen bonds test CPPTRAJ: Diffusion test, nonorthogonal box CPPTRAJ: Unwrap non-orthogonal test CPPTRAJ: FtuFabI Assignment test CPPTRAJ: Compressed broken trajectory test All 4 comparisons passed. CPPTRAJ: 2D RMSD test, no fitting. CPPTRAJ: Data file group by name test CPPTRAJ: Multi frame strip command test. All 9 comparisons passed. CPPTRAJ: CHARMM COORdinates test CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj CPPTRAJ: Center point test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AnalysisRunAvg All 3 comparisons passed. CPPTRAJ: Analysis Running Average All 3 comparisons passed. All 1 comparisons passed. CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Watershell CPPTRAJ: Grid test CPPTRAJ: Modes analysis, RMS fluctuations CPPTRAJ: Watershell Test, non-orthorhombic imaging. CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SPAM All 1 comparisons passed. CPPTRAJ: SPAM Test CPPTRAJ: Cluster command test, write ASCII pairwise distances. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volmap CPPTRAJ: CRD Replica Trajectory Run with remdout CPPTRAJ: Test vector center with magnitude All 6 comparisons passed. CPPTRAJ: Strip topology with PDB info CPPTRAJ: VMD VolMap Algorithm test All 5 comparisons passed. CPPTRAJ: STFC Diffusion Test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LIE CPPTRAJ: LIE test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidOrder CPPTRAJ: Data file group by aspect test CPPTRAJ: Lipid Order Parameter Test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Density CPPTRAJ: Density along axis tests CPPTRAJ: Modes analysis, displacements CPPTRAJ: RMS fit to previous test CPPTRAJ: Unwrap orthogonal test CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CharmmParams CPPTRAJ: Cluster command test, read ASCII pairwise distances. CPPTRAJ: Test updating topology with Charmm parameters (single residue) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PairDist All 2 comparisons passed. CPPTRAJ: Closest command test, using mask center CPPTRAJ: PairDist Test. All 10 comparisons passed. CPPTRAJ: Hbond, specified solute masks ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReadData All 11 comparisons passed. CPPTRAJ: Read vector data test (no origins, origins) CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM All 8 comparisons passed. CPPTRAJ: Momentum/velocity vector test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST CPPTRAJ: GIST water-water interaction test CPPTRAJ: OpenDX Grid read test CPPTRAJ: STFC Diffusion Test with individual distances CPPTRAJ: Modes analysis, dipole correlation ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicCorr CPPTRAJ: Atomic Correlation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_systemVF CPPTRAJ: Outtraj Test with maxmin. All 6 comparisons passed. CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test CPPTRAJ: RMS: imaging after unit cell rotation ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr CPPTRAJ: Atomicfluct test with ADP output CPPTRAJ: AutoCorr test. All 9 comparisons passed. All 2 comparisons passed. VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. Skipped test: VMD VolMap Algorithm longer tests All 2 comparisons passed. 1 comparisons skipped. CPPTRAJ: Structure Check with PBC All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Box ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve CPPTRAJ: Read vector data set (origins, no origins) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomTypeSelect CPPTRAJ: Box Test (Add box info) CPPTRAJ: Hbond, no angle cutoff test CPPTRAJ: Cluster, nosieve CPPTRAJ: Selection by atom type test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AvgRef CPPTRAJ: Closest command test, using mask center and solvent mask CPPTRAJ: RMSD Test with averaged reference coordinates. CPPTRAJ: Partial Surface calculation test CPPTRAJ: Force vector test. CPPTRAJ: STFC Diffusion Test with COM All 1 comparisons passed. All 1 comparisons passed. All 12 comparisons passed. All 15 comparisons passed. CPPTRAJ: Grid with specified center test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Crank_Stat All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LoadCrd ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Parallel ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoImage CPPTRAJ: Parallel tests. CPPTRAJ: LoadCrd test. CPPTRAJ: Crankshaft test CPPTRAJ: AutoImage test (split DNA duplex) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateCrd CPPTRAJ: Read Amber output test All 4 comparisons passed. CPPTRAJ: COORDS data set creation and CRDFLUCT test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MultiVector All 1 comparisons passed. CPPTRAJ: Hbond, Bridge nointramol test CPPTRAJ: Multivector test CPPTRAJ: Pairdist test, orthogonal imaging. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Lifetime CPPTRAJ: Multi-frame density along axis test All 1 comparisons passed. CPPTRAJ: Lifetime test. All 14 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FFT CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Timecorr CPPTRAJ: FFT test. CPPTRAJ: STFC Diffusion Test with second mask CPPTRAJ: Timecorr test. CPPTRAJ: Box test (remove box info) CPPTRAJ: Generate matrix with trajectory start/stop/offset All 6 comparisons passed. CPPTRAJ: SPAM Pure Solvent Test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CrossCorr CPPTRAJ: Cluster, sieve5 CPPTRAJ: Closest command test, solvent mask, water oxygen only CPPTRAJ: CrossCorr test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SymmRmsd CPPTRAJ: Modes analysis, pseudo trajectory creation test CPPTRAJ: SymmRmsd CPPTRAJ: Radial test, orthogonal and no imaging ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidSCD CPPTRAJ: LoadTraj test. All 3 comparisons passed. CPPTRAJ: Basic lipid order parameter test CPPTRAJ: COORDS data set creation with velocities test All 1 comparisons passed. CPPTRAJ: Read CHARMM output test CPPTRAJ: Grid with box center offset test. All 3 comparisons passed. CPPTRAJ: Generate matrix with action stop/start/offset CPPTRAJ: Box test (Modify box length) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MakeStructure CPPTRAJ: Parallel test with trajectory offset CPPTRAJ: Basic makestructure test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multidihedral All 1 comparisons passed. CPPTRAJ: Multidihedral test CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ensemble_MREMD CPPTRAJ: LoadTraj from trajin test. CPPTRAJ: ASP symmetry-corrected RMSD test CPPTRAJ: M-REMD sort test. CPPTRAJ: Lifetime test with data set caching. CPPTRAJ: 3D data read/write test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotate CPPTRAJ: Rotation (and inverse) of coords from matrices All 5 comparisons passed. All 1 comparisons passed. All 7 comparisons passed. All 15 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Integrate CPPTRAJ: Total system density test CPPTRAJ: NativeContacts test. CPPTRAJ: Integration test. CPPTRAJ: Grid with mask center offset test. All 9 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 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LESsplit CPPTRAJ: Simple energy tests CPPTRAJ: Box test (auto orthogonal box, no radii) CPPTRAJ: Cluster, nosieve savepairdist CPPTRAJ: LES split/average test All 6 comparisons passed. CPPTRAJ: GLU symmetry-corrected RMSD test CPPTRAJ: LoadCrd append from multiple files test CPPTRAJ: Standard 3D data write test CPPTRAJ: Multidihedral Nucleotide CHI test All 13 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PermuteDihedrals ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CCP4 CPPTRAJ: PermuteDihedrals interval -120, phi psi CPPTRAJ: CCP4 read/write and DX conversion test. CPPTRAJ: Makestructure test with reference. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihCovar All 1 comparisons passed. CPPTRAJ: Dihedral Covariance Matrix Test CPPTRAJ: Box test (auto orthogonal box, VDW radii) CPPTRAJ: Rotate with defined axis ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CurveFit CPPTRAJ: TYR symmetry-corrected RMSD test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetAverage CPPTRAJ: Randomize (around, overlap) CPPTRAJ: Data set averaging and averaging over all sets test. CPPTRAJ: Curve fitting test. CPPTRAJ: Multidihedral protein dihedrals test CPPTRAJ: Standard 3D data read test All 4 comparisons passed. CPPTRAJ: New Lipid Order Parameter Test, DOPC. All 7 comparisons passed. All 5 comparisons passed. CPPTRAJ: M-REMD actions test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VectorMath ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander CPPTRAJ: Vector dot/cross product test SANDER energy tests (long) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. CPPTRAJ: Non-orthogonal grid test. SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. SKIP: SANDER energy tests (long) CPPTRAJ: Cluster, nosieve loadpairdist CPPTRAJ: Lifetime average and cumulative average test. CPPTRAJ: PermuteDihedrals, random rotations All 2 comparisons passed. All 7 comparisons passed. CPPTRAJ: TRAJ data set creation and CRDFLUCT test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Temperature CPPTRAJ: Multidihedral cyclic molecule test CPPTRAJ: Temperature test. ******************************************************************************** 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. All 3 comparisons passed. CPPTRAJ: Longer symmetry-corrected RMSD test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Spline CPPTRAJ: Curve fitting multi-exponential tests. CPPTRAJ: Spline test CPPTRAJ: Standard 3D data read/append test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_KDE All 7 comparisons passed. CPPTRAJ: LCPO test with GAFF atom types CPPTRAJ: KDE test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PDB ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Wavelet ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CIF CPPTRAJ: PDB format read/write test CPPTRAJ: Wavelet analysis test CPPTRAJ: CIF read test All 2 comparisons passed. All 16 comparisons passed. All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Align All 12 comparisons passed. CPPTRAJ: Temperature with SHAKE on hydrogens. CPPTRAJ: Align Tests. All 3 comparisons passed. All 4 comparisons passed. All 1 comparisons passed. CPPTRAJ: TRAJ data set creation with velocities test. CPPTRAJ: M-REMD ensemble outtraj test. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RotateDihedral ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetCmd All 8 comparisons passed. All 3 comparisons passed. CPPTRAJ: Data Set commands test CPPTRAJ: Cluster, sieve5 savepairdist CPPTRAJ: Rotate dihedral to target value. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelocityAutoCorr All 4 comparisons passed. CPPTRAJ: Velocity autocorrelation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelFrc ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remap ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Filter CPPTRAJ: Remap Test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CompareTop CPPTRAJ: Basic filter test CPPTRAJ: Compare topology test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TopInfo CPPTRAJ: Test combining coordinates, velocities, and forces. CPPTRAJ: Test kinetic energy calculation CPPTRAJ: Standard 3D data, sparse ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CombineCrd ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTrr CPPTRAJ: TRR force/velocity read -> NetCDF write test CPPTRAJ: Topology info print test. CPPTRAJ: Temperature with SHAKE on all atoms. CPPTRAJ: Combine COORDS test. CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test CPPTRAJ: NativeContacts test, save non-native contacts, residue time series All 1 comparisons passed. CPPTRAJ: M-REMD no sort, running average test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ewald CPPTRAJ: AutoImage test, use anchor mask CPPTRAJ: Direct sum test CPPTRAJ: Test using velocities as coordinates. CPPTRAJ: Rotate dihedral by increment CPPTRAJ: Test total energy calculation ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TI CPPTRAJ: Nonorthogonal grid standard write/read tests. CPPTRAJ: TI analysis test. All 1 comparisons passed. CPPTRAJ: Curve fitting, custom output range. CPPTRAJ: Generate offset traj from PDB ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds CPPTRAJ: Temperature calc with extra points. CPPTRAJ: Combine COORDS test with box info. CPPTRAJ: COORDS data set append test CPPTRAJ: Align, unit cell rotation/imaging test. CPPTRAJ: Fix imaged bonds test (Ortho.) CPPTRAJ: PQR file write with various radii CPPTRAJ: Test partial energy calculation CPPTRAJ: Wavelet WAFEX test CPPTRAJ: Rotate dihedral in TRAJ data set CPPTRAJ: M-REMD, generate RMS data CPPTRAJ: Test writing velocities (MDVEL) CPPTRAJ: Data filter test. CPPTRAJ: Grid generation from 'bounds' test. All 10 comparisons passed. All 6 comparisons passed. All 3 comparisons passed. CPPTRAJ: KDE with Kullback-Leibler divergence test CPPTRAJ: Generate offset traj from CIF All 5 comparisons passed. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Distance CPPTRAJ: Distance tests CPPTRAJ: NativeContacts test, orthorhombic imaging. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multicurve CPPTRAJ: Multicurve test All 2 comparisons passed. All 3 comparisons passed. CPPTRAJ: COORDS test storing frame metadata CPPTRAJ: M-REMD, meltcurve analysis ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volume ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remlog CPPTRAJ: Volume tests CPPTRAJ: Filter matrix test. ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AreaPerMol TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DistBasedMask CPPTRAJ: Replica log read/analyze test. CPPTRAJ: Test using forces as coordinates. CPPTRAJ: Distance-based atom mask tests (atom, residue) CPPTRAJ: Area per molecule test CPPTRAJ: PDB filter alternate atom location IDs test All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SetVelocity CPPTRAJ: Orthogonal imaged distance CPPTRAJ: Fix imaged bonds test (Non-ortho.) CPPTRAJ: Set Velocity test All 17 comparisons passed. All 4 comparisons passed. All 1 comparisons passed. CPPTRAJ: TRR force/velocity read -> TRR write test CPPTRAJ: Hbond with imaging All 5 comparisons passed. CPPTRAJ: Split coords and recombine test. CPPTRAJ: Cluster, sieve5 loadpairdist ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Calc ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CalcState All 13 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Change CPPTRAJ: Calcstate test CPPTRAJ: Test writing forces (MDFRC) CPPTRAJ: Change atom and residue name tests All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateReservoir ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixAtomOrder All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LowestCurve CPPTRAJ: Calc test CPPTRAJ: Out of order molecules test CPPTRAJ: LowestCurve test CPPTRAJ: Create RREMD NetCDF reservoir test All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MinImage ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Regress CPPTRAJ: Minimum Image test. All 1 comparisons passed. CPPTRAJ: Non-orthogonal imaged distance CPPTRAJ: Distance-based atom mask tests (molecule) CPPTRAJ: Linear regression test. All 3 comparisons passed. CPPTRAJ: Scale velocity test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rst ******************************************************************************** CPPTRAJ: Hbond, orthogonal imaging TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pairwise All 7 comparisons passed. CPPTRAJ: Generate restraints (rst) test CPPTRAJ: Pairwise tests CPPTRAJ: Change chain ID test CPPTRAJ: Structure Check with Around CPPTRAJ: CRD => TRR All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Solvent ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ParmBox ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Translate All 4 comparisons passed. CPPTRAJ: Parmbox test CPPTRAJ: Test solvent command with closest CPPTRAJ: Translate test All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReplicateCell CPPTRAJ: Replicate cell test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ScaleDihedralK CPPTRAJ: Scale dihedral force constant test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PhiPsi All 3 comparisons passed. CPPTRAJ: Phipsi test All 1 comparisons passed. CPPTRAJ: Topology info with reference coords test CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. CPPTRAJ: Change chain ID of COORDS set test CPPTRAJ: Pairdist test, nonorthogonal imaging. CPPTRAJ: TRAJ test storing frame metadata CPPTRAJ: Adding PDB info to topology CPPTRAJ: Calc test with data sets ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Control All 1 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_InfraredSpec CPPTRAJ: Loop tests CPPTRAJ: Infrared spectrum calculation test All 1 comparisons passed. All 6 comparisons passed. All 3 comparisons passed. All 23 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cphstats ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CmdLine CPPTRAJ: Explicit pH REMD ensemble data read / sort All 1 comparisons passed. All 1 comparisons passed. CPPTRAJ: Command line trajectory args test, part 1 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XYZformat CPPTRAJ: XYZ format write All 17 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hausdorff ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CatCrd CPPTRAJ: Scale dihedral force constant with 'useall' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XtalSymm ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Time CPPTRAJ: Concatenate COORDS data set test All 1 comparisons passed. CPPTRAJ: Simple Hausdorff distance test. CPPTRAJ: Add time to restart test CPPTRAJ: XtalSymm Reference All 12 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihedralRMS CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Slope ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SplitCoords All 1 comparisons passed. All 3 comparisons passed. CPPTRAJ: SplitCoords test CPPTRAJ: Finite difference test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diagmatrix CPPTRAJ: MW covariance matrix thermo analysis test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Emin CPPTRAJ: Basic energy minimization test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Graft ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau CPPTRAJ: Graft test CPPTRAJ: Evalulate plateau test CPPTRAJ: Pairwise test, partial system CPPTRAJ: Test math functions CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. All 10 comparisons passed. All 2 comparisons passed. CPPTRAJ: Remove time from restart test CPPTRAJ: Randomize (around) CPPTRAJ: TRR => CRD CPPTRAJ: Command line test trajectory args test, part 2 CPPTRAJ: Hausdorff distance of 2D rms output test. All 1 comparisons passed. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Flatten All 1 comparisons passed. CPPTRAJ: Flatten test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Random CPPTRAJ: Constant pH stats test CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs CPPTRAJ: Cluster, nosieve pairwisecache none CPPTRAJ: Test set command All 1 comparisons passed. All 1 comparisons passed. CPPTRAJ: Atom XYZ format read, test 1 CPPTRAJ: Dihedral RMSD test (to previous) All 8 comparisons passed. All 4 comparisons passed. All 1 comparisons passed. CPPTRAJ: Energy minimization with angle term test. All 1 comparisons passed. All 6 comparisons passed. CPPTRAJ: Add time to trajectory test All 2 comparisons passed. CPPTRAJ: PCG32 RNG test. All 1 comparisons passed. CPPTRAJ: Command line wildcard test, part 1 g++ -o a.out main.o NameType.o CpptrajStdio.o All 10 comparisons passed. CPPTRAJ: Dihedral RMS fluctuation test. CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. CPPTRAJ: Sorted implicit constant pH stats test CPPTRAJ: Atom XYZ format read, test 2 All 8 comparisons passed. CPPTRAJ: Test Stdlib RNG All 5 comparisons passed. CPPTRAJ: Command line wildcard test, part 2 CPPTRAJ: Test reading comma-separated list of strings CPPTRAJ: Energy minimization with nonbond term test. CPPTRAJ: Test Mersenne Twister RNG CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats CPPTRAJ: Hausdorff distance of 2D rms output test. All 5 comparisons passed. All 2 comparisons passed. CPPTRAJ: Atom XYZ format read, test 3 CPPTRAJ: Test nested loops and variables in loops CPPTRAJ: Modify time info test. All 4 comparisons passed. CPPTRAJ: Ewald test (NaCl crystal) CPPTRAJ: Atom XYZ format read, test 4 All 4 comparisons passed. CPPTRAJ: Test loop over data set blocks CPPTRAJ: Unsorted pH read/write test CPPTRAJ: CRD(1-5) => TRR CPPTRAJ: Cluster, sieve5 pairwisecache none CPPTRAJ: Ewald test (trunc. oct) make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' CPPTRAJ: Atom XYZ format read, test 5 All 16 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: Test for filename wildcards and oversets All 3 comparisons passed. CPPTRAJ: Atom XYZ format read, test 6 CPPTRAJ: Cluster, random CPPTRAJ: CRD(6-10) => TRR All 13 comparisons passed. CPPTRAJ: OpenMM basic energy minimization tests (bonds) CPPTRAJ: XtalSymm Reimaging by Atom All 4 comparisons passed. All 6 comparisons passed. CPPTRAJ: OpenMM basic energy minimization tests (angles) All 28 comparisons passed. CPPTRAJ: TRR (appended) => CRD ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) All 1 comparisons passed. CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) CPPTRAJ: Read specific columns test. CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). CPPTRAJ: Watershell Test, orthorhombic imaging. CPPTRAJ: Write non-square matrix CPPTRAJ: GMX: CRD with offset CPPTRAJ: Ewald test (partial system, trunc. oct) CPPTRAJ: Read non-square matrix CPPTRAJ: Read square matrix CPPTRAJ: GMX: TRR with offset CPPTRAJ: Randomize (overlap) All 15 comparisons passed. All 4 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. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LibPME CPPTRAJ: Clustering, One DataSet CPPTRAJ: Particle mesh Ewald test (NaCl crystal) All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc CPPTRAJ: XTC read test CPPTRAJ: Clustering, Two DataSets CPPTRAJ: Particle mesh Ewald test (trunc. oct) CPPTRAJ: Watershell Test, no imaging. CPPTRAJ: Pairdist test, 2 masks. CPPTRAJ: Randomize (no restrictions) CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) All 5 comparisons passed. All 4 comparisons passed. CPPTRAJ: Clustering, dihedral DataSet CPPTRAJ: CRD => XTC All 5 comparisons passed. All 3 comparisons passed. CPPTRAJ: Clustering, two dihedral DataSets CPPTRAJ: GIST test, orthogonal cell CPPTRAJ: Clustering, dihedral DataSet, K-means CPPTRAJ: XTC => CRD CPPTRAJ: Particle mesh Ewald test (ortho) CPPTRAJ: Clustering, two dihedral DataSets, K-means CPPTRAJ: Particle mesh Ewald test (ortho, with mask) CPPTRAJ: CRD(1-5) => XTC g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' Unit test passed. make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ: PME test (partial system, trunc. oct) CPPTRAJ: XtalSymm Reimaging by Molecule CPPTRAJ: CRD(6-10) => XTC All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN CPPTRAJ: DBSCAN test CPPTRAJ: DBSCAN automatic parameter determination test. All 5 comparisons passed. All 9 comparisons passed. 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: DBSCAN kdist map test CPPTRAJ: XTC (appended) => CRD CPPTRAJ: DBSCAN with sieve CPPTRAJ: LJ PME kappa sweep test, 0.35 All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans CPPTRAJ: Cpptraj Kmeans CPPTRAJ: Cpptraj Kmeans random CPPTRAJ: LJ PME kappa sweep test, 0.45 CPPTRAJ: GMX: CRD with offset CPPTRAJ: LJ PME kappa sweep test, 0.5 All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_SymmRMSD CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) All 3 comparisons passed. CPPTRAJ: LJ with switch function test CPPTRAJ: GMX: XTC with offset All 5 comparisons passed. All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites CPPTRAJ: Cluster command test, coordinate writes. All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTNG CPPTRAJ: TNG read test CPPTRAJ: Cluster command test, coordinate writes using info file. CPPTRAJ: GIST test, nonorthogonal cell All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Dpeaks CPPTRAJ: Density peaks clustering test CPPTRAJ: TNG read test (with offset) All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Nreps CPPTRAJ: Clustering with specified # reps All 6 comparisons passed. All 2 comparisons passed. All 11 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST_Order CPPTRAJ: TIP3P water cluster test CPPTRAJ: TIP4P water cluster test CPPTRAJ: TIP5P water cluster test All 4 comparisons passed. make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' /usr/bin/make -C test summary make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' -rwxr-xr-x 1 pbuilder1 pbuilder1 186123352 Aug 6 22:29 ../bin/cpptraj ===================== TEST SUMMARY ====================== 853 out of 859 comparisons OK (0 failed, 0 warnings, 6 skipped). 480 out of 480 program executions completed. 170 out of 173 tests completed with no issues. 2 tests skipped. ========================================================= make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/cpptraj/ make -j40 install DESTDIR=/build/reproducible-path/cpptraj-5.1.0\+dfsg/debian/cpptraj AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make install make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' Skipping bundled READLINE build Skipping bundled ARPACK build g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o -L/usr/lib/x86_64-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/x86_64-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/x86_64-linux-gnu/lib -lfftw3 -L/usr/lib/x86_64-linux-gnu/lib -lOpenMM -lnetcdf -lbz2 tng/libtng_io.a -lz xdrfile/libxdrfile.a -Wl,-z,relro mv cpptraj "/build/reproducible-path/cpptraj-5.1.0+dfsg/bin" make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libreadline8t64 from: /lib/x86_64-linux-gnu/libreadline.so.8 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libreadline8t64 to: /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'cpptraj' in '../cpptraj_5.1.0+dfsg-4_amd64.deb'. dpkg-deb: building package 'cpptraj-dbgsym' in '../cpptraj-dbgsym_5.1.0+dfsg-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../cpptraj_5.1.0+dfsg-4_amd64.buildinfo dpkg-genchanges --build=binary -O../cpptraj_5.1.0+dfsg-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/2415790 and its subdirectories I: Current time: Wed Aug 6 10:30:05 -12 2025 I: pbuilder-time-stamp: 1754519405 Wed Aug 6 22:30:05 UTC 2025 I: Signing ./b1/cpptraj_5.1.0+dfsg-4_amd64.buildinfo as cpptraj_5.1.0+dfsg-4_amd64.buildinfo.asc Wed Aug 6 22:30:05 UTC 2025 I: Signed ./b1/cpptraj_5.1.0+dfsg-4_amd64.buildinfo as ./b1/cpptraj_5.1.0+dfsg-4_amd64.buildinfo.asc Wed Aug 6 22:30:05 UTC 2025 - build #1 for cpptraj/unstable/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Wed Aug 6 22:30:05 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-cjdqPoqN, removing. /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Aug 6 22:30 b1 drwxr-xr-x 2 jenkins jenkins 4096 Aug 6 22:26 b2 -rw-r--r-- 1 jenkins jenkins 2184 May 13 2024 cpptraj_5.1.0+dfsg-4.dsc -rw------- 1 jenkins jenkins 3311 Aug 6 22:26 rbuildlog.700T9Qk /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/b1: total 42748 -rw-r--r-- 1 jenkins jenkins 189248 Aug 6 22:30 build.log -rw-r--r-- 1 jenkins jenkins 41607356 Aug 6 22:30 cpptraj-dbgsym_5.1.0+dfsg-4_amd64.deb -rw-r--r-- 1 jenkins jenkins 6084 Aug 6 22:30 cpptraj_5.1.0+dfsg-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2184 Aug 6 22:30 cpptraj_5.1.0+dfsg-4.dsc -rw-r--r-- 1 jenkins jenkins 8233 Aug 6 22:30 cpptraj_5.1.0+dfsg-4_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 9115 Aug 6 22:30 cpptraj_5.1.0+dfsg-4_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1479 Aug 6 22:30 cpptraj_5.1.0+dfsg-4_amd64.changes -rw-r--r-- 1 jenkins jenkins 1924068 Aug 6 22:30 cpptraj_5.1.0+dfsg-4_amd64.deb -rw-r--r-- 1 jenkins jenkins 1313 Aug 6 22:30 cpptraj_5.1.0+dfsg-4_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/b2: total 0 Wed Aug 6 22:30:06 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Aug 6 10:26:58 -12 2025 I: pbuilder-time-stamp: 1754519218 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [cpptraj_5.1.0+dfsg-4.dsc] I: copying [./cpptraj_5.1.0+dfsg.orig.tar.xz] I: copying [./cpptraj_5.1.0+dfsg-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./cpptraj_5.1.0+dfsg-4.dsc: 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-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-system-libraries.patch dpkg-source: info: applying skip-failing-test.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2415790/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='bce42d0f097543b7a362b6996b6ac080' 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='2415790' 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.dE0NwvQ4/pbuilderrc_rHzM --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/b1 --logfile b1/build.log cpptraj_5.1.0+dfsg-4.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2415790/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), gfortran, libarpack2-dev, libbz2-dev, libfftw3-dev, libnetcdf-dev, libopenmm-dev, libreadline-dev, netcdf-bin dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19850 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on libarpack2-dev; however: Package libarpack2-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on libnetcdf-dev; however: Package libnetcdf-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmm-dev; however: Package libopenmm-dev is not installed. pbuilder-satisfydepends-dummy depends on libreadline-dev; however: Package libreadline-dev is not installed. pbuilder-satisfydepends-dummy depends on netcdf-bin; however: Package netcdf-bin is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran{a} gfortran-14{a} gfortran-14-x86-64-linux-gnu{a} gfortran-x86-64-linux-gnu{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarpack2-dev{a} libarpack2t64{a} libblas-dev{a} libblas3{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libffi8{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-quad3{a} libfftw3-single3{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-310{a} libhdf5-cpp-310{a} libhdf5-dev{a} libhdf5-fortran-310{a} libhdf5-hl-310{a} libhdf5-hl-cpp-310{a} libhdf5-hl-fortran-310{a} libidn2-0{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-dev{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnetcdf-dev{a} libnetcdf22{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libopenmm-dev{a} libopenmm8.1{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} libreadline-dev{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsz2{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2{a} libxml2-dev{a} libzstd-dev{a} m4{a} man-db{a} netcdf-bin{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 131 newly installed, 0 to remove and 0 not upgraded. Need to get 64.2 MB of archives. After unpacking 249 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b3 [56.7 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 25 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libgfortran-14-dev amd64 14.2.0-19 [880 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-19 [11.7 MB] Get: 36 http://deb.debian.org/debian unstable/main amd64 gfortran-14 amd64 14.2.0-19 [14.5 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1 [1284 B] Get: 38 http://deb.debian.org/debian unstable/main amd64 gfortran amd64 4:14.2.0-1 [1436 B] Get: 39 http://deb.debian.org/debian unstable/main amd64 hdf5-helpers amd64 1.14.5+repack-3 [26.6 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 43 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 52 http://deb.debian.org/debian unstable/main amd64 libaec-dev amd64 1.1.3-1+b1 [21.5 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-5 [159 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-5 [2448 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libarpack2t64 amd64 3.9.1-6 [104 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-5 [170 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.1-5 [4991 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libarpack2-dev amd64 3.9.1-6 [120 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.14.1-2 [384 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-2 [598 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-3 [455 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-3 [455 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-2 [103 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-3 [1406 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.10+dfsg-1 [312 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1 [116 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.5.1-1 [2954 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.14.1-2 [503 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.14.1-2 [391 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libfftw3-double3 amd64 3.3.10-2+b1 [781 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libfftw3-long3 amd64 3.3.10-2+b1 [347 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libfftw3-quad3 amd64 3.3.10-2+b1 [618 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libfftw3-single3 amd64 3.3.10-2+b1 [809 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libfftw3-bin amd64 3.3.10-2+b1 [51.3 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libfftw3-dev amd64 3.3.10-2+b1 [2118 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libhdf5-cpp-310 amd64 1.14.5+repack-3 [133 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libhdf5-fortran-310 amd64 1.14.5+repack-3 [111 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [69.3 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-fortran-310 amd64 1.14.5+repack-3 [43.9 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-cpp-310 amd64 1.14.5+repack-3 [24.4 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-4 [292 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-4 [72.2 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libhdf5-dev amd64 1.14.5+repack-3 [3165 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5+20250216-2 [353 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libnetcdf22 amd64 1:4.9.3-1 [517 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-2.1 [794 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libnetcdf-dev amd64 1:4.9.3-1 [116 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-11 [1059 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libopenmm-dev amd64 8.1.2+dfsg-11 [346 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libreadline-dev amd64 8.2-6 [153 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 netcdf-bin amd64 1:4.9.3-1 [260 kB] Fetched 64.2 MB in 1s (51.0 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 ... 19850 files and directories currently installed.) Preparing to unpack .../000-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/cpptraj-5.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../cpptraj_5.1.0+dfsg-4_source.changes dpkg-buildpackage: info: source package cpptraj dpkg-buildpackage: info: source version 5.1.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' touch config.h external.config.h dh_auto_clean make -j40 clean make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' /bin/rm -f SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o cpptraj *.LIBCPPTRAJ.o libcpptraj # cd readline && make clean cd xdrfile && make clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' /bin/rm -f *.o libxdrfile.a a.out test.trr test.xtc test.xdr make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' # cd arpack && make clean cd cuda_kernels && make clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/cuda_kernels' /bin/rm -f *.o libcpptraj_cuda.a make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/cuda_kernels' cd tng && make clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' /bin/rm -f *.o libtng_io.a tng_io_testing.o a.out tng_example_out.tng tng_test.tng make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' cd test && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' Cleaning all test directories: make test.complete test.libcpptraj OPT=clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' cd unitTests && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' Cleaning unit tests. make test.complete OPT=clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' rm -rf bin make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' ./configure gnu --with-arpack=/usr/lib/x86_64-linux-gnu --with-fftw3=/usr/lib/x86_64-linux-gnu --with-readline=/usr/lib/x86_64-linux-gnu --with-openmm=/usr/lib/x86_64-linux-gnu arpack specified: /usr/lib/x86_64-linux-gnu fftw3 specified: /usr/lib/x86_64-linux-gnu readline specified: /usr/lib/x86_64-linux-gnu openmm specified: /usr/lib/x86_64-linux-gnu Testing C++ compiler: OK Testing C compiler: OK Testing basic C++11 support: OK Testing system headers for C++11 support: OK Warning: Compilation of sanderlib requires AMBERHOME to be set Warning: if --with-sanderlib not specified. Checking BZLIB: OK Checking ZLIB: OK Checking NetCDF: OK Checking LAPACK/BLAS: OK Checking ARPACK: OK Checking FFTW3: OK Checking Readline: OK Checking OpenMM: OK vmdplugin disabled due to nonfree source. Configuration summary: Build type: Serial Options: netcdf bzlib tng zlib arpack lapack blas fftw3 readline xdrfile openmm Target platform: Linux, 64-bit. gnu compilers in use. C++11 support enabled. PME support enabled. Compiler optimizations are on. Cleaning source directory. -------------------------------------------------------------------------------- An environment resource file for CPPTRAJ has been created: /build/reproducible-path/cpptraj-5.1.0+dfsg/cpptraj.sh You may 'source' this file to set up your environment for CPPTRAJ. -------------------------------------------------------------------------------- CPPTRAJ configuration complete. make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_auto_build make -j40 make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make install make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' CXX SpaceGroup.cpp CXX ActionFrameCounter.cpp CXX ActionList.cpp CXX ActionTopWriter.cpp CXX Action_Align.cpp CXX Action_Angle.cpp CXX Action_AreaPerMol.cpp CXX Action_AtomMap.cpp CXX Action_AtomicCorr.cpp CXX Action_AtomicFluct.cpp CXX Action_AutoImage.cpp CXX Action_Average.cpp CXX Action_Bounds.cpp CXX Action_Box.cpp CXX Action_Center.cpp CXX Action_Channel.cpp CXX Action_CheckChirality.cpp CXX Action_CheckStructure.cpp CXX Action_Closest.cpp CXX Action_ClusterDihedral.cpp CXX Action_Contacts.cpp CXX Action_CreateCrd.cpp CXX Action_CreateReservoir.cpp CXX Action_DNAionTracker.cpp CXX Action_DSSP.cpp CXX Action_Density.cpp CXX Action_Diffusion.cpp CXX Action_Dihedral.cpp CXX Action_DihedralRMS.cpp CXX Action_Dipole.cpp CXX Action_Distance.cpp CXX Action_DistRmsd.cpp CXX Action_Energy.cpp CXX Action_FilterByData.cpp CXX Action_FixAtomOrder.cpp CXX Action_FixImagedBonds.cpp CXX Action_GIST.cpp CXX Action_Grid.cpp CXX Action_GridFreeEnergy.cpp CXX Action_HydrogenBond.cpp In file included from Ewald_ParticleMesh.h:5, from Action_Energy.cpp:4: helpme_standalone.h:2323: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2323 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:2343: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2343 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3014: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3014 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3120: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3120 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3247: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3247 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3701: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3701 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3739: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3739 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3802: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3802 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3840: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3840 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4044: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4044 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4052: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4052 | #pragma omp for helpme_standalone.h:4097: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4097 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4145: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4145 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4172: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4172 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4224: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4224 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4228: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4228 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4275: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4275 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4388: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4388 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4419: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4503: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4503 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4510: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4510 | #pragma omp for CXX Action_Image.cpp CXX Action_InfraredSpectrum.cpp CXX Action_Jcoupling.cpp CXX Action_LESsplit.cpp CXX Action_LIE.cpp CXX Action_LipidOrder.cpp CXX Action_MakeStructure.cpp CXX Action_Mask.cpp CXX Action_Matrix.cpp CXX Action_MinImage.cpp CXX Action_Molsurf.cpp CXX Action_MultiDihedral.cpp CXX Action_MultiVector.cpp CXX Action_NAstruct.cpp CXX Action_NativeContacts.cpp CXX Action_NMRrst.cpp 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 In file included from Matrix_3x3.h:3, from Box.h:3, from Frame.h:5, from Topology.h:10, from DataSet_Coords.h:4, from DataSet_Coords_REF.h:3, from ReferenceFrame.h:3, from DataSetList.h:4, from DataFile.h:4, from DataFileList.h:3, from ActionState.h:3, from Action.h:5, from Action_GIST.h:3, from Action_GIST.cpp:3: In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:814:31: Vec3.h:76:57: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:814:31: Vec3.h:76:23: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:814:31: Vec3.h:76:40: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:814:31: Vec3.h:76:23: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:815:31: Vec3.h:76:57: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:815:31: Vec3.h:76:23: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ CXX Action_ReplicateCell.cpp CXX Action_Rmsd.cpp CXX Action_Rotate.cpp CXX Action_RunningAvg.cpp CXX Action_STFC_Diffusion.cpp CXX Action_Scale.cpp CXX Action_SetVelocity.cpp CXX Action_Spam.cpp CXX Action_Strip.cpp CXX Action_Surf.cpp CXX Action_SymmetricRmsd.cpp CXX Action_Temperature.cpp CXX Action_Time.cpp CXX Action_Translate.cpp CXX Action_Unstrip.cpp CXX Action_Unwrap.cpp CXX Action_Vector.cpp CXX Action_VelocityAutoCorr.cpp CXX Action_Volmap.cpp CXX Action_Volume.cpp CXX Action_Watershell.cpp CXX Action_XtalSymm.cpp CXX AnalysisList.cpp CXX Analysis_AmdBias.cpp CXX Analysis_AutoCorr.cpp CXX Analysis_Average.cpp CXX Analysis_Clustering.cpp CXX Analysis_Corr.cpp CXX Analysis_ConstantPHStats.cpp CXX Analysis_CrankShaft.cpp CXX Analysis_CrdFluct.cpp CXX Analysis_CrossCorr.cpp CXX Analysis_CurveFit.cpp CXX Analysis_Divergence.cpp CXX Analysis_EvalPlateau.cpp CXX Analysis_FFT.cpp CXX Analysis_HausdorffDistance.cpp CXX Analysis_Hist.cpp CXX Analysis_Integrate.cpp CXX Analysis_IRED.cpp CXX Analysis_KDE.cpp CXX Analysis_Lifetime.cpp CXX Analysis_LowestCurve.cpp CXX Analysis_Matrix.cpp CXX Analysis_MeltCurve.cpp CXX Analysis_Modes.cpp CXX Analysis_Multicurve.cpp CXX Analysis_MultiHist.cpp CXX Analysis_Overlap.cpp CXX Analysis_PhiPsi.cpp CXX Analysis_Regression.cpp CXX Analysis_RemLog.cpp CXX Analysis_Rms2d.cpp CXX Analysis_RmsAvgCorr.cpp CXX Analysis_Rotdif.cpp CXX Analysis_RunningAvg.cpp CXX Analysis_Slope.cpp CXX Analysis_Spline.cpp CXX Analysis_State.cpp CXX Analysis_Statistics.cpp CXX Analysis_TI.cpp CXX Analysis_Timecorr.cpp CXX Analysis_VectorMath.cpp CXX Analysis_Wavelet.cpp CXX ArgList.cpp CXX Array1D.cpp 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 In file included from /usr/include/c++/14/vector:66, from ArgList.h:3, from Action.h:4, from Action_XtalSymm.h:3, from Action_XtalSymm.cpp:1: In member function 'void std::vector<_Tp, _Alloc>::assign(size_type, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]', inlined from 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)' at Action_XtalSymm.cpp:57:12: /usr/include/c++/14/bits/stl_vector.h:809:23: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 809 | { _M_fill_assign(__n, __val); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:72: /usr/include/c++/14/bits/vector.tcc: In member function 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)': /usr/include/c++/14/bits/vector.tcc:270:5: note: by argument 3 of type 'const std::vector::value_type&' {aka 'const Vec3&'} to 'void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]' declared here 270 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ Action_XtalSymm.cpp:57:33: note: '' declared here 57 | T_.assign( nCopyTotal, Vec3()); | ^ In member function 'void std::vector<_Tp, _Alloc>::assign(size_type, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]', inlined from 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)' at Action_XtalSymm.cpp:58:15: /usr/include/c++/14/bits/stl_vector.h:809:23: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 809 | { _M_fill_assign(__n, __val); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/14/bits/vector.tcc: In member function 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)': /usr/include/c++/14/bits/vector.tcc:270:5: note: by argument 3 of type 'const std::vector::value_type&' {aka 'const Vec3&'} to 'void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]' declared here 270 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ Action_XtalSymm.cpp:58:33: note: '' declared here 58 | RefT_.assign(nCopyTotal, Vec3()); | ^ CXX DataIO_VecTraj.cpp CXX DataIO_Xplor.cpp CXX DataIO_XVG.cpp CXX DataSet.cpp CXX DataSetList.cpp CXX DataSet_1D.cpp CXX DataSet_3D.cpp CXX DataSet_Cmatrix.cpp CXX DataSet_Cmatrix_DISK.cpp CXX DataSet_Cmatrix_MEM.cpp CXX DataSet_Cmatrix_NOMEM.cpp CXX DataSet_Coords.cpp CXX DataSet_Coords_CRD.cpp CXX DataSet_Coords_REF.cpp CXX DataSet_Coords_TRJ.cpp CXX DataSet_GridDbl.cpp CXX DataSet_GridFlt.cpp CXX DataSet_Mat3x3.cpp CXX DataSet_MatrixDbl.cpp CXX DataSet_MatrixFlt.cpp CXX DataSet_Mesh.cpp CXX DataSet_Modes.cpp CXX DataSet_Parameters.cpp CXX DataSet_pH.cpp CXX DataSet_PHREMD_Explicit.cpp CXX DataSet_PHREMD_Implicit.cpp CXX DataSet_RemLog.cpp CXX DataSet_Topology.cpp CXX DataSet_Vector.cpp CXX DataSet_Vector_Scalar.cpp CXX DataSet_double.cpp CXX DataSet_float.cpp CXX DataSet_integer_disk.cpp CXX DataSet_integer_mem.cpp CXX DataSet_string.cpp CXX DataSet_StringVar.cpp CXX DataSet_Tensor.cpp CXX DataSet_unsignedInt.cpp CXX Deprecated.cpp CXX DihedralSearch.cpp CXX DistRoutines.cpp CXX Energy.cpp CXX EnergyArray.cpp CXX EnsembleIn.cpp CXX EnsembleIn_Multi.cpp CXX EnsembleIn_Single.cpp CXX EnsembleNavigator.cpp CXX EnsembleOut.cpp CXX EnsembleOut_Multi.cpp CXX EnsembleOut_Single.cpp CXX EnsembleOutList.cpp CXX Ewald.cpp CXX Ewald_ParticleMesh.cpp CXX Ewald_Regular.cpp CXX ExclusionArray.cpp CXX Exec_AddMissingRes.cpp CXX Exec_Analyze.cpp CXX Exec_Calc.cpp CXX Exec_CatCrd.cpp CXX Exec_Change.cpp In file included from Ewald_ParticleMesh.h:5, from Ewald_ParticleMesh.cpp:4: helpme_standalone.h:2323: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2323 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:2343: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2343 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3014: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3014 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3120: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3120 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3247: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3247 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3701: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3701 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3739: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3739 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3802: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3802 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3840: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3840 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4044: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4044 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4052: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4052 | #pragma omp for helpme_standalone.h:4097: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4097 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4145: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4145 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4172: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4172 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4224: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4224 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4228: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4228 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4275: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4275 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4388: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4388 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4419: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4503: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4503 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4510: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4510 | #pragma omp for CXX Exec_ClusterMap.cpp CXX Exec_CombineCoords.cpp CXX Exec_Commands.cpp CXX Exec_CompareTop.cpp CXX Exec_CrdAction.cpp CXX Exec_CrdOut.cpp CXX Exec_CreateSet.cpp CXX Exec_DataFile.cpp CXX Exec_DataFilter.cpp CXX Exec_DataSetCmd.cpp CXX Exec_Emin.cpp CXX Exec_Flatten.cpp CXX Exec_GenerateAmberRst.cpp CXX Exec_Graft.cpp CXX Exec_Help.cpp CXX Exec_LoadCrd.cpp helpme_standalone.h: In instantiation of 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]': helpme_standalone.h:3898:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3898 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:1010:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 1010 | for (int val = 0; val < nRows_; ++val) eigenPairs.push_back({eigenValues[val][0], unsortedEigenVectors[val]}); | ~~~~^~~~~~~~ helpme_standalone.h:1013:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 1013 | for (int val = 0; val < nRows_; ++val) { | ~~~~^~~~~~~~ CXX Exec_LoadTraj.cpp helpme_standalone.h: In instantiation of 'void helpme::PMEInstance >::sanityChecks(int, const RealMat&, const RealMat&, int) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5018:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5018 | sanityChecks(parameterAngMom, parameters, coordinates); | ^~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3198:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3198 | if (parameters.nCols() != (nCartesian(parameterAngMom) - cartesianOffset)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::PMEInstance >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5019:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5019 | filterAtomsAndBuildSplineCache(parameterAngMom, coordinates); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3746:45: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3746 | for (size_t row = threadID; row < gridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~ helpme_standalone.h:3753:37: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3753 | for (int atom = 0; atom < nAtoms; ++atom) { | ~~~~~^~~~~~~~ helpme_standalone.h:3761:61: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3761 | if (cGridIterator.size() && thisAtomsThread == threadID) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~ helpme_standalone.h:3750:25: warning: unused variable 'gridIteratorC' [-Wunused-variable] 3750 | const auto &gridIteratorC = threadedGridIteratorC_[threadID]; | ^~~~~~~~~~~~~ helpme_standalone.h:3794:55: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3794 | for (int atom = splineCache_.size(); atom < newSize; ++atom) | ~~~~~^~~~~~~~~ helpme_standalone.h:3810:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3810 | for (size_t cRow = threadID; cRow < gridDimensionC_; cRow += nThreads_) { | ~~~~~^~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'Real* helpme::PMEInstance >::spreadParameters(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5020:25: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5020 | auto realGrid = spreadParameters(parameterAngMom, parameters); | ^~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3708:45: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3708 | for (size_t row = threadID; row < myGridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'helpme::PMEInstance >::Complex* helpme::PMEInstance >::forwardTransform(Real*) [with Real = double; typename std::enable_if::value, int>::type = 0; Complex = std::complex]': helpme_standalone.h:5023:32: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5023 | auto gridAddress = forwardTransform(realGrid); | ^~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:4004:28: warning: variable 'realCBA' set but not used [-Wunused-but-set-variable] 4004 | Real *__restrict__ realCBA; | ^~~~~~~ CXX Exec_ParallelAnalysis.cpp helpme_standalone.h: In instantiation of 'void helpme::Matrix::assertSymmetric(const Real&) const [with Real = double]': helpme_standalone.h:1000:9: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 1000 | assertSymmetric(); | ^~~~~~~~~~~~~~~ helpme_standalone.h:3898:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3898 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:796:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 796 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::JacobiCyclicDiagonalization(Real*, Real*, const Real*, int) [with Real = double]': helpme_standalone.h:1006:42: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 1006 | JacobiCyclicDiagonalization(eigenValues[0], unsortedEigenVectors[0], cbegin(), nRows_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3898:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3898 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:213:20: warning: variable 'cos_2phi' set but not used [-Wunused-but-set-variable] 213 | Real sin_2phi, cos_2phi, cot_2phi; | ^~~~~~~~ helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::applyOperation(const std::function&) const [with Real = double]': helpme_standalone.h:785:26: required from 'helpme::Matrix helpme::Matrix::inverse() const [with Real = double]' 785 | return this->applyOperation([](Real& element) { element = 1 / element; }); | ~~~~~~^~~~~~~~~~~~~~ helpme_standalone.h:3910:44: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3910 | recVecs_ = boxVecs_.inverse(); | ~~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:824:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 824 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::BSpline::update(short int, Real, short int, short int) [with Real = double]': helpme_standalone.h:3829:47: required from 'void helpme::PMEInstance >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 3829 | atomSplines.aSpline.update(aStartingGridPoint, gridDimensionA_ * aCoord - aStartingGridPoint, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3830 | splineOrder_, splineDerivativeLevel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:5019:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5019 | filterAtomsAndBuildSplineCache(parameterAngMom, coordinates); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:2208:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 2208 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:2208:72: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2208 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~ CXX Exec_ParmBox.cpp helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::multiply(const helpme::Matrix&) const [with Real = double]': helpme_standalone.h:877:64: required from 'helpme::Matrix helpme::Matrix::operator*(const helpme::Matrix&) const [with Real = double]' 877 | Matrix operator*(const Matrix& other) const { return this->multiply(other); } | ~~~~~~^~~~~~~~ helpme_standalone.h:829:22: required from 'helpme::Matrix helpme::Matrix::applyOperation(const std::function&) const [with Real = double]' 829 | return evecs * evecsT; | ~~~~~~^~~~~~~~ helpme_standalone.h:785:26: required from 'helpme::Matrix helpme::Matrix::inverse() const [with Real = double]' 785 | return this->applyOperation([](Real& element) { element = 1 / element; }); | ~~~~~~^~~~~~~~~~~~~~ helpme_standalone.h:3910:44: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3910 | recVecs_ = boxVecs_.inverse(); | ~~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:860:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 860 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h:862:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 862 | for (int col = 0; col < other.nCols_; ++col) { | ~~~~^~~~~~~~~~~~~~ helpme_standalone.h:863:41: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 863 | for (int link = 0; link < nCols_; ++link) { | ~~~~~^~~~~~~~ CXX Exec_ParmSolvent.cpp CXX Exec_ParmStrip.cpp CXX Exec_ParmWrite.cpp CXX Exec_PermuteDihedrals.cpp CXX Exec_Precision.cpp CXX Exec_PrepareForLeap.cpp CXX Exec_PrintData.cpp CXX Exec_Random.cpp CXX Exec_ReadData.cpp CXX Exec_ReadEnsembleData.cpp CXX Exec_ReadInput.cpp CXX Exec_RotateDihedral.cpp CXX Exec_RunAnalysis.cpp CXX Exec_ScaleDihedralK.cpp CXX Exec_Set.cpp CXX Exec_SequenceAlign.cpp CXX Exec_Show.cpp CXX Exec_SortEnsembleData.cpp CXX Exec_SplitCoords.cpp CXX Exec_System.cpp CXX Exec_Top.cpp CXX Exec_Traj.cpp CXX Exec_UpdateParameters.cpp CXX Exec_ViewRst.cpp CXX File_TempName.cpp CXX FileIO_Bzip2.cpp CXX FileIO_Gzip.cpp CXX FileIO_Mpi.cpp CXX FileIO_MpiShared.cpp CXX FileIO_Std.cpp CXX FileName.cpp CXX FileType.cpp CXX FileTypes.cpp CXX ForLoop.cpp CXX ForLoop_dataSetBlocks.cpp CXX ForLoop_integer.cpp CXX ForLoop_list.cpp CXX ForLoop_mask.cpp CXX ForLoop_overSets.cpp CXX Frame.cpp CXX GridAction.cpp CXX HistBin.cpp CXX Hungarian.cpp CXX ImageRoutines.cpp CXX Image_List_Mask.cpp CXX Image_List_Pair.cpp CXX Image_List_Unit.cpp CXX InputTrajCommon.cpp CXX KDE.cpp CXX MapAtom.cpp CXX MaskArray.cpp CXX MaskToken.cpp CXX Matrix_3x3.cpp CXX MdOpts.cpp CXX MetaData.cpp CXX Minimize_SteepestDescent.cpp CXX Mol.cpp CXX Mol2File.cpp CXX NameType.cpp CXX NC_Cmatrix.cpp CXX NC_Routines.cpp CXX NetcdfFile.cpp CXX OMM_helpers.cpp CXX OutputTrajCommon.cpp CXX ParameterSet.cpp CXX PDBfile.cpp CXX PairList.cpp CXX Parallel.cpp CXX ParallelNetcdf.cpp CXX ParmFile.cpp CXX Parm_Amber.cpp CXX Parm_CharmmPsf.cpp CXX Parm_CIF.cpp CXX Parm_Gromacs.cpp CXX Parm_Mol2.cpp CXX Parm_PDB.cpp CXX Parm_SDF.cpp CXX Parm_Tinker.cpp CXX PotentialFunction.cpp CXX PotentialTerm.cpp CXX PotentialTerm_Angle.cpp CXX PotentialTerm_Bond.cpp CXX PotentialTerm_Dihedral.cpp CXX PotentialTerm_LJ_Coulomb.cpp CXX PotentialTerm_OpenMM.cpp CXX ProgressBar.cpp CXX ProgressTimer.cpp CXX PubFFT.cpp CXX ExternalFxn.cpp CXX Random.cpp CXX Range.cpp CXX RNG.cpp CXX RNG_Marsaglia.cpp CXX RNG_MersenneTwister.cpp CXX RNG_PCG32.cpp CXX RNG_Stdlib.cpp CXX RPNcalc.cpp CXX RNG_Xoshiro128pp.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 helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3470:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3470 | fftHelperA_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3470:31: note: '' declared here 3470 | fftHelperA_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3471:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3471 | fftHelperB_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3471:31: note: '' declared here 3471 | fftHelperB_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3472:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3472 | fftHelperC_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3472:31: note: '' declared here 3472 | fftHelperC_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3503:43: helpme_standalone.h:519:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] 519 | class Matrix { | ^~~~~~ helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3503:45: note: '' declared here 3503 | compressionCoefficientsA_ = RealMat(); | ^~~~~~~~~ In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3504:43: helpme_standalone.h:519:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] 519 | class Matrix { | ^~~~~~ helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3504:45: note: '' declared here 3504 | compressionCoefficientsB_ = RealMat(); | ^~~~~~~~~ In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3505:43: helpme_standalone.h:519:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] 519 | class Matrix { | ^~~~~~ helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3505:45: note: '' declared here 3505 | compressionCoefficientsC_ = RealMat(); | ^~~~~~~~~ CXX 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 helpme_standalone.h: In member function 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:5031:16: warning: 'energy' may be used uninitialized [-Wmaybe-uninitialized] 5031 | return energy; | ^~~~~~ helpme_standalone.h:5021:14: note: 'energy' was declared here 5021 | Real energy; | ^~~~~~ CXX TrajinList.cpp CXX Trajin_Multi.cpp CXX Trajin_Single.cpp CXX TrajIOarray.cpp CXX Trajout_Single.cpp CXX TrajoutList.cpp CXX Vec3.cpp CXX ViewRst.cpp CXX xoshiro128plusplus.cpp CXX Action_Esander.cpp xoshiro128plusplus.cpp: In function 'void jump()': xoshiro128plusplus.cpp:60:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 60 | for(int i = 0; i < sizeof JUMP / sizeof *JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ xoshiro128plusplus.cpp: In function 'void long_jump()': xoshiro128plusplus.cpp:90:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 90 | for(int i = 0; i < sizeof LONG_JUMP / sizeof *LONG_JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CXX Command.cpp CXX Cpptraj.cpp CXX Energy_Sander.cpp CXX ReadLine.cpp CXX main.cpp CC molsurf.c Skipping bundled READLINE build cd xdrfile && make all make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' CC xdrfile.c Skipping bundled ARPACK build cd tng && make all make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' CC md5.c CC xdr_seek.c CC xdrfile_trr.c CC xdrfile_xtc.c CC tng_io.c CC tng_compress.c CC coder.c CC warnmalloc.c CC fixpoint.c CC xtc3.c CC bwlzh.c CC xtc2.c CC widemuldiv.c CC huffmem.c CC vals16.c CC bwt.c CC mtf.c CC rle.c CC lz77.c CC dict.c CC huffman.c CC merge_sort.c /bin/rm -f libxdrfile.a ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' tng_io.c: In function 'tng_gen_data_block_add': tng_io.c:12600:9: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tng_io.c:12600:47: note: length computed here 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ /bin/rm -f libtng_io.a ar cqs libtng_io.a md5.o tng_io.o tng_compress.o coder.o warnmalloc.o fixpoint.o xtc3.o bwlzh.o xtc2.o widemuldiv.o huffmem.o vals16.o bwt.o mtf.o rle.o lz77.o dict.o huffman.o merge_sort.o make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o -L/usr/lib/x86_64-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/x86_64-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/x86_64-linux-gnu/lib -lfftw3 -L/usr/lib/x86_64-linux-gnu/lib -lOpenMM -lnetcdf -lbz2 tng/libtng_io.a -lz xdrfile/libxdrfile.a -Wl,-z,relro mv cpptraj "/build/reproducible-path/cpptraj-5.1.0+dfsg/bin" make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_auto_test -- check unittest make -j40 test "TESTSUITEFLAGS=-j40 --verbose" VERBOSE=1 check unittest make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' make[2]: Nothing to be done for 'test'. cd test && make test.complete summary cd unitTests && make test.complete summary make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList CPPTRAJ: NameType class unit test. CPPTRAJ: ArgList class unit test. make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' g++ -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o NameType.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/NameType.cpp make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' g++ -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o ArgList.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/ArgList.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o StringRoutines.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/StringRoutines.cpp -rwxr-xr-x 1 pbuilder1 pbuilder1 186123352 Aug 6 22:29 ../bin/cpptraj -rwxr-xr-x 1 pbuilder1 pbuilder1 186123352 Aug 6 22:29 ../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_TrajinOffset TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Strip ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_General ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RemdTraj TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DSSP ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hbond CPPTRAJ: Normal trajectory read with offsets. CPPTRAJ: Broken Traj: Running good trajectory. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_trajout_framerange CPPTRAJ: One frame strip command test CPPTRAJ: CRD Replica Trajectory Run with offset CPPTRAJ: Secstruct (DSSP) command test. CPPTRAJ: Per-Residue RMSD Test. ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Center TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Image CPPTRAJ: Solute Hbond test ******************************************************************************** CPPTRAJ: General tests TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NCrestart ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radgyr CPPTRAJ: Trajout Frame Range [Amber Restart] ******************************************************************************** CPPTRAJ: Center command test. TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Jcoupling CPPTRAJ: Orthorhombic imaged distance test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diffusion ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf CPPTRAJ: Radius of gyration command test CPPTRAJ: NetCDF Restart Test - TXT->NetCDF TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotdif ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm ******************************************************************************** CPPTRAJ: J-Coupling single frame test TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_2DRMS ******************************************************************************** CPPTRAJ: RMSD Test with outtraj. TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mol2 CPPTRAJ: Surface calculation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Average ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RMSD ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Runavg CPPTRAJ: Diffusion test, no imaging. ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mask TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomMap ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pucker ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Datafile CPPTRAJ: NAstruct command test. ******************************************************************************** CPPTRAJ: Average Test. TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj CPPTRAJ: Mol2 Parm/Traj Read/Write Test. CPPTRAJ: Coordinate Running Average test. CPPTRAJ: 2D RMSD Test. CPPTRAJ: Basic RMSD tests CPPTRAJ: CHARMM PSF/DCD test CPPTRAJ: AtomMap Test CPPTRAJ: Pucker command test CPPTRAJ: Mask single frame test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial CPPTRAJ: Data file output precision test CPPTRAJ: Convert mdcrd -> NetCDF ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist CPPTRAJ: Rotational diffusion calculation test CPPTRAJ: 1D/2D Histogram Analysis test CPPTRAJ: Radial test, non-orthogonal imaging ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest CPPTRAJ: Gzipped trajectory read with offsets CPPTRAJ: Closest command test using first solvent atom. CPPTRAJ: CRD Replica Trajectory Run CPPTRAJ: NetCDF Restart Test - NetCDF->TXT J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DRMSD Skipped test: J-Coupling extended test CPPTRAJ: 2D RMSD Test, mass-weighted. All 1 comparisons passed. 1 comparisons skipped. CPPTRAJ: Distance RMSD test CPPTRAJ: Broken Traj: Running broken trajectory. CPPTRAJ: CHARMM DCD Write, step 1. All 2 comparisons passed. CPPTRAJ: Center origin command test. CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster CPPTRAJ: PDB => Mol2 CPPTRAJ: Non-orthorhombic imaged distance test. All 2 comparisons passed. CPPTRAJ: Cluster command test, in-memory pairwise distances. CPPTRAJ: Coordinate Running Average Traj Write CPPTRAJ: Diffusion test, old syntax. CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. CPPTRAJ: Per-Residue RMSD Test with averaging CPPTRAJ: Standard -> Grace Data ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_IRED All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons CPPTRAJ: Mask longer command test. CPPTRAJ: IRED vector/matrix test CPPTRAJ: randomizeions test (original algorithm) CPPTRAJ: Trajout Frame Range [Amber Coordinates] CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF CPPTRAJ: AtomMap with 'rmsfit' CPPTRAJ: Bzip2ed trajectory read with offsets ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Molsurf CPPTRAJ: Solute Hbond test with disk caching CPPTRAJ: NetCDF Replica Trajectory Run test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Corr CPPTRAJ: CHARMM DCD Write, step 2. CPPTRAJ: Molsurf test CPPTRAJ: Unstrip (Lig/Rec/Complex) command test CPPTRAJ: Correlation test CPPTRAJ: 2D RMSD Test with reference trajectory CPPTRAJ: Amber Top/Rst => Mol2 All 2 comparisons passed. CPPTRAJ: NAstruct command test, single strand CPPTRAJ: 3D histogram test. CPPTRAJ: Center origin mass command test. CPPTRAJ: Orthorhombic coordinate imaging test CPPTRAJ: Grace -> Standard Data CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckStructure CPPTRAJ: Structure Check All 6 comparisons passed. CPPTRAJ: Secstruct (DSSP) command with changing number of residues. CPPTRAJ: Atom map charmm->amber atom order CPPTRAJ: RMS coordinate rotation/rotation matrices test CPPTRAJ: Convert NetCDF -> mdcrd CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj CPPTRAJ: Per-Residue RMSD Test with residue centering. CPPTRAJ: CHAMBER topology read/strip test. CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt All 1 comparisons passed. 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: Cluster command test, read pairwise distances. CPPTRAJ: 2D DME Test. All 5 comparisons passed. CPPTRAJ: Start argument offset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RmsAvgCorr CPPTRAJ: RmsAvgCorr Reference CPPTRAJ: Solute-solvent hbond test All 11 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Contacts ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Principal CPPTRAJ: Contacts test. CPPTRAJ: Closest command test using all solvent atoms. All 7 comparisons passed. CPPTRAJ: Principal Test All 3 comparisons passed. All 2 comparisons passed. CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj CPPTRAJ: Diffusion test, new syntax. CPPTRAJ: Read CHARMM restart ******************************************************************************** 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_NAstruct_8OG ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Vector ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Matrix CPPTRAJ: NA test (8OG) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct CPPTRAJ: Basic vector tests CPPTRAJ: Matrix Tests CPPTRAJ: X column format/precision test. CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. CPPTRAJ: Center reference command test. All 4 comparisons passed. CPPTRAJ: Structure Check with Around and Skip CPPTRAJ: Nonorthorhombic coordinate imaging test CPPTRAJ: 2D RMSD with reference mask test. CPPTRAJ: Secstruct (DSSP): SS assign output test CPPTRAJ: Atom map charmm->amber atom order, by residue All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Grid All 3 comparisons passed. CPPTRAJ: RmsAvgCorr First CPPTRAJ: Dipole test CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj CPPTRAJ: RMS fit with no coordinates modification test. CPPTRAJ: CHARMM PSF write ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Project CPPTRAJ: Cluster command test, read NetCDF pairwise distances. All 3 comparisons passed. CPPTRAJ: Projection CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Unwrap CPPTRAJ: Hbond, no intramolecular hydrogen bonds test CPPTRAJ: Diffusion test, nonorthogonal box CPPTRAJ: Unwrap non-orthogonal test CPPTRAJ: FtuFabI Assignment test CPPTRAJ: Compressed broken trajectory test All 4 comparisons passed. CPPTRAJ: 2D RMSD test, no fitting. CPPTRAJ: Data file group by name test CPPTRAJ: Multi frame strip command test. All 9 comparisons passed. CPPTRAJ: CHARMM COORdinates test CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj CPPTRAJ: Center point test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AnalysisRunAvg All 3 comparisons passed. CPPTRAJ: Analysis Running Average All 3 comparisons passed. All 1 comparisons passed. CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Watershell CPPTRAJ: Grid test CPPTRAJ: Modes analysis, RMS fluctuations CPPTRAJ: Watershell Test, non-orthorhombic imaging. CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SPAM All 1 comparisons passed. CPPTRAJ: SPAM Test CPPTRAJ: Cluster command test, write ASCII pairwise distances. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volmap CPPTRAJ: CRD Replica Trajectory Run with remdout CPPTRAJ: Test vector center with magnitude All 6 comparisons passed. CPPTRAJ: Strip topology with PDB info CPPTRAJ: VMD VolMap Algorithm test All 5 comparisons passed. CPPTRAJ: STFC Diffusion Test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LIE CPPTRAJ: LIE test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidOrder CPPTRAJ: Data file group by aspect test CPPTRAJ: Lipid Order Parameter Test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Density CPPTRAJ: Density along axis tests CPPTRAJ: Modes analysis, displacements CPPTRAJ: RMS fit to previous test CPPTRAJ: Unwrap orthogonal test CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CharmmParams CPPTRAJ: Cluster command test, read ASCII pairwise distances. CPPTRAJ: Test updating topology with Charmm parameters (single residue) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PairDist All 2 comparisons passed. CPPTRAJ: Closest command test, using mask center CPPTRAJ: PairDist Test. All 10 comparisons passed. CPPTRAJ: Hbond, specified solute masks ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReadData All 11 comparisons passed. CPPTRAJ: Read vector data test (no origins, origins) CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM All 8 comparisons passed. CPPTRAJ: Momentum/velocity vector test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST CPPTRAJ: GIST water-water interaction test CPPTRAJ: OpenDX Grid read test CPPTRAJ: STFC Diffusion Test with individual distances CPPTRAJ: Modes analysis, dipole correlation ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicCorr CPPTRAJ: Atomic Correlation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_systemVF CPPTRAJ: Outtraj Test with maxmin. All 6 comparisons passed. CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test CPPTRAJ: RMS: imaging after unit cell rotation ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr CPPTRAJ: Atomicfluct test with ADP output CPPTRAJ: AutoCorr test. All 9 comparisons passed. All 2 comparisons passed. VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. Skipped test: VMD VolMap Algorithm longer tests All 2 comparisons passed. 1 comparisons skipped. CPPTRAJ: Structure Check with PBC All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Box ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve CPPTRAJ: Read vector data set (origins, no origins) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomTypeSelect CPPTRAJ: Box Test (Add box info) CPPTRAJ: Hbond, no angle cutoff test CPPTRAJ: Cluster, nosieve CPPTRAJ: Selection by atom type test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AvgRef CPPTRAJ: Closest command test, using mask center and solvent mask CPPTRAJ: RMSD Test with averaged reference coordinates. CPPTRAJ: Partial Surface calculation test CPPTRAJ: Force vector test. CPPTRAJ: STFC Diffusion Test with COM All 1 comparisons passed. All 1 comparisons passed. All 12 comparisons passed. All 15 comparisons passed. CPPTRAJ: Grid with specified center test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Crank_Stat All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LoadCrd ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Parallel ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoImage CPPTRAJ: Parallel tests. CPPTRAJ: LoadCrd test. CPPTRAJ: Crankshaft test CPPTRAJ: AutoImage test (split DNA duplex) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateCrd CPPTRAJ: Read Amber output test All 4 comparisons passed. CPPTRAJ: COORDS data set creation and CRDFLUCT test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MultiVector All 1 comparisons passed. CPPTRAJ: Hbond, Bridge nointramol test CPPTRAJ: Multivector test CPPTRAJ: Pairdist test, orthogonal imaging. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Lifetime CPPTRAJ: Multi-frame density along axis test All 1 comparisons passed. CPPTRAJ: Lifetime test. All 14 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FFT CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Timecorr CPPTRAJ: FFT test. CPPTRAJ: STFC Diffusion Test with second mask CPPTRAJ: Timecorr test. CPPTRAJ: Box test (remove box info) CPPTRAJ: Generate matrix with trajectory start/stop/offset All 6 comparisons passed. CPPTRAJ: SPAM Pure Solvent Test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CrossCorr CPPTRAJ: Cluster, sieve5 CPPTRAJ: Closest command test, solvent mask, water oxygen only CPPTRAJ: CrossCorr test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SymmRmsd CPPTRAJ: Modes analysis, pseudo trajectory creation test CPPTRAJ: SymmRmsd CPPTRAJ: Radial test, orthogonal and no imaging ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidSCD CPPTRAJ: LoadTraj test. All 3 comparisons passed. CPPTRAJ: Basic lipid order parameter test CPPTRAJ: COORDS data set creation with velocities test All 1 comparisons passed. CPPTRAJ: Read CHARMM output test CPPTRAJ: Grid with box center offset test. All 3 comparisons passed. CPPTRAJ: Generate matrix with action stop/start/offset CPPTRAJ: Box test (Modify box length) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MakeStructure CPPTRAJ: Parallel test with trajectory offset CPPTRAJ: Basic makestructure test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multidihedral All 1 comparisons passed. CPPTRAJ: Multidihedral test CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ensemble_MREMD CPPTRAJ: LoadTraj from trajin test. CPPTRAJ: ASP symmetry-corrected RMSD test CPPTRAJ: M-REMD sort test. CPPTRAJ: Lifetime test with data set caching. CPPTRAJ: 3D data read/write test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotate CPPTRAJ: Rotation (and inverse) of coords from matrices All 5 comparisons passed. All 1 comparisons passed. All 7 comparisons passed. All 15 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Integrate CPPTRAJ: Total system density test CPPTRAJ: NativeContacts test. CPPTRAJ: Integration test. CPPTRAJ: Grid with mask center offset test. All 9 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 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LESsplit CPPTRAJ: Simple energy tests CPPTRAJ: Box test (auto orthogonal box, no radii) CPPTRAJ: Cluster, nosieve savepairdist CPPTRAJ: LES split/average test All 6 comparisons passed. CPPTRAJ: GLU symmetry-corrected RMSD test CPPTRAJ: LoadCrd append from multiple files test CPPTRAJ: Standard 3D data write test CPPTRAJ: Multidihedral Nucleotide CHI test All 13 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PermuteDihedrals ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CCP4 CPPTRAJ: PermuteDihedrals interval -120, phi psi CPPTRAJ: CCP4 read/write and DX conversion test. CPPTRAJ: Makestructure test with reference. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihCovar All 1 comparisons passed. CPPTRAJ: Dihedral Covariance Matrix Test CPPTRAJ: Box test (auto orthogonal box, VDW radii) CPPTRAJ: Rotate with defined axis ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CurveFit CPPTRAJ: TYR symmetry-corrected RMSD test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetAverage CPPTRAJ: Randomize (around, overlap) CPPTRAJ: Data set averaging and averaging over all sets test. CPPTRAJ: Curve fitting test. CPPTRAJ: Multidihedral protein dihedrals test CPPTRAJ: Standard 3D data read test All 4 comparisons passed. CPPTRAJ: New Lipid Order Parameter Test, DOPC. All 7 comparisons passed. All 5 comparisons passed. CPPTRAJ: M-REMD actions test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VectorMath ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander CPPTRAJ: Vector dot/cross product test SANDER energy tests (long) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. CPPTRAJ: Non-orthogonal grid test. SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. SKIP: SANDER energy tests (long) CPPTRAJ: Cluster, nosieve loadpairdist CPPTRAJ: Lifetime average and cumulative average test. CPPTRAJ: PermuteDihedrals, random rotations All 2 comparisons passed. All 7 comparisons passed. CPPTRAJ: TRAJ data set creation and CRDFLUCT test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Temperature CPPTRAJ: Multidihedral cyclic molecule test CPPTRAJ: Temperature test. ******************************************************************************** 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. All 3 comparisons passed. CPPTRAJ: Longer symmetry-corrected RMSD test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Spline CPPTRAJ: Curve fitting multi-exponential tests. CPPTRAJ: Spline test CPPTRAJ: Standard 3D data read/append test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_KDE All 7 comparisons passed. CPPTRAJ: LCPO test with GAFF atom types CPPTRAJ: KDE test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PDB ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Wavelet ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CIF CPPTRAJ: PDB format read/write test CPPTRAJ: Wavelet analysis test CPPTRAJ: CIF read test All 2 comparisons passed. All 16 comparisons passed. All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Align All 12 comparisons passed. CPPTRAJ: Temperature with SHAKE on hydrogens. CPPTRAJ: Align Tests. All 3 comparisons passed. All 4 comparisons passed. All 1 comparisons passed. CPPTRAJ: TRAJ data set creation with velocities test. CPPTRAJ: M-REMD ensemble outtraj test. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RotateDihedral ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetCmd All 8 comparisons passed. All 3 comparisons passed. CPPTRAJ: Data Set commands test CPPTRAJ: Cluster, sieve5 savepairdist CPPTRAJ: Rotate dihedral to target value. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelocityAutoCorr All 4 comparisons passed. CPPTRAJ: Velocity autocorrelation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelFrc ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remap ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Filter CPPTRAJ: Remap Test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CompareTop CPPTRAJ: Basic filter test CPPTRAJ: Compare topology test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TopInfo CPPTRAJ: Test combining coordinates, velocities, and forces. CPPTRAJ: Test kinetic energy calculation CPPTRAJ: Standard 3D data, sparse ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CombineCrd ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTrr CPPTRAJ: TRR force/velocity read -> NetCDF write test CPPTRAJ: Topology info print test. CPPTRAJ: Temperature with SHAKE on all atoms. CPPTRAJ: Combine COORDS test. CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test CPPTRAJ: NativeContacts test, save non-native contacts, residue time series All 1 comparisons passed. CPPTRAJ: M-REMD no sort, running average test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ewald CPPTRAJ: AutoImage test, use anchor mask CPPTRAJ: Direct sum test CPPTRAJ: Test using velocities as coordinates. CPPTRAJ: Rotate dihedral by increment CPPTRAJ: Test total energy calculation ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TI CPPTRAJ: Nonorthogonal grid standard write/read tests. CPPTRAJ: TI analysis test. All 1 comparisons passed. CPPTRAJ: Curve fitting, custom output range. CPPTRAJ: Generate offset traj from PDB ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds CPPTRAJ: Temperature calc with extra points. CPPTRAJ: Combine COORDS test with box info. CPPTRAJ: COORDS data set append test CPPTRAJ: Align, unit cell rotation/imaging test. CPPTRAJ: Fix imaged bonds test (Ortho.) CPPTRAJ: PQR file write with various radii CPPTRAJ: Test partial energy calculation CPPTRAJ: Wavelet WAFEX test CPPTRAJ: Rotate dihedral in TRAJ data set CPPTRAJ: M-REMD, generate RMS data CPPTRAJ: Test writing velocities (MDVEL) CPPTRAJ: Data filter test. CPPTRAJ: Grid generation from 'bounds' test. All 10 comparisons passed. All 6 comparisons passed. All 3 comparisons passed. CPPTRAJ: KDE with Kullback-Leibler divergence test CPPTRAJ: Generate offset traj from CIF All 5 comparisons passed. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Distance CPPTRAJ: Distance tests CPPTRAJ: NativeContacts test, orthorhombic imaging. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multicurve CPPTRAJ: Multicurve test All 2 comparisons passed. All 3 comparisons passed. CPPTRAJ: COORDS test storing frame metadata CPPTRAJ: M-REMD, meltcurve analysis ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volume ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remlog CPPTRAJ: Volume tests CPPTRAJ: Filter matrix test. ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AreaPerMol TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DistBasedMask CPPTRAJ: Replica log read/analyze test. CPPTRAJ: Test using forces as coordinates. CPPTRAJ: Distance-based atom mask tests (atom, residue) CPPTRAJ: Area per molecule test CPPTRAJ: PDB filter alternate atom location IDs test All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SetVelocity CPPTRAJ: Orthogonal imaged distance CPPTRAJ: Fix imaged bonds test (Non-ortho.) CPPTRAJ: Set Velocity test All 17 comparisons passed. All 4 comparisons passed. All 1 comparisons passed. CPPTRAJ: TRR force/velocity read -> TRR write test CPPTRAJ: Hbond with imaging All 5 comparisons passed. CPPTRAJ: Split coords and recombine test. CPPTRAJ: Cluster, sieve5 loadpairdist ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Calc ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CalcState All 13 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Change CPPTRAJ: Calcstate test CPPTRAJ: Test writing forces (MDFRC) CPPTRAJ: Change atom and residue name tests All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateReservoir ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixAtomOrder All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LowestCurve CPPTRAJ: Calc test CPPTRAJ: Out of order molecules test CPPTRAJ: LowestCurve test CPPTRAJ: Create RREMD NetCDF reservoir test All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MinImage ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Regress CPPTRAJ: Minimum Image test. All 1 comparisons passed. CPPTRAJ: Non-orthogonal imaged distance CPPTRAJ: Distance-based atom mask tests (molecule) CPPTRAJ: Linear regression test. All 3 comparisons passed. CPPTRAJ: Scale velocity test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rst ******************************************************************************** CPPTRAJ: Hbond, orthogonal imaging TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pairwise All 7 comparisons passed. CPPTRAJ: Generate restraints (rst) test CPPTRAJ: Pairwise tests CPPTRAJ: Change chain ID test CPPTRAJ: Structure Check with Around CPPTRAJ: CRD => TRR All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Solvent ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ParmBox ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Translate All 4 comparisons passed. CPPTRAJ: Parmbox test CPPTRAJ: Test solvent command with closest CPPTRAJ: Translate test All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReplicateCell CPPTRAJ: Replicate cell test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ScaleDihedralK CPPTRAJ: Scale dihedral force constant test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PhiPsi All 3 comparisons passed. CPPTRAJ: Phipsi test All 1 comparisons passed. CPPTRAJ: Topology info with reference coords test CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. CPPTRAJ: Change chain ID of COORDS set test CPPTRAJ: Pairdist test, nonorthogonal imaging. CPPTRAJ: TRAJ test storing frame metadata CPPTRAJ: Adding PDB info to topology CPPTRAJ: Calc test with data sets ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Control All 1 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_InfraredSpec CPPTRAJ: Loop tests CPPTRAJ: Infrared spectrum calculation test All 1 comparisons passed. All 6 comparisons passed. All 3 comparisons passed. All 23 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cphstats ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CmdLine CPPTRAJ: Explicit pH REMD ensemble data read / sort All 1 comparisons passed. All 1 comparisons passed. CPPTRAJ: Command line trajectory args test, part 1 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XYZformat CPPTRAJ: XYZ format write All 17 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hausdorff ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CatCrd CPPTRAJ: Scale dihedral force constant with 'useall' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XtalSymm ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Time CPPTRAJ: Concatenate COORDS data set test All 1 comparisons passed. CPPTRAJ: Simple Hausdorff distance test. CPPTRAJ: Add time to restart test CPPTRAJ: XtalSymm Reference All 12 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihedralRMS CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Slope ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SplitCoords All 1 comparisons passed. All 3 comparisons passed. CPPTRAJ: SplitCoords test CPPTRAJ: Finite difference test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diagmatrix CPPTRAJ: MW covariance matrix thermo analysis test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Emin CPPTRAJ: Basic energy minimization test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Graft ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau CPPTRAJ: Graft test CPPTRAJ: Evalulate plateau test CPPTRAJ: Pairwise test, partial system CPPTRAJ: Test math functions CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. All 10 comparisons passed. All 2 comparisons passed. CPPTRAJ: Remove time from restart test CPPTRAJ: Randomize (around) CPPTRAJ: TRR => CRD CPPTRAJ: Command line test trajectory args test, part 2 CPPTRAJ: Hausdorff distance of 2D rms output test. All 1 comparisons passed. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Flatten All 1 comparisons passed. CPPTRAJ: Flatten test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Random CPPTRAJ: Constant pH stats test CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs CPPTRAJ: Cluster, nosieve pairwisecache none CPPTRAJ: Test set command All 1 comparisons passed. All 1 comparisons passed. CPPTRAJ: Atom XYZ format read, test 1 CPPTRAJ: Dihedral RMSD test (to previous) All 8 comparisons passed. All 4 comparisons passed. All 1 comparisons passed. CPPTRAJ: Energy minimization with angle term test. All 1 comparisons passed. All 6 comparisons passed. CPPTRAJ: Add time to trajectory test All 2 comparisons passed. CPPTRAJ: PCG32 RNG test. All 1 comparisons passed. CPPTRAJ: Command line wildcard test, part 1 g++ -o a.out main.o NameType.o CpptrajStdio.o All 10 comparisons passed. CPPTRAJ: Dihedral RMS fluctuation test. CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. CPPTRAJ: Sorted implicit constant pH stats test CPPTRAJ: Atom XYZ format read, test 2 All 8 comparisons passed. CPPTRAJ: Test Stdlib RNG All 5 comparisons passed. CPPTRAJ: Command line wildcard test, part 2 CPPTRAJ: Test reading comma-separated list of strings CPPTRAJ: Energy minimization with nonbond term test. CPPTRAJ: Test Mersenne Twister RNG CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats CPPTRAJ: Hausdorff distance of 2D rms output test. All 5 comparisons passed. All 2 comparisons passed. CPPTRAJ: Atom XYZ format read, test 3 CPPTRAJ: Test nested loops and variables in loops CPPTRAJ: Modify time info test. All 4 comparisons passed. CPPTRAJ: Ewald test (NaCl crystal) CPPTRAJ: Atom XYZ format read, test 4 All 4 comparisons passed. CPPTRAJ: Test loop over data set blocks CPPTRAJ: Unsorted pH read/write test CPPTRAJ: CRD(1-5) => TRR CPPTRAJ: Cluster, sieve5 pairwisecache none CPPTRAJ: Ewald test (trunc. oct) make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' CPPTRAJ: Atom XYZ format read, test 5 All 16 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: Test for filename wildcards and oversets All 3 comparisons passed. CPPTRAJ: Atom XYZ format read, test 6 CPPTRAJ: Cluster, random CPPTRAJ: CRD(6-10) => TRR All 13 comparisons passed. CPPTRAJ: OpenMM basic energy minimization tests (bonds) CPPTRAJ: XtalSymm Reimaging by Atom All 4 comparisons passed. All 6 comparisons passed. CPPTRAJ: OpenMM basic energy minimization tests (angles) All 28 comparisons passed. CPPTRAJ: TRR (appended) => CRD ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) All 1 comparisons passed. CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) CPPTRAJ: Read specific columns test. CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). CPPTRAJ: Watershell Test, orthorhombic imaging. CPPTRAJ: Write non-square matrix CPPTRAJ: GMX: CRD with offset CPPTRAJ: Ewald test (partial system, trunc. oct) CPPTRAJ: Read non-square matrix CPPTRAJ: Read square matrix CPPTRAJ: GMX: TRR with offset CPPTRAJ: Randomize (overlap) All 15 comparisons passed. All 4 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. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LibPME CPPTRAJ: Clustering, One DataSet CPPTRAJ: Particle mesh Ewald test (NaCl crystal) All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc CPPTRAJ: XTC read test CPPTRAJ: Clustering, Two DataSets CPPTRAJ: Particle mesh Ewald test (trunc. oct) CPPTRAJ: Watershell Test, no imaging. CPPTRAJ: Pairdist test, 2 masks. CPPTRAJ: Randomize (no restrictions) CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) All 5 comparisons passed. All 4 comparisons passed. CPPTRAJ: Clustering, dihedral DataSet CPPTRAJ: CRD => XTC All 5 comparisons passed. All 3 comparisons passed. CPPTRAJ: Clustering, two dihedral DataSets CPPTRAJ: GIST test, orthogonal cell CPPTRAJ: Clustering, dihedral DataSet, K-means CPPTRAJ: XTC => CRD CPPTRAJ: Particle mesh Ewald test (ortho) CPPTRAJ: Clustering, two dihedral DataSets, K-means CPPTRAJ: Particle mesh Ewald test (ortho, with mask) CPPTRAJ: CRD(1-5) => XTC g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' Unit test passed. make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ: PME test (partial system, trunc. oct) CPPTRAJ: XtalSymm Reimaging by Molecule CPPTRAJ: CRD(6-10) => XTC All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN CPPTRAJ: DBSCAN test CPPTRAJ: DBSCAN automatic parameter determination test. All 5 comparisons passed. All 9 comparisons passed. 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: DBSCAN kdist map test CPPTRAJ: XTC (appended) => CRD CPPTRAJ: DBSCAN with sieve CPPTRAJ: LJ PME kappa sweep test, 0.35 All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans CPPTRAJ: Cpptraj Kmeans CPPTRAJ: Cpptraj Kmeans random CPPTRAJ: LJ PME kappa sweep test, 0.45 CPPTRAJ: GMX: CRD with offset CPPTRAJ: LJ PME kappa sweep test, 0.5 All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_SymmRMSD CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) All 3 comparisons passed. CPPTRAJ: LJ with switch function test CPPTRAJ: GMX: XTC with offset All 5 comparisons passed. All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites CPPTRAJ: Cluster command test, coordinate writes. All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTNG CPPTRAJ: TNG read test CPPTRAJ: Cluster command test, coordinate writes using info file. CPPTRAJ: GIST test, nonorthogonal cell All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Dpeaks CPPTRAJ: Density peaks clustering test CPPTRAJ: TNG read test (with offset) All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Nreps CPPTRAJ: Clustering with specified # reps All 6 comparisons passed. All 2 comparisons passed. All 11 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST_Order CPPTRAJ: TIP3P water cluster test CPPTRAJ: TIP4P water cluster test CPPTRAJ: TIP5P water cluster test All 4 comparisons passed. make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' /usr/bin/make -C test summary make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' -rwxr-xr-x 1 pbuilder1 pbuilder1 186123352 Aug 6 22:29 ../bin/cpptraj ===================== TEST SUMMARY ====================== 853 out of 859 comparisons OK (0 failed, 0 warnings, 6 skipped). 480 out of 480 program executions completed. 170 out of 173 tests completed with no issues. 2 tests skipped. ========================================================= make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/cpptraj/ make -j40 install DESTDIR=/build/reproducible-path/cpptraj-5.1.0\+dfsg/debian/cpptraj AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make install make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' Skipping bundled READLINE build Skipping bundled ARPACK build g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o -L/usr/lib/x86_64-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/x86_64-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/x86_64-linux-gnu/lib -lfftw3 -L/usr/lib/x86_64-linux-gnu/lib -lOpenMM -lnetcdf -lbz2 tng/libtng_io.a -lz xdrfile/libxdrfile.a -Wl,-z,relro mv cpptraj "/build/reproducible-path/cpptraj-5.1.0+dfsg/bin" make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libreadline8t64 from: /lib/x86_64-linux-gnu/libreadline.so.8 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libreadline8t64 to: /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'cpptraj' in '../cpptraj_5.1.0+dfsg-4_amd64.deb'. dpkg-deb: building package 'cpptraj-dbgsym' in '../cpptraj-dbgsym_5.1.0+dfsg-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../cpptraj_5.1.0+dfsg-4_amd64.buildinfo dpkg-genchanges --build=binary -O../cpptraj_5.1.0+dfsg-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/2415790 and its subdirectories I: Current time: Wed Aug 6 10:30:05 -12 2025 I: pbuilder-time-stamp: 1754519405 Wed Aug 6 22:30:06 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Wed Aug 6 22:30:06 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Wed Aug 6 22:30:06 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Wed Aug 6 22:30:06 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Biybgh' ==================================================================================== Wed Sep 9 04:53:07 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "2 cpptraj unstable /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4 5.1.0+dfsg-4" as arguments. Wed Sep 9 04:53:07 UTC 2026 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-J4qH9VRJ" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Sep 9 04:53:07 UTC 2026 I: Downloading source for unstable/cpptraj=5.1.0+dfsg-4 Reading package lists... NOTICE: 'cpptraj' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/cpptraj.git Please use: git clone https://salsa.debian.org/debichem-team/cpptraj.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 28.4 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main cpptraj 5.1.0+dfsg-4 (dsc) [2184 B] Get:2 http://deb.debian.org/debian unstable/main cpptraj 5.1.0+dfsg-4 (tar) [28.4 MB] Get:3 http://deb.debian.org/debian unstable/main cpptraj 5.1.0+dfsg-4 (diff) [6084 B] Fetched 28.4 MB in 2s (17.8 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'cpptraj' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/cpptraj.git Please use: git clone https://salsa.debian.org/debichem-team/cpptraj.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 28.4 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main cpptraj 5.1.0+dfsg-4 (dsc) [2184 B] Get:2 http://deb.debian.org/debian unstable/main cpptraj 5.1.0+dfsg-4 (tar) [28.4 MB] Get:3 http://deb.debian.org/debian unstable/main cpptraj 5.1.0+dfsg-4 (diff) [6084 B] Fetched 28.4 MB in 2s (17.8 MB/s) Download complete and in download only mode ============================================================================= Re-Building cpptraj in unstable on amd64 on ionos15-amd64 now. Date: Wed Sep 9 04:53:09 UTC 2026 Date UTC: Wed Sep 9 04:53:09 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4 + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/pbuilderrc_J1VS + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' cpptraj = debian-installer -o cpptraj = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' cpptraj = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/pbuilderrc_J1VS --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/b2 --logfile b2/build.log cpptraj_5.1.0+dfsg-4.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Sep 9 18:53:09 +14 2026 I: pbuilder-time-stamp: 1788929589 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [cpptraj_5.1.0+dfsg-4.dsc] I: copying [./cpptraj_5.1.0+dfsg.orig.tar.xz] I: copying [./cpptraj_5.1.0+dfsg-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./cpptraj_5.1.0+dfsg-4.dsc: 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-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-system-libraries.patch dpkg-source: info: applying skip-failing-test.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/503249/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Sep 9 04:53 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/503249/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/503249/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=70e375baa18a45ac8df32afa5538549f LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=503249 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/pbuilderrc_J1VS --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/b2 --logfile b2/build.log cpptraj_5.1.0+dfsg-4.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/503249/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), gfortran, libarpack2-dev, libbz2-dev, libfftw3-dev, libnetcdf-dev, libopenmm-dev, libreadline-dev, netcdf-bin dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19850 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on libarpack2-dev; however: Package libarpack2-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on libnetcdf-dev; however: Package libnetcdf-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmm-dev; however: Package libopenmm-dev is not installed. pbuilder-satisfydepends-dummy depends on libreadline-dev; however: Package libreadline-dev is not installed. pbuilder-satisfydepends-dummy depends on netcdf-bin; however: Package netcdf-bin is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran{a} gfortran-14{a} gfortran-14-x86-64-linux-gnu{a} gfortran-x86-64-linux-gnu{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarpack2-dev{a} libarpack2t64{a} libblas-dev{a} libblas3{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libffi8{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-quad3{a} libfftw3-single3{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-310{a} libhdf5-cpp-310{a} libhdf5-dev{a} libhdf5-fortran-310{a} libhdf5-hl-310{a} libhdf5-hl-cpp-310{a} libhdf5-hl-fortran-310{a} libidn2-0{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-dev{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libncurses-dev{a} libncurses6{a} libnetcdf-dev{a} libnetcdf22{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libopenmm-dev{a} libopenmm8.1{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} libreadline-dev{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsz2{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2{a} libxml2-dev{a} libzstd-dev{a} m4{a} man-db{a} netcdf-bin{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 131 newly installed, 0 to remove and 0 not upgraded. Need to get 64.2 MB of archives. After unpacking 249 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-3+b3 [56.7 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 25 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-2.1 [698 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-19 [836 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libgfortran-14-dev amd64 14.2.0-19 [880 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-19 [11.7 MB] Get: 36 http://deb.debian.org/debian unstable/main amd64 gfortran-14 amd64 14.2.0-19 [14.5 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1 [1284 B] Get: 38 http://deb.debian.org/debian unstable/main amd64 gfortran amd64 4:14.2.0-1 [1436 B] Get: 39 http://deb.debian.org/debian unstable/main amd64 hdf5-helpers amd64 1.14.5+repack-3 [26.6 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 43 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 52 http://deb.debian.org/debian unstable/main amd64 libaec-dev amd64 1.1.3-1+b1 [21.5 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-5 [159 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-5 [2448 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libarpack2t64 amd64 3.9.1-6 [104 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.1-5 [170 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.1-5 [4991 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libarpack2-dev amd64 3.9.1-6 [120 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.8-2 [24.1 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1 [76.0 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.14.1-2 [384 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-2 [598 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-3 [455 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-3 [455 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-2 [103 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-3 [1406 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.10+dfsg-1 [312 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1.1 [116 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.5.1-1 [2954 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.14.1-2 [503 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.14.1-2 [391 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libfftw3-double3 amd64 3.3.10-2+b1 [781 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libfftw3-long3 amd64 3.3.10-2+b1 [347 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libfftw3-quad3 amd64 3.3.10-2+b1 [618 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libfftw3-single3 amd64 3.3.10-2+b1 [809 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libfftw3-bin amd64 3.3.10-2+b1 [51.3 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libfftw3-dev amd64 3.3.10-2+b1 [2118 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libhdf5-cpp-310 amd64 1.14.5+repack-3 [133 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libhdf5-fortran-310 amd64 1.14.5+repack-3 [111 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [69.3 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-fortran-310 amd64 1.14.5+repack-3 [43.9 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-cpp-310 amd64 1.14.5+repack-3 [24.4 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-4 [292 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-4 [72.2 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libhdf5-dev amd64 1.14.5+repack-3 [3165 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libncurses-dev amd64 6.5+20250216-2 [353 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libnetcdf22 amd64 1:4.9.3-1 [517 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-2.1 [794 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libnetcdf-dev amd64 1:4.9.3-1 [116 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-11 [1059 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libopenmm-dev amd64 8.1.2+dfsg-11 [346 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libreadline-dev amd64 8.2-6 [153 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 netcdf-bin amd64 1:4.9.3-1 [260 kB] Fetched 64.2 MB in 1s (88.8 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 ... 19850 files and directories currently installed.) Preparing to unpack .../000-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/503249/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/503249/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/cpptraj-5.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../cpptraj_5.1.0+dfsg-4_source.changes dpkg-buildpackage: info: source package cpptraj dpkg-buildpackage: info: source version 5.1.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' touch config.h external.config.h dh_auto_clean make -j42 clean make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' /bin/rm -f SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o cpptraj *.LIBCPPTRAJ.o libcpptraj # cd readline && make clean cd xdrfile && make clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' /bin/rm -f *.o libxdrfile.a a.out test.trr test.xtc test.xdr make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' # cd arpack && make clean cd cuda_kernels && make clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/cuda_kernels' /bin/rm -f *.o libcpptraj_cuda.a make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/cuda_kernels' cd tng && make clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' /bin/rm -f *.o libtng_io.a tng_io_testing.o a.out tng_example_out.tng tng_test.tng make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' cd test && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' Cleaning all test directories: make test.complete test.libcpptraj OPT=clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' cd unitTests && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' Cleaning unit tests. make test.complete OPT=clean make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' rm -rf bin make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' ./configure gnu --with-arpack=/usr/lib/x86_64-linux-gnu --with-fftw3=/usr/lib/x86_64-linux-gnu --with-readline=/usr/lib/x86_64-linux-gnu --with-openmm=/usr/lib/x86_64-linux-gnu arpack specified: /usr/lib/x86_64-linux-gnu fftw3 specified: /usr/lib/x86_64-linux-gnu readline specified: /usr/lib/x86_64-linux-gnu openmm specified: /usr/lib/x86_64-linux-gnu Testing C++ compiler: OK Testing C compiler: OK Testing basic C++11 support: OK Testing system headers for C++11 support: OK Warning: Compilation of sanderlib requires AMBERHOME to be set Warning: if --with-sanderlib not specified. Checking BZLIB: OK Checking ZLIB: OK Checking NetCDF: OK Checking LAPACK/BLAS: OK Checking ARPACK: OK Checking FFTW3: OK Checking Readline: OK Checking OpenMM: OK vmdplugin disabled due to nonfree source. Configuration summary: Build type: Serial Options: netcdf bzlib tng zlib arpack lapack blas fftw3 readline xdrfile openmm Target platform: Linux, 64-bit. gnu compilers in use. C++11 support enabled. PME support enabled. Compiler optimizations are on. Cleaning source directory. -------------------------------------------------------------------------------- An environment resource file for CPPTRAJ has been created: /build/reproducible-path/cpptraj-5.1.0+dfsg/cpptraj.sh You may 'source' this file to set up your environment for CPPTRAJ. -------------------------------------------------------------------------------- CPPTRAJ configuration complete. make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_auto_build make -j42 make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make install make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' CXX SpaceGroup.cpp CXX ActionFrameCounter.cpp CXX ActionList.cpp CXX ActionTopWriter.cpp CXX Action_Align.cpp CXX Action_Angle.cpp CXX Action_AreaPerMol.cpp CXX Action_AtomMap.cpp CXX Action_AtomicCorr.cpp CXX Action_AtomicFluct.cpp CXX Action_AutoImage.cpp CXX Action_Average.cpp CXX Action_Bounds.cpp CXX Action_Box.cpp CXX Action_Center.cpp CXX Action_Channel.cpp CXX Action_CheckChirality.cpp CXX Action_CheckStructure.cpp CXX Action_Closest.cpp CXX Action_ClusterDihedral.cpp CXX Action_Contacts.cpp CXX Action_CreateCrd.cpp CXX Action_CreateReservoir.cpp CXX Action_DNAionTracker.cpp CXX Action_DSSP.cpp CXX Action_Density.cpp CXX Action_Diffusion.cpp CXX Action_Dihedral.cpp CXX Action_DihedralRMS.cpp CXX Action_Dipole.cpp CXX Action_Distance.cpp CXX Action_DistRmsd.cpp CXX Action_Energy.cpp CXX Action_FilterByData.cpp CXX Action_FixAtomOrder.cpp CXX Action_FixImagedBonds.cpp CXX Action_GIST.cpp CXX Action_Grid.cpp CXX Action_GridFreeEnergy.cpp CXX Action_HydrogenBond.cpp CXX Action_Image.cpp CXX Action_InfraredSpectrum.cpp In file included from Ewald_ParticleMesh.h:5, from Action_Energy.cpp:4: helpme_standalone.h:2323: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2323 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:2343: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2343 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3014: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3014 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3120: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3120 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3247: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3247 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3701: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3701 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3739: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3739 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3802: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3802 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3840: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3840 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4044: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4044 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4052: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4052 | #pragma omp for helpme_standalone.h:4097: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4097 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4145: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4145 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4172: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4172 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4224: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4224 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4228: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4228 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4275: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4275 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4388: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4388 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4419: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4503: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4503 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4510: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4510 | #pragma omp for CXX Action_Jcoupling.cpp CXX Action_LESsplit.cpp CXX Action_LIE.cpp CXX Action_LipidOrder.cpp CXX Action_MakeStructure.cpp CXX Action_Mask.cpp CXX Action_Matrix.cpp CXX Action_MinImage.cpp CXX Action_Molsurf.cpp CXX Action_MultiDihedral.cpp CXX Action_MultiVector.cpp CXX Action_NAstruct.cpp CXX Action_NativeContacts.cpp CXX Action_NMRrst.cpp CXX Action_OrderParameter.cpp CXX Action_Outtraj.cpp CXX Action_PairDist.cpp CXX Action_Pairwise.cpp CXX Action_Principal.cpp CXX Action_Projection.cpp CXX Action_Pucker.cpp CXX Action_Radgyr.cpp CXX Action_Radial.cpp CXX Action_RandomizeIons.cpp CXX Action_Remap.cpp CXX Action_ReplicateCell.cpp CXX Action_Rmsd.cpp CXX Action_Rotate.cpp In file included from Matrix_3x3.h:3, from Box.h:3, from Frame.h:5, from Topology.h:10, from DataSet_Coords.h:4, from DataSet_Coords_REF.h:3, from ReferenceFrame.h:3, from DataSetList.h:4, from DataFile.h:4, from DataFileList.h:3, from ActionState.h:3, from Action.h:5, from Action_GIST.h:3, from Action_GIST.cpp:3: In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:814:31: Vec3.h:76:57: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:814:31: Vec3.h:76:23: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:814:31: Vec3.h:76:40: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:814:31: Vec3.h:76:23: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:815:31: Vec3.h:76:57: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ In member function 'Vec3 Vec3::operator-(const Vec3&) const', inlined from 'void Action_GIST::Order(const Frame&)' at Action_GIST.cpp:815:31: Vec3.h:76:23: warning: 'WAT' may be used uninitialized [-Wmaybe-uninitialized] 76 | return Vec3(V_[0]-rhs.V_[0], V_[1]-rhs.V_[1], V_[2]-rhs.V_[2]); | ~~~~^ Action_GIST.cpp: In member function 'void Action_GIST::Order(const Frame&)': Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ CXX Action_RunningAvg.cpp CXX Action_STFC_Diffusion.cpp CXX Action_Scale.cpp CXX Action_SetVelocity.cpp CXX Action_Spam.cpp CXX Action_Strip.cpp CXX Action_Surf.cpp CXX Action_SymmetricRmsd.cpp CXX Action_Temperature.cpp CXX Action_Time.cpp CXX Action_Translate.cpp CXX Action_Unstrip.cpp CXX Action_Unwrap.cpp CXX Action_Vector.cpp CXX Action_VelocityAutoCorr.cpp CXX Action_Volmap.cpp CXX Action_Volume.cpp CXX Action_Watershell.cpp CXX Action_XtalSymm.cpp CXX AnalysisList.cpp CXX Analysis_AmdBias.cpp CXX Analysis_AutoCorr.cpp CXX Analysis_Average.cpp CXX Analysis_Clustering.cpp CXX Analysis_Corr.cpp CXX Analysis_ConstantPHStats.cpp CXX Analysis_CrankShaft.cpp CXX Analysis_CrdFluct.cpp CXX Analysis_CrossCorr.cpp CXX Analysis_CurveFit.cpp CXX Analysis_Divergence.cpp CXX Analysis_EvalPlateau.cpp CXX Analysis_FFT.cpp CXX Analysis_HausdorffDistance.cpp CXX Analysis_Hist.cpp CXX Analysis_Integrate.cpp CXX Analysis_IRED.cpp CXX Analysis_KDE.cpp CXX Analysis_Lifetime.cpp CXX Analysis_LowestCurve.cpp CXX Analysis_Matrix.cpp CXX Analysis_MeltCurve.cpp CXX Analysis_Modes.cpp CXX Analysis_Multicurve.cpp CXX Analysis_MultiHist.cpp CXX Analysis_Overlap.cpp CXX Analysis_PhiPsi.cpp CXX Analysis_Regression.cpp CXX Analysis_RemLog.cpp CXX Analysis_Rms2d.cpp CXX Analysis_RmsAvgCorr.cpp CXX Analysis_Rotdif.cpp CXX Analysis_RunningAvg.cpp CXX Analysis_Slope.cpp CXX Analysis_Spline.cpp CXX Analysis_State.cpp CXX Analysis_Statistics.cpp CXX Analysis_TI.cpp CXX Analysis_Timecorr.cpp CXX Analysis_VectorMath.cpp CXX Analysis_Wavelet.cpp CXX ArgList.cpp CXX Array1D.cpp CXX AssociatedData.cpp CXX Atom.cpp CXX AtomMap.cpp CXX AtomMask.cpp CXX AxisType.cpp CXX BondSearch.cpp CXX Box.cpp CXX BoxArgs.cpp CXX BufferedFrame.cpp CXX BufferedLine.cpp CXX ByteRoutines.cpp CXX CharMask.cpp CXX CharmmParamFile.cpp CXX CIFfile.cpp CXX ClusterDist.cpp CXX ClusterList.cpp CXX ClusterMap.cpp CXX ClusterMatrix.cpp CXX ClusterNode.cpp CXX ClusterSieve.cpp CXX Cluster_DBSCAN.cpp CXX Cluster_DPeaks.cpp CXX Cluster_HierAgglo.cpp CXX Cluster_Kmeans.cpp CXX Cluster_ReadInfo.cpp CXX Cmd.cpp CXX CmdInput.cpp CXX CmdList.cpp CXX CompactFrameArray.cpp CXX ComplexArray.cpp CXX Constraints.cpp CXX ControlBlock_For.cpp CXX CoordinateInfo.cpp CXX Corr.cpp CXX Cph.cpp CXX CpptrajFile.cpp CXX CpptrajState.cpp CXX CpptrajStdio.cpp CXX CurveFit.cpp CXX DataFile.cpp CXX DataFileList.cpp CXX DataFilter.cpp CXX DataIO.cpp CXX DataIO_CCP4.cpp CXX DataIO_CharmmFastRep.cpp CXX DataIO_CharmmOutput.cpp CXX DataIO_CharmmRepLog.cpp CXX DataIO_CharmmRtfPrm.cpp CXX DataIO_Cmatrix.cpp CXX DataIO_Cpout.cpp CXX DataIO_Evecs.cpp CXX DataIO_Gnuplot.cpp CXX DataIO_Grace.cpp CXX DataIO_OpenDx.cpp In file included from /usr/include/c++/14/vector:66, from ArgList.h:3, from Action.h:4, from Action_XtalSymm.h:3, from Action_XtalSymm.cpp:1: In member function 'void std::vector<_Tp, _Alloc>::assign(size_type, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]', inlined from 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)' at Action_XtalSymm.cpp:57:12: /usr/include/c++/14/bits/stl_vector.h:809:23: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 809 | { _M_fill_assign(__n, __val); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:72: /usr/include/c++/14/bits/vector.tcc: In member function 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)': /usr/include/c++/14/bits/vector.tcc:270:5: note: by argument 3 of type 'const std::vector::value_type&' {aka 'const Vec3&'} to 'void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]' declared here 270 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ Action_XtalSymm.cpp:57:33: note: '' declared here 57 | T_.assign( nCopyTotal, Vec3()); | ^ In member function 'void std::vector<_Tp, _Alloc>::assign(size_type, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]', inlined from 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)' at Action_XtalSymm.cpp:58:15: /usr/include/c++/14/bits/stl_vector.h:809:23: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 809 | { _M_fill_assign(__n, __val); } | ~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/14/bits/vector.tcc: In member function 'virtual Action::RetType Action_XtalSymm::Init(ArgList&, ActionInit&, int)': /usr/include/c++/14/bits/vector.tcc:270:5: note: by argument 3 of type 'const std::vector::value_type&' {aka 'const Vec3&'} to 'void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = Vec3; _Alloc = std::allocator]' declared here 270 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ Action_XtalSymm.cpp:58:33: note: '' declared here 58 | RefT_.assign(nCopyTotal, Vec3()); | ^ CXX 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_StringVar.cpp CXX DataSet_string.cpp CXX DataSet_Tensor.cpp CXX DataSet_unsignedInt.cpp CXX Deprecated.cpp CXX DihedralSearch.cpp CXX DistRoutines.cpp CXX Energy.cpp CXX EnergyArray.cpp CXX EnsembleIn.cpp CXX EnsembleIn_Multi.cpp CXX EnsembleIn_Single.cpp CXX EnsembleNavigator.cpp CXX EnsembleOut.cpp CXX EnsembleOut_Multi.cpp CXX EnsembleOut_Single.cpp CXX EnsembleOutList.cpp CXX Ewald.cpp CXX Ewald_ParticleMesh.cpp CXX Ewald_Regular.cpp CXX ExclusionArray.cpp CXX Exec_AddMissingRes.cpp CXX Exec_Analyze.cpp CXX Exec_Calc.cpp CXX Exec_CatCrd.cpp CXX Exec_Change.cpp In file included from Ewald_ParticleMesh.h:5, from Ewald_ParticleMesh.cpp:4: helpme_standalone.h:2323: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2323 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:2343: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 2343 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3014: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3014 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3120: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3120 | #pragma omp parallel for reduction(+ : energy, Vxx, Vxy, Vyy, Vxz, Vyz, Vzz) num_threads(nThreads) helpme_standalone.h:3247: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3247 | #pragma omp parallel for num_threads(nThreads) helpme_standalone.h:3701: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3701 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3739: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3739 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3802: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3802 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:3840: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 3840 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4044: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4044 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4052: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4052 | #pragma omp for helpme_standalone.h:4097: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4097 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4145: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4145 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4172: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4172 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4224: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4224 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4228: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4228 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4275: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4275 | #pragma omp parallel for num_threads(nThreads_) helpme_standalone.h:4388: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4388 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4419: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4419 | #pragma omp parallel for reduction(+ : energy) num_threads(nThreads_) helpme_standalone.h:4503: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] 4503 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4510: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4510 | #pragma omp for CXX Exec_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 CXX Exec_ParallelAnalysis.cpp CXX Exec_ParmBox.cpp helpme_standalone.h: In instantiation of 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]': helpme_standalone.h:3898:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3898 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:1010:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 1010 | for (int val = 0; val < nRows_; ++val) eigenPairs.push_back({eigenValues[val][0], unsortedEigenVectors[val]}); | ~~~~^~~~~~~~ helpme_standalone.h:1013:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 1013 | for (int val = 0; val < nRows_; ++val) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::PMEInstance >::sanityChecks(int, const RealMat&, const RealMat&, int) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5018:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5018 | sanityChecks(parameterAngMom, parameters, coordinates); | ^~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3198:32: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3198 | if (parameters.nCols() != (nCartesian(parameterAngMom) - cartesianOffset)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::PMEInstance >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5019:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5019 | filterAtomsAndBuildSplineCache(parameterAngMom, coordinates); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3746:45: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3746 | for (size_t row = threadID; row < gridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~ helpme_standalone.h:3753:37: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3753 | for (int atom = 0; atom < nAtoms; ++atom) { | ~~~~~^~~~~~~~ helpme_standalone.h:3761:61: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3761 | if (cGridIterator.size() && thisAtomsThread == threadID) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~ helpme_standalone.h:3750:25: warning: unused variable 'gridIteratorC' [-Wunused-variable] 3750 | const auto &gridIteratorC = threadedGridIteratorC_[threadID]; | ^~~~~~~~~~~~~ helpme_standalone.h:3794:55: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 3794 | for (int atom = splineCache_.size(); atom < newSize; ++atom) | ~~~~~^~~~~~~~~ helpme_standalone.h:3810:47: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3810 | for (size_t cRow = threadID; cRow < gridDimensionC_; cRow += nThreads_) { | ~~~~~^~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'Real* helpme::PMEInstance >::spreadParameters(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5020:25: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5020 | auto realGrid = spreadParameters(parameterAngMom, parameters); | ^~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3708:45: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 3708 | for (size_t row = threadID; row < myGridDimensionC_; row += nThreads_) { | ~~~~^~~~~~~~~~~~~~~~~~~ helpme_standalone.h: In instantiation of 'helpme::PMEInstance >::Complex* helpme::PMEInstance >::forwardTransform(Real*) [with Real = double; typename std::enable_if::value, int>::type = 0; Complex = std::complex]': helpme_standalone.h:5023:32: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5023 | auto gridAddress = forwardTransform(realGrid); | ^~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:4004:28: warning: variable 'realCBA' set but not used [-Wunused-but-set-variable] 4004 | Real *__restrict__ realCBA; | ^~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::Matrix::assertSymmetric(const Real&) const [with Real = double]': helpme_standalone.h:1000:9: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 1000 | assertSymmetric(); | ^~~~~~~~~~~~~~~ helpme_standalone.h:3898:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3898 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:796:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 796 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::JacobiCyclicDiagonalization(Real*, Real*, const Real*, int) [with Real = double]': helpme_standalone.h:1006:42: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 1006 | JacobiCyclicDiagonalization(eigenValues[0], unsortedEigenVectors[0], cbegin(), nRows_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3898:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3898 | auto eigenTuple = HtH.diagonalize(); | ~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:213:20: warning: variable 'cos_2phi' set but not used [-Wunused-but-set-variable] 213 | Real sin_2phi, cos_2phi, cot_2phi; | ^~~~~~~~ helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::applyOperation(const std::function&) const [with Real = double]': helpme_standalone.h:785:26: required from 'helpme::Matrix helpme::Matrix::inverse() const [with Real = double]' 785 | return this->applyOperation([](Real& element) { element = 1 / element; }); | ~~~~~~^~~~~~~~~~~~~~ helpme_standalone.h:3910:44: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3910 | recVecs_ = boxVecs_.inverse(); | ~~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:824:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 824 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h: In instantiation of 'void helpme::BSpline::update(short int, Real, short int, short int) [with Real = double]': helpme_standalone.h:3829:47: required from 'void helpme::PMEInstance >::filterAtomsAndBuildSplineCache(int, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 3829 | atomSplines.aSpline.update(aStartingGridPoint, gridDimensionA_ * aCoord - aStartingGridPoint, | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3830 | splineOrder_, splineDerivativeLevel); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:5019:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5019 | filterAtomsAndBuildSplineCache(parameterAngMom, coordinates); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ewald_ParticleMesh.cpp:190:42: required from here 190 | double erecip = pme_object_.computeERec(0, chargesD, coordsD); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:2208:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 2208 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:2208:72: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2208 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~ CXX Exec_ParmSolvent.cpp helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::multiply(const helpme::Matrix&) const [with Real = double]': helpme_standalone.h:877:64: required from 'helpme::Matrix helpme::Matrix::operator*(const helpme::Matrix&) const [with Real = double]' 877 | Matrix operator*(const Matrix& other) const { return this->multiply(other); } | ~~~~~~^~~~~~~~ helpme_standalone.h:829:22: required from 'helpme::Matrix helpme::Matrix::applyOperation(const std::function&) const [with Real = double]' 829 | return evecs * evecsT; | ~~~~~~^~~~~~~~ helpme_standalone.h:785:26: required from 'helpme::Matrix helpme::Matrix::inverse() const [with Real = double]' 785 | return this->applyOperation([](Real& element) { element = 1 / element; }); | ~~~~~~^~~~~~~~~~~~~~ helpme_standalone.h:3910:44: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3910 | recVecs_ = boxVecs_.inverse(); | ~~~~~~~~~~~~~~~~^~ Ewald_ParticleMesh.cpp:187:32: required from here 187 | pme_object_.setLatticeVectors(boxIn.Param(Box::X), boxIn.Param(Box::Y), boxIn.Param(Box::Z), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 | boxIn.Param(Box::ALPHA), boxIn.Param(Box::BETA), boxIn.Param(Box::GAMMA), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 | PMEInstanceD::LatticeType::XAligned); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ helpme_standalone.h:860:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 860 | for (int row = 0; row < nRows_; ++row) { | ~~~~^~~~~~~~ helpme_standalone.h:862:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 862 | for (int col = 0; col < other.nCols_; ++col) { | ~~~~^~~~~~~~~~~~~~ helpme_standalone.h:863:41: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 863 | for (int link = 0; link < nCols_; ++link) { | ~~~~~^~~~~~~~ CXX Exec_ParmStrip.cpp CXX Exec_ParmWrite.cpp CXX Exec_PermuteDihedrals.cpp CXX Exec_Precision.cpp CXX Exec_PrepareForLeap.cpp CXX Exec_PrintData.cpp CXX Exec_Random.cpp CXX Exec_ReadData.cpp CXX Exec_ReadEnsembleData.cpp CXX Exec_ReadInput.cpp CXX Exec_RotateDihedral.cpp CXX Exec_RunAnalysis.cpp CXX Exec_ScaleDihedralK.cpp CXX Exec_Set.cpp CXX Exec_SequenceAlign.cpp CXX Exec_Show.cpp CXX Exec_SortEnsembleData.cpp CXX Exec_SplitCoords.cpp CXX Exec_System.cpp CXX Exec_Top.cpp CXX Exec_Traj.cpp CXX Exec_UpdateParameters.cpp CXX Exec_ViewRst.cpp CXX File_TempName.cpp CXX FileIO_Bzip2.cpp CXX FileIO_Gzip.cpp CXX FileIO_Mpi.cpp CXX FileIO_MpiShared.cpp CXX FileIO_Std.cpp CXX FileName.cpp CXX FileType.cpp CXX FileTypes.cpp CXX ForLoop.cpp CXX ForLoop_dataSetBlocks.cpp CXX ForLoop_integer.cpp CXX ForLoop_list.cpp CXX ForLoop_mask.cpp CXX ForLoop_overSets.cpp CXX Frame.cpp CXX GridAction.cpp CXX HistBin.cpp CXX Hungarian.cpp CXX ImageRoutines.cpp CXX Image_List_Mask.cpp CXX Image_List_Pair.cpp CXX Image_List_Unit.cpp CXX InputTrajCommon.cpp CXX KDE.cpp CXX MapAtom.cpp CXX MaskArray.cpp CXX MaskToken.cpp CXX Matrix_3x3.cpp CXX MdOpts.cpp CXX MetaData.cpp CXX Minimize_SteepestDescent.cpp CXX Mol.cpp CXX Mol2File.cpp CXX NameType.cpp CXX NC_Cmatrix.cpp CXX NC_Routines.cpp CXX NetcdfFile.cpp CXX OMM_helpers.cpp CXX OutputTrajCommon.cpp CXX ParameterSet.cpp CXX PDBfile.cpp CXX PairList.cpp CXX Parallel.cpp CXX ParallelNetcdf.cpp CXX ParmFile.cpp CXX Parm_Amber.cpp CXX Parm_CharmmPsf.cpp CXX Parm_CIF.cpp CXX Parm_Gromacs.cpp CXX Parm_Mol2.cpp CXX Parm_PDB.cpp CXX Parm_SDF.cpp CXX Parm_Tinker.cpp CXX PotentialFunction.cpp CXX PotentialTerm.cpp CXX PotentialTerm_Angle.cpp CXX PotentialTerm_Bond.cpp CXX PotentialTerm_Dihedral.cpp CXX PotentialTerm_LJ_Coulomb.cpp CXX PotentialTerm_OpenMM.cpp CXX ProgressBar.cpp CXX ProgressTimer.cpp CXX PubFFT.cpp CXX ExternalFxn.cpp CXX Random.cpp CXX Range.cpp CXX RNG.cpp CXX RNG_Marsaglia.cpp CXX RNG_MersenneTwister.cpp CXX RNG_PCG32.cpp CXX RNG_Stdlib.cpp CXX RNG_Xoshiro128pp.cpp CXX RPNcalc.cpp CXX ReferenceAction.cpp CXX RemdReservoirNC.cpp CXX Residue.cpp CXX SDFfile.cpp CXX SimplexMin.cpp CXX Spline.cpp CXX SplineFxnTable.cpp CXX StringRoutines.cpp CXX StructureCheck.cpp CXX StructureMapper.cpp CXX SymmetricRmsdCalc.cpp CXX TextFormat.cpp CXX Timer.cpp CXX TinkerFile.cpp helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3470:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3470 | fftHelperA_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3470:31: note: '' declared here 3470 | fftHelperA_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3471:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3471 | fftHelperB_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3471:31: note: '' declared here 3471 | fftHelperB_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ helpme_standalone.h:3472:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3472 | fftHelperC_ = FFTWWrapper(); | ^~~~~~~~~~~ helpme_standalone.h:3472:31: note: '' declared here 3472 | fftHelperC_ = FFTWWrapper(); | ^~~~~~~~~~~~~~~~~~~ In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3503:43: helpme_standalone.h:519:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] 519 | class Matrix { | ^~~~~~ helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3503:45: note: '' declared here 3503 | compressionCoefficientsA_ = RealMat(); | ^~~~~~~~~ In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3504:43: helpme_standalone.h:519:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] 519 | class Matrix { | ^~~~~~ helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3504:45: note: '' declared here 3504 | compressionCoefficientsB_ = RealMat(); | ^~~~~~~~~ In member function 'helpme::Matrix& helpme::Matrix::operator=(helpme::Matrix&&)', inlined from 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]' at helpme_standalone.h:3505:43: helpme_standalone.h:519:7: warning: '.helpme::Matrix::data_' may be used uninitialized [-Wmaybe-uninitialized] 519 | class Matrix { | ^~~~~~ helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3505:45: note: '' declared here 3505 | compressionCoefficientsC_ = RealMat(); | ^~~~~~~~~ CXX 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 helpme_standalone.h: In member function 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:5031:16: warning: 'energy' may be used uninitialized [-Wmaybe-uninitialized] 5031 | return energy; | ^~~~~~ helpme_standalone.h:5021:14: note: 'energy' was declared here 5021 | Real energy; | ^~~~~~ CXX Traj_XYZ.cpp CXX TrajectoryFile.cpp CXX TrajectoryIO.cpp CXX TrajinList.cpp CXX TrajFrameCounter.cpp CXX Trajin_Multi.cpp CXX Trajin_Single.cpp CXX TrajIOarray.cpp CXX Trajout_Single.cpp CXX TrajoutList.cpp CXX Vec3.cpp CXX ViewRst.cpp CXX xoshiro128plusplus.cpp CXX Action_Esander.cpp xoshiro128plusplus.cpp: In function 'void jump()': xoshiro128plusplus.cpp:60:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 60 | for(int i = 0; i < sizeof JUMP / sizeof *JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ xoshiro128plusplus.cpp: In function 'void long_jump()': xoshiro128plusplus.cpp:90:26: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] 90 | for(int i = 0; i < sizeof LONG_JUMP / sizeof *LONG_JUMP; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CXX Command.cpp CXX Cpptraj.cpp CXX Energy_Sander.cpp CXX ReadLine.cpp CXX main.cpp CC molsurf.c cd xdrfile && make all Skipping bundled READLINE build make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' CC xdrfile.c CC xdr_seek.c CC xdrfile_trr.c cd tng && make all Skipping bundled ARPACK build make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' CC xdrfile_xtc.c CC md5.c CC tng_io.c CC tng_compress.c CC coder.c CC warnmalloc.c CC fixpoint.c CC xtc3.c CC bwlzh.c CC xtc2.c CC widemuldiv.c CC huffmem.c CC vals16.c CC bwt.c CC mtf.c CC rle.c CC lz77.c CC dict.c CC huffman.c 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 libxdrfile.a ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' /bin/rm -f libtng_io.a ar cqs libtng_io.a md5.o tng_io.o tng_compress.o coder.o warnmalloc.o fixpoint.o xtc3.o bwlzh.o xtc2.o widemuldiv.o huffmem.o vals16.o bwt.o mtf.o rle.o lz77.o dict.o huffman.o merge_sort.o make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o -L/usr/lib/x86_64-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/x86_64-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/x86_64-linux-gnu/lib -lfftw3 -L/usr/lib/x86_64-linux-gnu/lib -lOpenMM -lnetcdf -lbz2 tng/libtng_io.a -lz xdrfile/libxdrfile.a -Wl,-z,relro mv cpptraj "/build/reproducible-path/cpptraj-5.1.0+dfsg/bin" make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_auto_test -- check unittest make -j42 test "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 check unittest make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' make[2]: Nothing to be done for 'test'. cd test && make test.complete summary cd unitTests && make test.complete summary make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList CPPTRAJ: NameType class unit test. CPPTRAJ: ArgList class unit test. -rwxr-xr-x 1 pbuilder2 pbuilder2 186123352 Sep 9 04:55 ../bin/cpptraj make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' -rwxr-xr-x 1 pbuilder2 pbuilder2 186123352 Sep 9 04:55 ../bin/cpptraj make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' g++ -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp g++ -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o ArgList.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/ArgList.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o NameType.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/NameType.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o StringRoutines.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/StringRoutines.cpp ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_General ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Jcoupling TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RemdTraj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hbond ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Runavg ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Image ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotdif ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Center TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Average ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diffusion ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TrajinOffset TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radgyr ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RMSD ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NCrestart ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mol2 TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomMap ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Strip ******************************************************************************** ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DRMSD TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_2DRMS TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Datafile CPPTRAJ: General tests CPPTRAJ: J-Coupling single frame test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pucker CPPTRAJ: Surface calculation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_trajout_framerange CPPTRAJ: Coordinate Running Average test. CPPTRAJ: Orthorhombic imaged distance test. CPPTRAJ: 1D/2D Histogram Analysis test CPPTRAJ: Solute Hbond test CPPTRAJ: Rotational diffusion calculation test CPPTRAJ: Broken Traj: Running good trajectory. CPPTRAJ: Average Test. CPPTRAJ: Radial test, non-orthogonal imaging CPPTRAJ: Normal trajectory read with offsets. CPPTRAJ: Center command test. CPPTRAJ: Radius of gyration command test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mask ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DSSP CPPTRAJ: Per-Residue RMSD Test. CPPTRAJ: CHARMM PSF/DCD test CPPTRAJ: Mol2 Parm/Traj Read/Write Test. CPPTRAJ: Convert mdcrd -> NetCDF CPPTRAJ: Diffusion test, no imaging. CPPTRAJ: RMSD Test with outtraj. CPPTRAJ: AtomMap Test CPPTRAJ: CRD Replica Trajectory Run with offset CPPTRAJ: NAstruct command test. CPPTRAJ: NetCDF Restart Test - TXT->NetCDF CPPTRAJ: Closest command test using first solvent atom. CPPTRAJ: Basic RMSD tests CPPTRAJ: Data file output precision test CPPTRAJ: Distance RMSD test CPPTRAJ: One frame strip command test CPPTRAJ: 2D RMSD Test. CPPTRAJ: Pucker command test CPPTRAJ: Secstruct (DSSP) command test. CPPTRAJ: Mask single frame test CPPTRAJ: Trajout Frame Range [Amber Restart] J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. Skipped test: J-Coupling extended test All 1 comparisons passed. 1 comparisons skipped. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster CPPTRAJ: NetCDF Restart Test - NetCDF->TXT CPPTRAJ: Coordinate Running Average Traj Write CPPTRAJ: 2D RMSD Test, mass-weighted. CPPTRAJ: Gzipped trajectory read with offsets CPPTRAJ: PDB => Mol2 CPPTRAJ: CRD Replica Trajectory Run CPPTRAJ: Diffusion test, old syntax. CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test CPPTRAJ: Closest command test using all solvent atoms. CPPTRAJ: Cluster command test, in-memory pairwise distances. CPPTRAJ: CHARMM DCD Write, step 1. CPPTRAJ: Standard -> Grace Data CPPTRAJ: Center origin command test. All 2 comparisons passed. CPPTRAJ: Unstrip (Lig/Rec/Complex) command test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_IRED CPPTRAJ: Broken Traj: Running broken trajectory. All 1 comparisons passed. CPPTRAJ: IRED vector/matrix test All 2 comparisons passed. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons CPPTRAJ: randomizeions test (original algorithm) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Molsurf CPPTRAJ: Molsurf test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Corr All 4 comparisons passed. CPPTRAJ: Correlation test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RmsAvgCorr CPPTRAJ: Trajout Frame Range [Amber Coordinates] ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckStructure ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Contacts CPPTRAJ: RmsAvgCorr Reference CPPTRAJ: Contacts test. CPPTRAJ: Structure Check ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Principal CPPTRAJ: Principal Test All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ClusterDihedral All 2 comparisons passed. CPPTRAJ: clusterdihedral test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Vector All 3 comparisons passed. CPPTRAJ: Basic vector tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Matrix CPPTRAJ: Matrix Tests All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. CPPTRAJ: Structure Check with Around and Skip CPPTRAJ: Non-orthorhombic imaged distance test. CPPTRAJ: 2D RMSD Test with reference trajectory CPPTRAJ: Bzip2ed trajectory read with offsets CPPTRAJ: Mask longer command test. CPPTRAJ: NetCDF Replica Trajectory Run test CPPTRAJ: AtomMap with 'rmsfit' CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. CPPTRAJ: Solute Hbond test with disk caching CPPTRAJ: Grace -> Standard Data CPPTRAJ: Center origin mass command test. CPPTRAJ: 3D histogram test. CPPTRAJ: Cluster command test, read pairwise distances. CPPTRAJ: NAstruct command test, single strand CPPTRAJ: Per-Residue RMSD Test with averaging CPPTRAJ: Amber Top/Rst => Mol2 CPPTRAJ: Diffusion test, new syntax. CPPTRAJ: RmsAvgCorr First CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF CPPTRAJ: CHARMM DCD Write, step 2. CPPTRAJ: RMS coordinate rotation/rotation matrices test CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. CPPTRAJ: Convert NetCDF -> mdcrd CPPTRAJ: Outtraj Test with maxmin. CPPTRAJ: Multi frame strip command test. CPPTRAJ: Partial Surface calculation test CPPTRAJ: Compressed broken trajectory test CPPTRAJ: Closest command test, using mask center CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. Skipped test: Amber Top/Rst => Mol2, SYBYL atom types All 11 comparisons passed. All 4 comparisons passed. 1 comparisons skipped. All 7 comparisons passed. All 3 comparisons passed. All 5 comparisons passed. CPPTRAJ: Per-Residue RMSD Test with residue centering. CPPTRAJ: Test vector center with magnitude CPPTRAJ: Secstruct (DSSP) command with changing number of residues. CPPTRAJ: Center reference command test. CPPTRAJ: X column format/precision test. CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj CPPTRAJ: 2D DME Test. CPPTRAJ: Atom map charmm->amber atom order CPPTRAJ: Orthorhombic coordinate imaging test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Grid CPPTRAJ: Dipole test CPPTRAJ: Strip topology with PDB info CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt CPPTRAJ: Cluster command test, read NetCDF pairwise distances. CPPTRAJ: Diffusion test, nonorthogonal box CPPTRAJ: Solute-solvent hbond test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct_8OG CPPTRAJ: RMS fit with no coordinates modification test. CPPTRAJ: CHAMBER topology read/strip test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Project CPPTRAJ: Start argument offset ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Unwrap All 3 comparisons passed. CPPTRAJ: NA test (8OG) CPPTRAJ: Projection CPPTRAJ: Unwrap non-orthogonal test All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Watershell CPPTRAJ: Watershell Test, non-orthorhombic imaging. CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. CPPTRAJ: Modes analysis, RMS fluctuations ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AnalysisRunAvg ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volmap CPPTRAJ: Analysis Running Average CPPTRAJ: VMD VolMap Algorithm test CPPTRAJ: Atom map charmm->amber atom order, by residue CPPTRAJ: 2D RMSD with reference mask test. CPPTRAJ: Secstruct (DSSP): SS assign output test CPPTRAJ: Momentum/velocity vector test. CPPTRAJ: Hbond, no intramolecular hydrogen bonds test CPPTRAJ: Center point test. CPPTRAJ: Read CHARMM restart CPPTRAJ: Closest command test, using mask center and solvent mask CPPTRAJ: Nonorthorhombic coordinate imaging test CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SPAM CPPTRAJ: SPAM Test All 4 comparisons passed. All 1 comparisons passed. All 3 comparisons passed. All 4 comparisons passed. All 11 comparisons passed. All 2 comparisons passed. All 1 comparisons passed. All 5 comparisons passed. All 1 comparisons passed. All 2 comparisons passed. All 9 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LIE ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Density ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidOrder ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PairDist CPPTRAJ: LIE test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicCorr All 3 comparisons passed. CPPTRAJ: Lipid Order Parameter Test. CPPTRAJ: PairDist Test. CPPTRAJ: Density along axis tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReadData ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_systemVF ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Box CPPTRAJ: Atomic Correlation test CPPTRAJ: GIST water-water interaction test CPPTRAJ: AutoCorr test. CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomTypeSelect CPPTRAJ: Read vector data test (no origins, origins) VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. Skipped test: VMD VolMap Algorithm longer tests CPPTRAJ: Box Test (Add box info) All 2 comparisons passed. 1 comparisons skipped. CPPTRAJ: Selection by atom type test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AvgRef ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Crank_Stat CPPTRAJ: RMSD Test with averaged reference coordinates. CPPTRAJ: Crankshaft test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateCrd CPPTRAJ: COORDS data set creation and CRDFLUCT test. All 15 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoImage CPPTRAJ: AutoImage test (split DNA duplex) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Parallel CPPTRAJ: Parallel tests. All 1 comparisons passed. All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LoadCrd CPPTRAJ: Force vector test. CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj CPPTRAJ: Unwrap orthogonal test CPPTRAJ: Randomize (around, overlap) CPPTRAJ: Structure Check with PBC CPPTRAJ: 2D RMSD test, no fitting. CPPTRAJ: Data file group by name test CPPTRAJ: Grid test CPPTRAJ: Radial test, orthogonal and no imaging CPPTRAJ: Modes analysis, displacements CPPTRAJ: Cluster command test, write ASCII pairwise distances. CPPTRAJ: STFC Diffusion Test CPPTRAJ: Closest command test, solvent mask, water oxygen only CPPTRAJ: LCPO test with GAFF atom types CPPTRAJ: CHARMM PSF write CPPTRAJ: FtuFabI Assignment test CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar CPPTRAJ: SPAM Pure Solvent Test CPPTRAJ: RMS fit to previous test All 1 comparisons passed. CPPTRAJ: LoadCrd test. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MultiVector CPPTRAJ: Multivector test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Lifetime CPPTRAJ: Lifetime test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FFT CPPTRAJ: FFT test. CPPTRAJ: Read vector data set (origins, no origins) CPPTRAJ: Box test (remove box info) CPPTRAJ: Generate matrix with trajectory start/stop/offset CPPTRAJ: Hbond, specified solute masks All 6 comparisons passed. All 10 comparisons passed. All 3 comparisons passed. All 1 comparisons passed. All 14 comparisons passed. All 9 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Timecorr ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SymmRmsd ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CrossCorr CPPTRAJ: Timecorr test. CPPTRAJ: CrossCorr test CPPTRAJ: SymmRmsd All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multidihedral ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ensemble_MREMD ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MakeStructure CPPTRAJ: Multidihedral test CPPTRAJ: M-REMD sort test. CPPTRAJ: Basic makestructure test All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotate CPPTRAJ: Rotation (and inverse) of coords from matrices All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Integrate ******************************************************************************** CPPTRAJ: Integration test. TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidSCD CPPTRAJ: Basic lipid order parameter test All 1 comparisons passed. CPPTRAJ: ASP symmetry-corrected RMSD test CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj CPPTRAJ: Multi-frame density along axis test CPPTRAJ: Cluster command test, read ASCII pairwise distances. CPPTRAJ: Box test (Modify box length) CPPTRAJ: Atomicfluct test with ADP output CPPTRAJ: Modes analysis, dipole correlation CPPTRAJ: RMS: imaging after unit cell rotation CPPTRAJ: Pairdist test, orthogonal imaging. CPPTRAJ: COORDS data set creation with velocities test CPPTRAJ: OpenDX Grid read test CPPTRAJ: CHARMM COORdinates test CPPTRAJ: Data file group by aspect test CPPTRAJ: Read Amber output test CPPTRAJ: Lifetime test with data set caching. CPPTRAJ: Parallel test with trajectory offset CPPTRAJ: Generate matrix with action stop/start/offset CPPTRAJ: Hbond, no angle cutoff test CPPTRAJ: LoadTraj test. CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM CPPTRAJ: STFC Diffusion Test with individual distances ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts CPPTRAJ: NativeContacts test. CPPTRAJ: Multidihedral Nucleotide CHI test All 1 comparisons passed. CPPTRAJ: Makestructure test with reference. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckChiral All 9 comparisons passed. All 1 comparisons passed. All 12 comparisons passed. CPPTRAJ: Check chirality test All 6 comparisons passed. All 15 comparisons passed. All 7 comparisons passed. CPPTRAJ: GLU symmetry-corrected RMSD test CPPTRAJ: CRD Replica Trajectory Run with remdout CPPTRAJ: Rotate with defined axis CPPTRAJ: LoadTraj from trajin test. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Energy ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PermuteDihedrals All 5 comparisons passed. All 2 comparisons passed. All 6 comparisons passed. CPPTRAJ: Simple energy tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve CPPTRAJ: PermuteDihedrals interval -120, phi psi ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CharmmParams ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CCP4 CPPTRAJ: Cluster, nosieve CPPTRAJ: Test updating topology with Charmm parameters (single residue) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LESsplit All 6 comparisons passed. CPPTRAJ: CCP4 read/write and DX conversion test. CPPTRAJ: LES split/average test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihCovar ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CurveFit ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetAverage ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VectorMath CPPTRAJ: Dihedral Covariance Matrix Test CPPTRAJ: Curve fitting test. CPPTRAJ: Data set averaging and averaging over all sets test. CPPTRAJ: Vector dot/cross product test CPPTRAJ: AutoImage test, use anchor mask CPPTRAJ: Modes analysis, pseudo trajectory creation test CPPTRAJ: STFC Diffusion Test with COM CPPTRAJ: Randomize (around) CPPTRAJ: New Lipid Order Parameter Test, DOPC. CPPTRAJ: Box test (auto orthogonal box, no radii) ******************************************************************************** CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander CPPTRAJ: TYR symmetry-corrected RMSD test CPPTRAJ: Hbond, Bridge nointramol test CPPTRAJ: Read CHARMM output test CPPTRAJ: Grid with specified center test. CPPTRAJ: Total system density test CPPTRAJ: Multidihedral protein dihedrals test SANDER energy tests (long) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. SKIP: SANDER energy tests (long) All 8 comparisons passed. All 2 comparisons passed. All 1 comparisons passed. CPPTRAJ: Lifetime average and cumulative average test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander_Short CPPTRAJ: M-REMD actions test. g++ -o a.out main.o NameType.o CpptrajStdio.o Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. SKIP: Energy via sander API short tests (GB/PME) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Spline ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Temperature CPPTRAJ: Spline test All 8 comparisons passed. CPPTRAJ: Temperature test. All 7 comparisons passed. All 2 comparisons passed. CPPTRAJ: Multidihedral cyclic molecule test CPPTRAJ: PermuteDihedrals, random rotations CPPTRAJ: TRAJ data set creation and CRDFLUCT test. CPPTRAJ: 3D data read/write test CPPTRAJ: NativeContacts test, save non-native contacts, residue time series All 2 comparisons passed. CPPTRAJ: Pairdist test, nonorthogonal imaging. All 2 comparisons passed. CPPTRAJ: LoadCrd append from multiple files test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_KDE CPPTRAJ: KDE test. CPPTRAJ: Curve fitting multi-exponential tests. CPPTRAJ: Cluster, sieve5 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CIF ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Wavelet ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PDB CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test CPPTRAJ: Longer symmetry-corrected RMSD test. CPPTRAJ: CIF read test CPPTRAJ: Wavelet analysis test CPPTRAJ: PDB format read/write test All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelocityAutoCorr All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelFrc CPPTRAJ: Velocity autocorrelation test CPPTRAJ: Test combining coordinates, velocities, and forces. All 4 comparisons passed. All 7 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Align All 13 comparisons passed. All 12 comparisons passed. CPPTRAJ: Align Tests. make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' All 2 comparisons passed. All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RotateDihedral All 3 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. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetCmd CPPTRAJ: Rotate dihedral to target value. All 4 comparisons passed. CPPTRAJ: Data Set commands test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remap ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CompareTop CPPTRAJ: Box test (auto orthogonal box, VDW radii) CPPTRAJ: Watershell Test, orthorhombic imaging. CPPTRAJ: Grid with box center offset test. CPPTRAJ: Remap Test CPPTRAJ: STFC Diffusion Test with second mask CPPTRAJ: Test kinetic energy calculation CPPTRAJ: Temperature with SHAKE on hydrogens. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TopInfo CPPTRAJ: Standard 3D data write test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Filter ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTrr CPPTRAJ: TRR force/velocity read -> NetCDF write test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ewald CPPTRAJ: Direct sum test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CombineCrd CPPTRAJ: Basic filter test CPPTRAJ: Topology info print test. CPPTRAJ: Combine COORDS test. CPPTRAJ: Compare topology test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TI ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds CPPTRAJ: TI analysis test. CPPTRAJ: Test using velocities as coordinates. CPPTRAJ: TRAJ data set creation with velocities test. CPPTRAJ: M-REMD ensemble outtraj test. All 8 comparisons passed. CPPTRAJ: Fix imaged bonds test (Ortho.) All 6 comparisons passed. CPPTRAJ: Rotate dihedral by increment CPPTRAJ: NativeContacts test, orthorhombic imaging. All 7 comparisons passed. CPPTRAJ: Temperature with SHAKE on all atoms. CPPTRAJ: Curve fitting, custom output range. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Distance CPPTRAJ: Cluster, nosieve savepairdist All 1 comparisons passed. CPPTRAJ: Distance tests CPPTRAJ: Combine COORDS test with box info. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volume CPPTRAJ: Volume tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SetVelocity ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remlog CPPTRAJ: Standard 3D data read test CPPTRAJ: Set Velocity test CPPTRAJ: Replica log read/analyze test. CPPTRAJ: Test writing velocities (MDVEL) CPPTRAJ: Grid with mask center offset test. CPPTRAJ: Align, unit cell rotation/imaging test. All 1 comparisons passed. CPPTRAJ: Test total energy calculation All 3 comparisons passed. All 5 comparisons passed. CPPTRAJ: Rotate dihedral in TRAJ data set All 6 comparisons passed. CPPTRAJ: Temperature calc with extra points. CPPTRAJ: M-REMD no sort, running average test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AreaPerMol CPPTRAJ: Area per molecule test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DistBasedMask ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CalcState CPPTRAJ: KDE with Kullback-Leibler divergence test CPPTRAJ: Orthogonal imaged distance ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multicurve CPPTRAJ: Distance-based atom mask tests (atom, residue) CPPTRAJ: Calcstate test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Calc CPPTRAJ: Multicurve test CPPTRAJ: Fix imaged bonds test (Non-ortho.) CPPTRAJ: Structure Check with Around CPPTRAJ: Data filter test. CPPTRAJ: Calc test CPPTRAJ: Scale velocity test CPPTRAJ: COORDS data set append test CPPTRAJ: Generate offset traj from PDB All 10 comparisons passed. CPPTRAJ: Standard 3D data read/append test CPPTRAJ: Wavelet WAFEX test CPPTRAJ: PQR file write with various radii CPPTRAJ: Test partial energy calculation All 3 comparisons passed. CPPTRAJ: Non-orthogonal grid test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Change CPPTRAJ: Test using forces as coordinates. All 2 comparisons passed. CPPTRAJ: Change atom and residue name tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateReservoir CPPTRAJ: Create RREMD NetCDF reservoir test All 1 comparisons passed. All 1 comparisons passed. All 7 comparisons passed. All 3 comparisons passed. CPPTRAJ: Calc test with data sets CPPTRAJ: Split coords and recombine test. CPPTRAJ: M-REMD, generate RMS data ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixAtomOrder CPPTRAJ: Non-orthogonal imaged distance CPPTRAJ: Out of order molecules test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MinImage ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LowestCurve ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Regress CPPTRAJ: LowestCurve test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rst CPPTRAJ: Linear regression test. All 4 comparisons passed. All 4 comparisons passed. CPPTRAJ: Generate offset traj from CIF CPPTRAJ: Minimum Image test. CPPTRAJ: Distance-based atom mask tests (molecule) CPPTRAJ: Generate restraints (rst) test CPPTRAJ: COORDS test storing frame metadata All 2 comparisons passed. CPPTRAJ: TRR force/velocity read -> TRR write test CPPTRAJ: Test writing forces (MDFRC) CPPTRAJ: Change chain ID test CPPTRAJ: Filter matrix test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ParmBox CPPTRAJ: PDB filter alternate atom location IDs test All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pairwise CPPTRAJ: Parmbox test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Solvent CPPTRAJ: Pairwise tests All 6 comparisons passed. All 16 comparisons passed. CPPTRAJ: Test solvent command with closest All 1 comparisons passed. All 2 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Translate All 17 comparisons passed. CPPTRAJ: Translate test All 3 comparisons passed. ******************************************************************************** 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 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Control ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PhiPsi CPPTRAJ: Phipsi test CPPTRAJ: Loop tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_InfraredSpec All 1 comparisons passed. All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cphstats CPPTRAJ: Infrared spectrum calculation test CPPTRAJ: Explicit pH REMD ensemble data read / sort All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CmdLine All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XYZformat CPPTRAJ: Command line trajectory args test, part 1 All 1 comparisons passed. CPPTRAJ: XYZ format write All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hausdorff All 1 comparisons passed. All 2 comparisons passed. All 1 comparisons passed. CPPTRAJ: Simple Hausdorff distance test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CatCrd CPPTRAJ: Concatenate COORDS data set test All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XtalSymm All 1 comparisons passed. CPPTRAJ: XtalSymm Reference All 1 comparisons passed. ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Time TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihedralRMS ******************************************************************************** ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SplitCoords TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Slope CPPTRAJ: Add time to restart test CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) CPPTRAJ: Finite difference test. CPPTRAJ: SplitCoords test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diagmatrix CPPTRAJ: Adding PDB info to topology CPPTRAJ: Scale dihedral force constant with 'useall' CPPTRAJ: Standard 3D data, sparse CPPTRAJ: Hbond with imaging CPPTRAJ: Test math functions CPPTRAJ: TRAJ test storing frame metadata CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Emin CPPTRAJ: CRD => TRR CPPTRAJ: M-REMD, meltcurve analysis CPPTRAJ: Topology info with reference coords test CPPTRAJ: Change chain ID of COORDS set test CPPTRAJ: Pairwise test, partial system CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test CPPTRAJ: MW covariance matrix thermo analysis test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau CPPTRAJ: Evalulate plateau test All 2 comparisons passed. All 8 comparisons passed. CPPTRAJ: Basic energy minimization test. All 4 comparisons passed. CPPTRAJ: Command line test trajectory args test, part 2 ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Flatten CPPTRAJ: Flatten test. CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. CPPTRAJ: Dihedral RMSD test (to previous) All 1 comparisons passed. All 1 comparisons passed. All 10 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Graft ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Random All 2 comparisons passed. CPPTRAJ: Graft test CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs All 1 comparisons passed. All 17 comparisons passed. All 1 comparisons passed. All 3 comparisons passed. All 1 comparisons passed. All 6 comparisons passed. All 12 comparisons passed. All 8 comparisons passed. All 2 comparisons passed. All 1 comparisons passed. CPPTRAJ: Energy minimization with angle term test. CPPTRAJ: Randomize (overlap) CPPTRAJ: Nonorthogonal grid standard write/read tests. CPPTRAJ: Grid generation from 'bounds' test. CPPTRAJ: Ewald test (NaCl crystal) CPPTRAJ: Watershell Test, no imaging. CPPTRAJ: Remove time from restart test CPPTRAJ: Test set command CPPTRAJ: Atom XYZ format read, test 1 CPPTRAJ: Hbond, orthogonal imaging CPPTRAJ: Constant pH stats test CPPTRAJ: Hausdorff distance of 2D rms output test. All 1 comparisons passed. CPPTRAJ: Dihedral RMS fluctuation test. g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o All 1 comparisons passed. All 5 comparisons passed. All 10 comparisons passed. CPPTRAJ: Ewald test (trunc. oct) CPPTRAJ: PCG32 RNG test. CPPTRAJ: Add time to trajectory test CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. CPPTRAJ: Sorted implicit constant pH stats test CPPTRAJ: Cluster, nosieve loadpairdist CPPTRAJ: Atom XYZ format read, test 2 CPPTRAJ: Command line wildcard test, part 1 CPPTRAJ: Test reading comma-separated list of strings CPPTRAJ: TRR => CRD All 5 comparisons passed. All 23 comparisons passed. CPPTRAJ: Command line wildcard test, part 2 CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats All 13 comparisons passed. make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' Unit test passed. make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' CPPTRAJ: Test nested loops and variables in loops CPPTRAJ: Energy minimization with nonbond term test. CPPTRAJ: Atom XYZ format read, test 3 CPPTRAJ: Test Stdlib RNG CPPTRAJ: Pairdist test, 2 masks. CPPTRAJ: Hausdorff distance of 2D rms output test. All 2 comparisons passed. CPPTRAJ: Randomize (no restrictions) CPPTRAJ: Unsorted pH read/write test All 4 comparisons passed. All 3 comparisons passed. All 16 comparisons passed. All 4 comparisons passed. All 3 comparisons passed. All 5 comparisons passed. CPPTRAJ: OpenMM basic energy minimization tests (bonds) CPPTRAJ: Modify time info test. CPPTRAJ: Atom XYZ format read, test 4 CPPTRAJ: Ewald test (partial system, trunc. oct) CPPTRAJ: GIST test, orthogonal cell CPPTRAJ: CRD(1-5) => TRR CPPTRAJ: Test Mersenne Twister RNG CPPTRAJ: Cluster, sieve5 savepairdist CPPTRAJ: XtalSymm Reimaging by Atom CPPTRAJ: Test loop over data set blocks All 4 comparisons passed. All 4 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 All 5 comparisons passed. 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: Test for filename wildcards and oversets CPPTRAJ: Atom XYZ format read, test 5 CPPTRAJ: OpenMM basic energy minimization tests (angles) CPPTRAJ: CRD(6-10) => TRR ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LibPME CPPTRAJ: Particle mesh Ewald test (NaCl crystal) All 13 comparisons passed. CPPTRAJ: Particle mesh Ewald test (trunc. oct) CPPTRAJ: Atom XYZ format read, test 6 CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) All 6 comparisons passed. CPPTRAJ: Read specific columns test. CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) CPPTRAJ: TRR (appended) => CRD CPPTRAJ: Write non-square matrix CPPTRAJ: GMX: CRD with offset CPPTRAJ: Cluster, sieve5 loadpairdist CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) CPPTRAJ: Read non-square matrix CPPTRAJ: Particle mesh Ewald test (ortho) All 5 comparisons passed. CPPTRAJ: Cluster, nosieve pairwisecache none CPPTRAJ: Read square matrix CPPTRAJ: GMX: TRR with offset All 15 comparisons passed. All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc CPPTRAJ: XTC read test CPPTRAJ: Cluster, sieve5 pairwisecache none CPPTRAJ: Particle mesh Ewald test (ortho, with mask) CPPTRAJ: CRD => XTC CPPTRAJ: Cluster, random CPPTRAJ: PME test (partial system, trunc. oct) All 28 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). CPPTRAJ: XTC => CRD CPPTRAJ: XtalSymm Reimaging by Molecule CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). 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: CRD(1-5) => XTC CPPTRAJ: LJ PME kappa sweep test, 0.25 All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet CPPTRAJ: Clustering, One DataSet CPPTRAJ: CRD(6-10) => XTC CPPTRAJ: Clustering, Two DataSets CPPTRAJ: LJ PME kappa sweep test, 0.35 CPPTRAJ: Clustering, dihedral DataSet CPPTRAJ: XTC (appended) => CRD CPPTRAJ: Clustering, two dihedral DataSets CPPTRAJ: Clustering, dihedral DataSet, K-means CPPTRAJ: LJ PME kappa sweep test, 0.45 CPPTRAJ: Clustering, two dihedral DataSets, K-means CPPTRAJ: GMX: CRD with offset All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN CPPTRAJ: DBSCAN test CPPTRAJ: LJ PME kappa sweep test, 0.5 All 9 comparisons passed. CPPTRAJ: DBSCAN automatic parameter determination test. CPPTRAJ: GMX: XTC with offset CPPTRAJ: DBSCAN kdist map test CPPTRAJ: LJ with switch function test CPPTRAJ: DBSCAN with sieve All 5 comparisons passed. All 4 comparisons passed. All 4 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTNG CPPTRAJ: TNG read test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans CPPTRAJ: Cpptraj Kmeans CPPTRAJ: Cpptraj Kmeans random CPPTRAJ: GIST test, nonorthogonal cell All 6 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_SymmRMSD CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) CPPTRAJ: TNG read test (with offset) All 5 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites CPPTRAJ: Cluster command test, coordinate writes. CPPTRAJ: Cluster command test, coordinate writes using info file. All 6 comparisons passed. All 8 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Dpeaks CPPTRAJ: Density peaks clustering test All 3 comparisons passed. All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Nreps CPPTRAJ: Clustering with specified # reps All 2 comparisons passed. All 11 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST_Order CPPTRAJ: TIP3P water cluster test CPPTRAJ: TIP4P water cluster test CPPTRAJ: TIP5P water cluster test All 4 comparisons passed. make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' /usr/bin/make -C test summary make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' -rwxr-xr-x 1 pbuilder2 pbuilder2 186123352 Sep 9 04:55 ../bin/cpptraj ===================== TEST SUMMARY ====================== 853 out of 859 comparisons OK (0 failed, 0 warnings, 6 skipped). 480 out of 480 program executions completed. 170 out of 173 tests completed with no issues. 2 tests skipped. ========================================================= make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/cpptraj/ make -j42 install DESTDIR=/build/reproducible-path/cpptraj-5.1.0\+dfsg/debian/cpptraj AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make install make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' Skipping bundled READLINE build Skipping bundled ARPACK build g++ -o cpptraj SpaceGroup.o ActionFrameCounter.o ActionList.o ActionTopWriter.o Action_Align.o Action_Angle.o Action_AreaPerMol.o Action_AtomMap.o Action_AtomicCorr.o Action_AtomicFluct.o Action_AutoImage.o Action_Average.o Action_Bounds.o Action_Box.o Action_Center.o Action_Channel.o Action_CheckChirality.o Action_CheckStructure.o Action_Closest.o Action_ClusterDihedral.o Action_Contacts.o Action_CreateCrd.o Action_CreateReservoir.o Action_DNAionTracker.o Action_DSSP.o Action_Density.o Action_Diffusion.o Action_Dihedral.o Action_DihedralRMS.o Action_Dipole.o Action_Distance.o Action_DistRmsd.o Action_Energy.o Action_FilterByData.o Action_FixAtomOrder.o Action_FixImagedBonds.o Action_GIST.o Action_Grid.o Action_GridFreeEnergy.o Action_HydrogenBond.o Action_Image.o Action_InfraredSpectrum.o Action_Jcoupling.o Action_LESsplit.o Action_LIE.o Action_LipidOrder.o Action_MakeStructure.o Action_Mask.o Action_Matrix.o Action_MinImage.o Action_Molsurf.o Action_MultiDihedral.o Action_MultiVector.o Action_NAstruct.o Action_NativeContacts.o Action_NMRrst.o Action_OrderParameter.o Action_Outtraj.o Action_PairDist.o Action_Pairwise.o Action_Principal.o Action_Projection.o Action_Pucker.o Action_Radgyr.o Action_Radial.o Action_RandomizeIons.o Action_Remap.o Action_ReplicateCell.o Action_Rmsd.o Action_Rotate.o Action_RunningAvg.o Action_STFC_Diffusion.o Action_Scale.o Action_SetVelocity.o Action_Spam.o Action_Strip.o Action_Surf.o Action_SymmetricRmsd.o Action_Temperature.o Action_Time.o Action_Translate.o Action_Unstrip.o Action_Unwrap.o Action_Vector.o Action_VelocityAutoCorr.o Action_Volmap.o Action_Volume.o Action_Watershell.o Action_XtalSymm.o AnalysisList.o Analysis_AmdBias.o Analysis_AutoCorr.o Analysis_Average.o Analysis_Clustering.o Analysis_Corr.o Analysis_ConstantPHStats.o Analysis_CrankShaft.o Analysis_CrdFluct.o Analysis_CrossCorr.o Analysis_CurveFit.o Analysis_Divergence.o Analysis_EvalPlateau.o Analysis_FFT.o Analysis_HausdorffDistance.o Analysis_Hist.o Analysis_Integrate.o Analysis_IRED.o Analysis_KDE.o Analysis_Lifetime.o Analysis_LowestCurve.o Analysis_Matrix.o Analysis_MeltCurve.o Analysis_Modes.o Analysis_Multicurve.o Analysis_MultiHist.o Analysis_Overlap.o Analysis_PhiPsi.o Analysis_Regression.o Analysis_RemLog.o Analysis_Rms2d.o Analysis_RmsAvgCorr.o Analysis_Rotdif.o Analysis_RunningAvg.o Analysis_Slope.o Analysis_Spline.o Analysis_State.o Analysis_Statistics.o Analysis_TI.o Analysis_Timecorr.o Analysis_VectorMath.o Analysis_Wavelet.o ArgList.o Array1D.o AssociatedData.o Atom.o AtomMap.o AtomMask.o AxisType.o BondSearch.o Box.o BoxArgs.o BufferedFrame.o BufferedLine.o ByteRoutines.o CharMask.o CharmmParamFile.o CIFfile.o ClusterDist.o ClusterList.o ClusterMap.o ClusterMatrix.o ClusterNode.o ClusterSieve.o Cluster_DBSCAN.o Cluster_DPeaks.o Cluster_HierAgglo.o Cluster_Kmeans.o Cluster_ReadInfo.o Cmd.o CmdInput.o CmdList.o CompactFrameArray.o ComplexArray.o Constraints.o ControlBlock_For.o CoordinateInfo.o Corr.o Cph.o CpptrajFile.o CpptrajState.o CpptrajStdio.o CurveFit.o DataFile.o DataFileList.o DataFilter.o DataIO.o DataIO_CCP4.o DataIO_CharmmFastRep.o DataIO_CharmmOutput.o DataIO_CharmmRepLog.o DataIO_CharmmRtfPrm.o DataIO_Cmatrix.o DataIO_Cpout.o DataIO_Evecs.o DataIO_Gnuplot.o DataIO_Grace.o DataIO_OpenDx.o DataIO_Peaks.o DataIO_Mdout.o DataIO_NC_Cmatrix.o DataIO_RemLog.o DataIO_Std.o DataIO_VecTraj.o DataIO_Xplor.o DataIO_XVG.o DataSet.o DataSetList.o DataSet_1D.o DataSet_3D.o DataSet_Cmatrix.o DataSet_Cmatrix_DISK.o DataSet_Cmatrix_MEM.o DataSet_Cmatrix_NOMEM.o DataSet_Coords.o DataSet_Coords_CRD.o DataSet_Coords_REF.o DataSet_Coords_TRJ.o DataSet_GridDbl.o DataSet_GridFlt.o DataSet_Mat3x3.o DataSet_MatrixDbl.o DataSet_MatrixFlt.o DataSet_Mesh.o DataSet_Modes.o DataSet_Parameters.o DataSet_pH.o DataSet_PHREMD_Explicit.o DataSet_PHREMD_Implicit.o DataSet_RemLog.o DataSet_Topology.o DataSet_Vector.o DataSet_Vector_Scalar.o DataSet_double.o DataSet_float.o DataSet_integer_disk.o DataSet_integer_mem.o DataSet_string.o DataSet_StringVar.o DataSet_Tensor.o DataSet_unsignedInt.o Deprecated.o DihedralSearch.o DistRoutines.o Energy.o EnergyArray.o EnsembleIn.o EnsembleIn_Multi.o EnsembleIn_Single.o EnsembleNavigator.o EnsembleOut.o EnsembleOut_Multi.o EnsembleOut_Single.o EnsembleOutList.o Ewald.o Ewald_ParticleMesh.o Ewald_Regular.o ExclusionArray.o Exec_AddMissingRes.o Exec_Analyze.o Exec_Calc.o Exec_CatCrd.o Exec_Change.o Exec_ClusterMap.o Exec_CombineCoords.o Exec_Commands.o Exec_CompareTop.o Exec_CrdAction.o Exec_CrdOut.o Exec_CreateSet.o Exec_DataFile.o Exec_DataFilter.o Exec_DataSetCmd.o Exec_Emin.o Exec_Flatten.o Exec_GenerateAmberRst.o Exec_Graft.o Exec_Help.o Exec_LoadCrd.o Exec_LoadTraj.o Exec_ParallelAnalysis.o Exec_ParmBox.o Exec_ParmSolvent.o Exec_ParmStrip.o Exec_ParmWrite.o Exec_PermuteDihedrals.o Exec_Precision.o Exec_PrepareForLeap.o Exec_PrintData.o Exec_Random.o Exec_ReadData.o Exec_ReadEnsembleData.o Exec_ReadInput.o Exec_RotateDihedral.o Exec_RunAnalysis.o Exec_ScaleDihedralK.o Exec_Set.o Exec_SequenceAlign.o Exec_Show.o Exec_SortEnsembleData.o Exec_SplitCoords.o Exec_System.o Exec_Top.o Exec_Traj.o Exec_UpdateParameters.o Exec_ViewRst.o File_TempName.o FileIO_Bzip2.o FileIO_Gzip.o FileIO_Mpi.o FileIO_MpiShared.o FileIO_Std.o FileName.o FileType.o FileTypes.o ForLoop.o ForLoop_dataSetBlocks.o ForLoop_integer.o ForLoop_list.o ForLoop_mask.o ForLoop_overSets.o Frame.o GridAction.o HistBin.o Hungarian.o ImageRoutines.o Image_List_Mask.o Image_List_Pair.o Image_List_Unit.o InputTrajCommon.o KDE.o MapAtom.o MaskArray.o MaskToken.o Matrix_3x3.o MdOpts.o MetaData.o Minimize_SteepestDescent.o Mol.o Mol2File.o NameType.o NC_Cmatrix.o NC_Routines.o NetcdfFile.o OMM_helpers.o OutputTrajCommon.o ParameterSet.o PDBfile.o PairList.o Parallel.o ParallelNetcdf.o ParmFile.o Parm_Amber.o Parm_CharmmPsf.o Parm_CIF.o Parm_Gromacs.o Parm_Mol2.o Parm_PDB.o Parm_SDF.o Parm_Tinker.o PotentialFunction.o PotentialTerm.o PotentialTerm_Angle.o PotentialTerm_Bond.o PotentialTerm_Dihedral.o PotentialTerm_LJ_Coulomb.o PotentialTerm_OpenMM.o ProgressBar.o ProgressTimer.o PubFFT.o ExternalFxn.o Random.o Range.o RNG.o RNG_Marsaglia.o RNG_MersenneTwister.o RNG_PCG32.o RNG_Stdlib.o RNG_Xoshiro128pp.o RPNcalc.o ReferenceAction.o RemdReservoirNC.o Residue.o SDFfile.o SimplexMin.o Spline.o SplineFxnTable.o StringRoutines.o StructureCheck.o StructureMapper.o SymmetricRmsdCalc.o TextFormat.o Timer.o TinkerFile.o TopInfo.o Topology.o TorsionRoutines.o Traj_AmberCoord.o Traj_AmberNetcdf.o Traj_AmberRestart.o Traj_AmberRestartNC.o Traj_Binpos.o Traj_CharmmCor.o Traj_CharmmDcd.o Traj_CharmmRestart.o Traj_CIF.o Traj_Conflib.o Traj_DTR.o Traj_GmxDump.o Traj_GmxTng.o Traj_GmxTrX.o Traj_GmxXtc.o Traj_Gro.o Traj_Mol2File.o Traj_NcEnsemble.o Traj_PDBfile.o Traj_SDF.o Traj_SQM.o Traj_Tinker.o Traj_XYZ.o TrajectoryFile.o TrajectoryIO.o TrajFrameCounter.o TrajinList.o Trajin_Multi.o Trajin_Single.o TrajIOarray.o Trajout_Single.o TrajoutList.o Vec3.o ViewRst.o xoshiro128plusplus.o Action_Esander.o Command.o Cpptraj.o Energy_Sander.o ReadLine.o main.o molsurf.o -L/usr/lib/x86_64-linux-gnu/lib -lreadline -ltermcap -L/usr/lib/x86_64-linux-gnu/lib -larpack -llapack -lblas -L/usr/lib/x86_64-linux-gnu/lib -lfftw3 -L/usr/lib/x86_64-linux-gnu/lib -lOpenMM -lnetcdf -lbz2 tng/libtng_io.a -lz xdrfile/libxdrfile.a -Wl,-z,relro mv cpptraj "/build/reproducible-path/cpptraj-5.1.0+dfsg/bin" make[2]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libreadline8t64 from: /lib/x86_64-linux-gnu/libreadline.so.8 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libreadline8t64 to: /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'cpptraj' in '../cpptraj_5.1.0+dfsg-4_amd64.deb'. dpkg-deb: building package 'cpptraj-dbgsym' in '../cpptraj-dbgsym_5.1.0+dfsg-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../cpptraj_5.1.0+dfsg-4_amd64.buildinfo dpkg-genchanges --build=binary -O../cpptraj_5.1.0+dfsg-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/503249/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/503249/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/503249 and its subdirectories I: Current time: Wed Sep 9 18:56:07 +14 2026 I: pbuilder-time-stamp: 1788929767 + false + set +x Wed Sep 9 04:56:07 UTC 2026 I: Signing ./b2/cpptraj_5.1.0+dfsg-4_amd64.buildinfo as cpptraj_5.1.0+dfsg-4_amd64.buildinfo.asc Wed Sep 9 04:56:07 UTC 2026 I: Signed ./b2/cpptraj_5.1.0+dfsg-4_amd64.buildinfo as ./b2/cpptraj_5.1.0+dfsg-4_amd64.buildinfo.asc Wed Sep 9 04:56:07 UTC 2026 - build #2 for cpptraj/unstable/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Wed Sep 9 04:56:07 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-J4qH9VRJ, removing. /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4: total 208 drwxr-xr-x 2 jenkins jenkins 4096 Aug 6 22:30 b1 drwxr-xr-x 2 jenkins jenkins 4096 Aug 6 22:33 b2 -rw-r--r-- 1 jenkins jenkins 2184 May 13 2024 cpptraj_5.1.0+dfsg-4.dsc -rw------- 1 jenkins jenkins 192847 Aug 6 22:30 rbuildlog.700T9Qk /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/b1: total 42800 -rw-r--r-- 1 jenkins jenkins 189248 Aug 6 22:30 build.log -rw-r--r-- 1 jenkins jenkins 41607356 Aug 6 22:30 cpptraj-dbgsym_5.1.0+dfsg-4_amd64.deb -rw-r--r-- 1 jenkins jenkins 6084 Aug 6 22:30 cpptraj_5.1.0+dfsg-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2184 Aug 6 22:30 cpptraj_5.1.0+dfsg-4.dsc -rw-r--r-- 1 jenkins jenkins 8233 Aug 6 22:30 cpptraj_5.1.0+dfsg-4_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 9115 Aug 6 22:30 cpptraj_5.1.0+dfsg-4_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1479 Aug 6 22:30 cpptraj_5.1.0+dfsg-4_amd64.changes -rw-r--r-- 1 jenkins jenkins 1924068 Aug 6 22:30 cpptraj_5.1.0+dfsg-4_amd64.deb -rw-r--r-- 1 jenkins jenkins 1313 Aug 6 22:30 cpptraj_5.1.0+dfsg-4_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/b2: total 42748 -rw-r--r-- 1 jenkins jenkins 191186 Aug 6 22:33 build.log -rw-r--r-- 1 jenkins jenkins 41607356 Aug 6 22:33 cpptraj-dbgsym_5.1.0+dfsg-4_amd64.deb -rw-r--r-- 1 jenkins jenkins 6084 Aug 6 22:33 cpptraj_5.1.0+dfsg-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2184 Aug 6 22:33 cpptraj_5.1.0+dfsg-4.dsc -rw-r--r-- 1 jenkins jenkins 8246 Aug 6 22:33 cpptraj_5.1.0+dfsg-4_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 9128 Aug 6 22:33 cpptraj_5.1.0+dfsg-4_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1479 Aug 6 22:33 cpptraj_5.1.0+dfsg-4_amd64.changes -rw-r--r-- 1 jenkins jenkins 1924068 Aug 6 22:33 cpptraj_5.1.0+dfsg-4_amd64.deb -rw-r--r-- 1 jenkins jenkins 1313 Aug 6 22:33 cpptraj_5.1.0+dfsg-4_source.changes Wed Aug 6 22:33:08 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Wed Aug 6 22:33:08 UTC 2025 I: cpptraj_5.1.0+dfsg-4_amd64.changes: Format: 1.8 Date: Mon, 13 May 2024 10:39:49 -0400 Source: cpptraj Binary: cpptraj cpptraj-dbgsym Architecture: amd64 Version: 5.1.0+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Andrius Merkys Description: cpptraj - fast, parallelized molecular dynamics trajectory data analysis Changes: cpptraj (5.1.0+dfsg-4) unstable; urgency=medium . * Stop the build on test failures. * Build with OpenMM support on armhf, mips64el and riscv64 as well. * Bump copyright years. Checksums-Sha1: 80c8d3b6ff6bdcf4bb78d62abf91eea89c6fe7b8 41607356 cpptraj-dbgsym_5.1.0+dfsg-4_amd64.deb 9a43ad5ecb692b8cf727fc587ac11d0c0cd2cdd4 8233 cpptraj_5.1.0+dfsg-4_amd64.buildinfo e2250e25de21bc65cf0f3905e3e27657bd645413 1924068 cpptraj_5.1.0+dfsg-4_amd64.deb Checksums-Sha256: f36239eb10f7a92f2a373ab5904d00de2049499ba513c066d60abf0098376e17 41607356 cpptraj-dbgsym_5.1.0+dfsg-4_amd64.deb ed8c2abd66ac29f6e3defb32888fdda76a1f2ebe750f132a3679895bfe02f830 8233 cpptraj_5.1.0+dfsg-4_amd64.buildinfo ceda1e077ef68c0a5967803e8b4cf571340235b8a75fe89c75d9acca62fcc03e 1924068 cpptraj_5.1.0+dfsg-4_amd64.deb Files: ea6e49d65b8a00cb79e0428afb8301e9 41607356 debug optional cpptraj-dbgsym_5.1.0+dfsg-4_amd64.deb ca1becf30907f3102bd65560b3bb10b3 8233 science optional cpptraj_5.1.0+dfsg-4_amd64.buildinfo 9914a7ecec0a95ec98180c6253506dff 1924068 science optional cpptraj_5.1.0+dfsg-4_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/cpptraj_5.1.0+dfsg-4.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/cpptraj_5.1.0+dfsg-4.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/cpptraj_5.1.0+dfsg-4.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/cpptraj_5.1.0+dfsg-4.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/cpptraj_5.1.0+dfsg-4_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/cpptraj_5.1.0+dfsg-4.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-08-06 22:30:06.137172377 +0000 +++ b2/build.log 2025-08-06 22:33:07.993408368 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Aug 6 10:26:58 -12 2025 -I: pbuilder-time-stamp: 1754519218 +I: Current time: Wed Sep 9 18:53:09 +14 2026 +I: pbuilder-time-stamp: 1788929589 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: applying skip-failing-test.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2415790/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/503249/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 9 04:53 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/503249/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/503249/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='bce42d0f097543b7a362b6996b6ac080' - 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='2415790' - PS1='# ' - PS2='> ' + INVOCATION_ID=70e375baa18a45ac8df32afa5538549f + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=503249 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.dE0NwvQ4/pbuilderrc_rHzM --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/b1 --logfile b1/build.log cpptraj_5.1.0+dfsg-4.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/pbuilderrc_J1VS --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/b2 --logfile b2/build.log cpptraj_5.1.0+dfsg-4.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-37-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.140-1 (2025-05-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.33+deb12-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.33-1~bpo12+1 (2025-07-09) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2415790/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/503249/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -253,7 +285,7 @@ Get: 129 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libreadline-dev amd64 8.2-6 [153 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 netcdf-bin amd64 1:4.9.3-1 [260 kB] -Fetched 64.2 MB in 1s (51.0 MB/s) +Fetched 64.2 MB in 1s (88.8 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 ... 19850 files and directories currently installed.) @@ -803,7 +835,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/cpptraj-5.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../cpptraj_5.1.0+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/503249/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/503249/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/cpptraj-5.1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../cpptraj_5.1.0+dfsg-4_source.changes dpkg-buildpackage: info: source package cpptraj dpkg-buildpackage: info: source version 5.1.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -816,7 +852,7 @@ make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' touch config.h external.config.h dh_auto_clean - make -j40 clean + make -j42 clean make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make clean make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' @@ -909,7 +945,7 @@ make[1]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_auto_build - make -j40 + make -j42 make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make install make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' @@ -953,6 +989,8 @@ CXX Action_Grid.cpp CXX Action_GridFreeEnergy.cpp CXX Action_HydrogenBond.cpp +CXX Action_Image.cpp +CXX Action_InfraredSpectrum.cpp In file included from Ewald_ParticleMesh.h:5, from Action_Energy.cpp:4: helpme_standalone.h:2323: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas] @@ -997,8 +1035,6 @@ 4503 | #pragma omp parallel num_threads(nThreads_) helpme_standalone.h:4510: warning: ignoring '#pragma omp for' [-Wunknown-pragmas] 4510 | #pragma omp for -CXX Action_Image.cpp -CXX Action_InfraredSpectrum.cpp CXX Action_Jcoupling.cpp CXX Action_LESsplit.cpp CXX Action_LIE.cpp @@ -1024,6 +1060,9 @@ CXX Action_Radial.cpp CXX Action_RandomizeIons.cpp CXX Action_Remap.cpp +CXX Action_ReplicateCell.cpp +CXX Action_Rmsd.cpp +CXX Action_Rotate.cpp In file included from Matrix_3x3.h:3, from Box.h:3, from Frame.h:5, @@ -1092,9 +1131,6 @@ Action_GIST.cpp:783:10: note: 'WAT' declared here 783 | Vec3 WAT[4]; | ^~~ -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 @@ -1212,11 +1248,6 @@ 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 In file included from /usr/include/c++/14/vector:66, from ArgList.h:3, from Action.h:4, @@ -1247,6 +1278,11 @@ Action_XtalSymm.cpp:58:33: note: '' declared here 58 | RefT_.assign(nCopyTotal, Vec3()); | ^ +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 @@ -1281,8 +1317,8 @@ CXX DataSet_float.cpp CXX DataSet_integer_disk.cpp CXX DataSet_integer_mem.cpp -CXX DataSet_string.cpp CXX DataSet_StringVar.cpp +CXX DataSet_string.cpp CXX DataSet_Tensor.cpp CXX DataSet_unsignedInt.cpp CXX Deprecated.cpp @@ -1367,6 +1403,9 @@ CXX Exec_Graft.cpp CXX Exec_Help.cpp CXX Exec_LoadCrd.cpp +CXX Exec_LoadTraj.cpp +CXX Exec_ParallelAnalysis.cpp +CXX Exec_ParmBox.cpp helpme_standalone.h: In instantiation of 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]': helpme_standalone.h:3898:50: required from 'void helpme::PMEInstance >::setLatticeVectors(Real, Real, Real, Real, Real, Real, LatticeType) [with Real = double; typename std::enable_if::value, int>::type = 0]' 3898 | auto eigenTuple = HtH.diagonalize(); @@ -1384,7 +1423,6 @@ helpme_standalone.h:1013:31: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 1013 | for (int val = 0; val < nRows_; ++val) { | ~~~~^~~~~~~~ -CXX Exec_LoadTraj.cpp helpme_standalone.h: In instantiation of 'void helpme::PMEInstance >::sanityChecks(int, const RealMat&, const RealMat&, int) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]': helpme_standalone.h:5018:9: required from 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0; RealMat = helpme::Matrix]' 5018 | sanityChecks(parameterAngMom, parameters, coordinates); @@ -1440,7 +1478,6 @@ helpme_standalone.h:4004:28: warning: variable 'realCBA' set but not used [-Wunused-but-set-variable] 4004 | Real *__restrict__ realCBA; | ^~~~~~~ -CXX Exec_ParallelAnalysis.cpp helpme_standalone.h: In instantiation of 'void helpme::Matrix::assertSymmetric(const Real&) const [with Real = double]': helpme_standalone.h:1000:9: required from 'std::pair, helpme::Matrix > helpme::Matrix::diagonalize(SortOrder) const [with Real = double]' 1000 | assertSymmetric(); @@ -1510,7 +1547,7 @@ helpme_standalone.h:2208:72: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'short int' [-Wsign-compare] 2208 | if (splines_.nRows() < derivativeLevel + 1 || splines_.nCols() != order) | ~~~~~~~~~~~~~~~~~^~~~~~~~ -CXX Exec_ParmBox.cpp +CXX Exec_ParmSolvent.cpp helpme_standalone.h: In instantiation of 'helpme::Matrix helpme::Matrix::multiply(const helpme::Matrix&) const [with Real = double]': helpme_standalone.h:877:64: required from 'helpme::Matrix helpme::Matrix::operator*(const helpme::Matrix&) const [with Real = double]' 877 | Matrix operator*(const Matrix& other) const { return this->multiply(other); } @@ -1540,7 +1577,6 @@ helpme_standalone.h:863:41: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare] 863 | for (int link = 0; link < nCols_; ++link) { | ~~~~~^~~~~~~~ -CXX Exec_ParmSolvent.cpp CXX Exec_ParmStrip.cpp CXX Exec_ParmWrite.cpp CXX Exec_PermuteDihedrals.cpp @@ -1636,8 +1672,8 @@ CXX RNG_MersenneTwister.cpp CXX RNG_PCG32.cpp CXX RNG_Stdlib.cpp -CXX RPNcalc.cpp CXX RNG_Xoshiro128pp.cpp +CXX RPNcalc.cpp CXX ReferenceAction.cpp CXX RemdReservoirNC.cpp CXX Residue.cpp @@ -1649,6 +1685,9 @@ CXX StructureCheck.cpp CXX StructureMapper.cpp CXX SymmetricRmsdCalc.cpp +CXX TextFormat.cpp +CXX Timer.cpp +CXX TinkerFile.cpp helpme_standalone.h: In function 'void helpme::PMEInstance >::setupCalculationMetadata(int, Real, int, int, int, int, int, int, int, Real, int, void*, NodeOrder, int, int, int) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:3470:17: warning: '*(unsigned char (*)[60])((char*)& + offsetof(helpme::FFTWWrapper,helpme::FFTWWrapper::forwardPlan_))' may be used uninitialized [-Wmaybe-uninitialized] 3470 | fftHelperA_ = FFTWWrapper(); @@ -1695,9 +1734,6 @@ helpme_standalone.h:3505:45: note: '' declared here 3505 | compressionCoefficientsC_ = RealMat(); | ^~~~~~~~~ -CXX TextFormat.cpp -CXX Timer.cpp -CXX TinkerFile.cpp CXX TopInfo.cpp CXX Topology.cpp CXX TorsionRoutines.cpp @@ -1723,10 +1759,6 @@ 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 helpme_standalone.h: In member function 'Real helpme::PMEInstance >::computeERec(int, const RealMat&, const RealMat&) [with Real = double; typename std::enable_if::value, int>::type = 0]': helpme_standalone.h:5031:16: warning: 'energy' may be used uninitialized [-Wmaybe-uninitialized] 5031 | return energy; @@ -1734,7 +1766,11 @@ helpme_standalone.h:5021:14: note: 'energy' was declared here 5021 | Real energy; | ^~~~~~ +CXX Traj_XYZ.cpp +CXX TrajectoryFile.cpp +CXX TrajectoryIO.cpp CXX TrajinList.cpp +CXX TrajFrameCounter.cpp CXX Trajin_Multi.cpp CXX Trajin_Single.cpp CXX TrajIOarray.cpp @@ -1759,20 +1795,20 @@ CXX main.cpp CC molsurf.c -Skipping bundled READLINE build - cd xdrfile && make all +Skipping bundled READLINE build make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' + CC xdrfile.c +CC xdr_seek.c +CC xdrfile_trr.c +cd tng && make all Skipping bundled ARPACK build -cd tng && make all make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/tng' -CC md5.c -CC xdr_seek.c -CC xdrfile_trr.c CC xdrfile_xtc.c +CC md5.c CC tng_io.c CC tng_compress.c CC coder.c @@ -1791,9 +1827,6 @@ CC dict.c CC huffman.c CC merge_sort.c -/bin/rm -f libxdrfile.a -ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o -make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' tng_io.c: In function 'tng_gen_data_block_add': tng_io.c:12600:9: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-truncation] 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); @@ -1801,6 +1834,9 @@ tng_io.c:12600:47: note: length computed here 12600 | strncpy(data->block_name, block_name, strlen(block_name) + 1); | ^~~~~~~~~~~~~~~~~~ +/bin/rm -f libxdrfile.a +ar cqs libxdrfile.a xdrfile.o xdr_seek.o xdrfile_trr.o xdrfile_xtc.o +make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src/xdrfile' /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' @@ -1811,7 +1847,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' dh_auto_test -- check unittest - make -j40 test "TESTSUITEFLAGS=-j40 --verbose" VERBOSE=1 check unittest + make -j42 test "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 check unittest make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' make[2]: Nothing to be done for 'test'. cd test && make test.complete summary @@ -1819,8 +1855,8 @@ make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' make[3]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src - CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h + CPPTRAJ source directory: /build/reproducible-path/cpptraj-5.1.0+dfsg/src CPPTRAJ config.h file: /build/reproducible-path/cpptraj-5.1.0+dfsg/config.h make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' ******************************************************************************** @@ -1831,1771 +1867,1738 @@ CPPTRAJ: NameType class unit test. CPPTRAJ: ArgList class unit test. +-rwxr-xr-x 1 pbuilder2 pbuilder2 186123352 Sep 9 04:55 ../bin/cpptraj +make[4]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/test' +-rwxr-xr-x 1 pbuilder2 pbuilder2 186123352 Sep 9 04:55 ../bin/cpptraj make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' -g++ -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o NameType.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/NameType.cpp make[5]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' g++ -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp -g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp +g++ -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o main.o main.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o ArgList.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/ArgList.cpp +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o NameType.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/NameType.cpp +g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o CpptrajStdio.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/CpptrajStdio.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DC11_SUPPORT -DLIBPME -DHAVE_FFTWD=1 -DBUILDTYPE='"GitHub"' -DBINTRAJ -DHASBZ2 -DHAS_TNGFILE -DHASGZ -DFFTW_FFT -DHAS_OPENMM -Wall -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/cpptraj-5.1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=gnu++11 -I/build/reproducible-path/cpptraj-5.1.0+dfsg/src -c -o StringRoutines.o /build/reproducible-path/cpptraj-5.1.0+dfsg/src/StringRoutines.cpp --rwxr-xr-x 1 pbuilder1 pbuilder1 186123352 Aug 6 22:29 ../bin/cpptraj --rwxr-xr-x 1 pbuilder1 pbuilder1 186123352 Aug 6 22:29 ../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_TrajinOffset -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Strip ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_General ******************************************************************************** ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Jcoupling TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RemdTraj -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DSSP -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hbond - - CPPTRAJ: Normal trajectory read with offsets. - - CPPTRAJ: Broken Traj: Running good trajectory. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_trajout_framerange - - CPPTRAJ: One frame strip command test - - CPPTRAJ: CRD Replica Trajectory Run with offset - - CPPTRAJ: Secstruct (DSSP) command test. - - CPPTRAJ: Per-Residue RMSD Test. ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Runavg ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Center TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Image - - CPPTRAJ: Solute Hbond test ******************************************************************************** - - CPPTRAJ: General tests -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NCrestart ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radgyr - - CPPTRAJ: Trajout Frame Range [Amber Restart] +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf ******************************************************************************** - - CPPTRAJ: Center command test. -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Jcoupling - - CPPTRAJ: Orthorhombic imaged distance test. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotdif ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diffusion +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_BrokenTraj ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PerResRMSD ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Surf - - CPPTRAJ: Radius of gyration command test - - CPPTRAJ: NetCDF Restart Test - TXT->NetCDF -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotdif ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Center +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Average ******************************************************************************** - - CPPTRAJ: J-Coupling single frame test -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_2DRMS +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diffusion ******************************************************************************** - - CPPTRAJ: RMSD Test with outtraj. - -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mol2 - CPPTRAJ: Surface calculation test +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TrajinOffset +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radgyr ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Average +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Charmm ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RMSD ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Runavg - - CPPTRAJ: Diffusion test, no imaging. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NCrestart ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Outtraj +******************************************************************************** +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mol2 +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mask TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomMap ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pucker +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Strip +******************************************************************************** ******************************************************************************** +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DRMSD +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_2DRMS +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct +******************************************************************************** + TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Datafile + CPPTRAJ: General tests - CPPTRAJ: NAstruct command test. + CPPTRAJ: J-Coupling single frame test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pucker + CPPTRAJ: Surface calculation test ******************************************************************************** - CPPTRAJ: Average Test. -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NetcdfTraj +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_trajout_framerange + CPPTRAJ: Coordinate Running Average test. - CPPTRAJ: Mol2 Parm/Traj Read/Write Test. + CPPTRAJ: Orthorhombic imaged distance test. - CPPTRAJ: Coordinate Running Average test. + CPPTRAJ: 1D/2D Histogram Analysis test - CPPTRAJ: 2D RMSD Test. - CPPTRAJ: Basic RMSD tests - CPPTRAJ: CHARMM PSF/DCD test + CPPTRAJ: Solute Hbond test + CPPTRAJ: Rotational diffusion calculation test + CPPTRAJ: Broken Traj: Running good trajectory. + CPPTRAJ: Average Test. - CPPTRAJ: AtomMap Test - CPPTRAJ: Pucker command test - CPPTRAJ: Mask single frame test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Radial + CPPTRAJ: Radial test, non-orthogonal imaging - CPPTRAJ: Data file output precision test + CPPTRAJ: Normal trajectory read with offsets. - CPPTRAJ: Convert mdcrd -> NetCDF + + CPPTRAJ: Center command test. + CPPTRAJ: Radius of gyration command test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hist +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Mask +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DSSP - CPPTRAJ: Rotational diffusion calculation test + CPPTRAJ: Per-Residue RMSD Test. - CPPTRAJ: 1D/2D Histogram Analysis test + CPPTRAJ: CHARMM PSF/DCD test - CPPTRAJ: Radial test, non-orthogonal imaging -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Closest + CPPTRAJ: Mol2 Parm/Traj Read/Write Test. + CPPTRAJ: Convert mdcrd -> NetCDF - CPPTRAJ: Gzipped trajectory read with offsets - CPPTRAJ: Closest command test using first solvent atom. - CPPTRAJ: CRD Replica Trajectory Run + CPPTRAJ: Diffusion test, no imaging. + CPPTRAJ: RMSD Test with outtraj. - CPPTRAJ: NetCDF Restart Test - NetCDF->TXT - J-Coupling extended test requires CPPTRAJHOME or AMBERHOME to be set. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DRMSD - Skipped test: J-Coupling extended test - CPPTRAJ: 2D RMSD Test, mass-weighted. + CPPTRAJ: AtomMap Test + CPPTRAJ: CRD Replica Trajectory Run with offset -All 1 comparisons passed. -1 comparisons skipped. + + CPPTRAJ: NAstruct command test. + CPPTRAJ: NetCDF Restart Test - TXT->NetCDF + + CPPTRAJ: Closest command test using first solvent atom. + + CPPTRAJ: Basic RMSD tests + CPPTRAJ: Data file output precision test CPPTRAJ: Distance RMSD test + CPPTRAJ: One frame strip command test - CPPTRAJ: Broken Traj: Running broken trajectory. - CPPTRAJ: CHARMM DCD Write, step 1. + CPPTRAJ: 2D RMSD Test. -All 2 comparisons passed. + CPPTRAJ: Pucker command test - CPPTRAJ: Center origin command test. + CPPTRAJ: Secstruct (DSSP) command test. + CPPTRAJ: Mask single frame test + + CPPTRAJ: Trajout Frame Range [Amber Restart] + 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: 5-member ring pucker, Cremer & Pople Furanoid test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster - CPPTRAJ: PDB => Mol2 - CPPTRAJ: Non-orthorhombic imaged distance test. -All 2 comparisons passed. + CPPTRAJ: NetCDF Restart Test - NetCDF->TXT + CPPTRAJ: Coordinate Running Average Traj Write + CPPTRAJ: 2D RMSD Test, mass-weighted. + CPPTRAJ: Gzipped trajectory read with offsets - CPPTRAJ: Cluster command test, in-memory pairwise distances. + CPPTRAJ: PDB => Mol2 - CPPTRAJ: Coordinate Running Average Traj Write + CPPTRAJ: CRD Replica Trajectory Run CPPTRAJ: Diffusion test, old syntax. - CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. + CPPTRAJ: 5-member ring pucker, Cremer & Pople Furanoid test - CPPTRAJ: Per-Residue RMSD Test with averaging + CPPTRAJ: Closest command test using all solvent atoms. + + CPPTRAJ: Cluster command test, in-memory pairwise distances. + + CPPTRAJ: CHARMM DCD Write, step 1. CPPTRAJ: Standard -> Grace Data + + CPPTRAJ: Center origin command test. + +All 2 comparisons passed. + + CPPTRAJ: Unstrip (Lig/Rec/Complex) command test + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_IRED -All 4 comparisons passed. + CPPTRAJ: Broken Traj: Running broken trajectory. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons +All 1 comparisons passed. - CPPTRAJ: Mask longer command test. CPPTRAJ: IRED vector/matrix test - CPPTRAJ: randomizeions test (original algorithm) +All 2 comparisons passed. - CPPTRAJ: Trajout Frame Range [Amber Coordinates] - CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF +All 2 comparisons passed. - CPPTRAJ: AtomMap with 'rmsfit' +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RandomizeIons - CPPTRAJ: Bzip2ed trajectory read with offsets + CPPTRAJ: randomizeions test (original algorithm) ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Molsurf - CPPTRAJ: Solute Hbond test with disk caching - - CPPTRAJ: NetCDF Replica Trajectory Run test + CPPTRAJ: Molsurf test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Corr - CPPTRAJ: CHARMM DCD Write, step 2. - - CPPTRAJ: Molsurf test +All 4 comparisons passed. - CPPTRAJ: Unstrip (Lig/Rec/Complex) command test CPPTRAJ: Correlation test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RmsAvgCorr - CPPTRAJ: 2D RMSD Test with reference trajectory + CPPTRAJ: Trajout Frame Range [Amber Coordinates] +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckStructure +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Contacts - CPPTRAJ: Amber Top/Rst => Mol2 + CPPTRAJ: RmsAvgCorr Reference -All 2 comparisons passed. + CPPTRAJ: Contacts test. + CPPTRAJ: Structure Check +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Principal - CPPTRAJ: NAstruct command test, single strand + CPPTRAJ: Principal Test - CPPTRAJ: 3D histogram test. +All 6 comparisons passed. - CPPTRAJ: Center origin mass command test. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ClusterDihedral - CPPTRAJ: Orthorhombic coordinate imaging test +All 2 comparisons passed. - CPPTRAJ: Grace -> Standard Data - CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. + CPPTRAJ: clusterdihedral test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckStructure +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Vector - CPPTRAJ: Structure Check +All 3 comparisons passed. -All 6 comparisons passed. + CPPTRAJ: Basic vector tests +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Matrix - CPPTRAJ: Secstruct (DSSP) command with changing number of residues. + CPPTRAJ: Matrix Tests - CPPTRAJ: Atom map charmm->amber atom order +All 4 comparisons passed. - CPPTRAJ: RMS coordinate rotation/rotation matrices test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct - CPPTRAJ: Convert NetCDF -> mdcrd + CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. - CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj - CPPTRAJ: Per-Residue RMSD Test with residue centering. - CPPTRAJ: CHAMBER topology read/strip test. + CPPTRAJ: Structure Check with Around and Skip + CPPTRAJ: Non-orthorhombic imaged distance test. + CPPTRAJ: 2D RMSD Test with reference trajectory - CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt -All 1 comparisons passed. + CPPTRAJ: Bzip2ed trajectory read with offsets - Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. - Skipped test: Amber Top/Rst => Mol2, SYBYL atom types + CPPTRAJ: Mask longer command test. + CPPTRAJ: NetCDF Replica Trajectory Run test -All 4 comparisons passed. -1 comparisons skipped. - CPPTRAJ: Cluster command test, read pairwise distances. + CPPTRAJ: AtomMap with 'rmsfit' + CPPTRAJ: 6-member ring pucker, Cremer & Pople Pyranoid test. + CPPTRAJ: Solute Hbond test with disk caching - CPPTRAJ: 2D DME Test. + CPPTRAJ: Grace -> Standard Data -All 5 comparisons passed. + CPPTRAJ: Center origin mass command test. + CPPTRAJ: 3D histogram test. - CPPTRAJ: Start argument offset -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RmsAvgCorr - CPPTRAJ: RmsAvgCorr Reference + CPPTRAJ: Cluster command test, read pairwise distances. + CPPTRAJ: NAstruct command test, single strand - CPPTRAJ: Solute-solvent hbond test + CPPTRAJ: Per-Residue RMSD Test with averaging -All 11 comparisons passed. + CPPTRAJ: Amber Top/Rst => Mol2 -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Contacts -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Principal - CPPTRAJ: Contacts test. + CPPTRAJ: Diffusion test, new syntax. + CPPTRAJ: RmsAvgCorr First - CPPTRAJ: Closest command test using all solvent atoms. + CPPTRAJ: NetCDF Restart w/ box Test - Txt->NetCDF -All 7 comparisons passed. + CPPTRAJ: CHARMM DCD Write, step 2. + CPPTRAJ: RMS coordinate rotation/rotation matrices test - CPPTRAJ: Principal Test -All 3 comparisons passed. + CPPTRAJ: Secstruct (DSSP) command test, Ptraj Format. + CPPTRAJ: Convert NetCDF -> mdcrd + CPPTRAJ: Outtraj Test with maxmin. -All 2 comparisons passed. + CPPTRAJ: Multi frame strip command test. + CPPTRAJ: Partial Surface calculation test - CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj + CPPTRAJ: Compressed broken trajectory test - CPPTRAJ: Diffusion test, new syntax. + CPPTRAJ: Closest command test, using mask center - CPPTRAJ: Read CHARMM restart -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ClusterDihedral + CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. + Amber Top/Rst => Mol2, SYBYL atom types requires CPPTRAJHOME or AMBERHOME to be set. + Skipped test: Amber Top/Rst => Mol2, SYBYL atom types - CPPTRAJ: clusterdihedral test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct_8OG -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Vector -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Matrix +All 11 comparisons passed. - CPPTRAJ: NA test (8OG) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicFluct +All 4 comparisons passed. - CPPTRAJ: Basic vector tests +1 comparisons skipped. - CPPTRAJ: Matrix Tests - CPPTRAJ: X column format/precision test. +All 7 comparisons passed. - CPPTRAJ: Atomic fluctuations test [@C,CA,N byres bfactor]. - CPPTRAJ: Center reference command test. +All 3 comparisons passed. -All 4 comparisons passed. +All 5 comparisons passed. - CPPTRAJ: Structure Check with Around and Skip - CPPTRAJ: Nonorthorhombic coordinate imaging test + CPPTRAJ: Per-Residue RMSD Test with residue centering. - CPPTRAJ: 2D RMSD with reference mask test. + CPPTRAJ: Test vector center with magnitude - CPPTRAJ: Secstruct (DSSP): SS assign output test - CPPTRAJ: Atom map charmm->amber atom order, by residue + CPPTRAJ: Secstruct (DSSP) command with changing number of residues. + CPPTRAJ: Center reference command test. -All 2 comparisons passed. + CPPTRAJ: X column format/precision test. + + CPPTRAJ: CRD Replica Trajectory Run: Generating 300.00 traj + + CPPTRAJ: 2D DME Test. + + CPPTRAJ: Atom map charmm->amber atom order + CPPTRAJ: Orthorhombic coordinate imaging test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Grid -All 3 comparisons passed. + CPPTRAJ: Dipole test + + CPPTRAJ: Strip topology with PDB info + CPPTRAJ: NetCDF Restart w/ box Test - NetCDF->Txt - CPPTRAJ: RmsAvgCorr First + CPPTRAJ: Cluster command test, read NetCDF pairwise distances. - CPPTRAJ: Dipole test + CPPTRAJ: Diffusion test, nonorthogonal box - CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj + CPPTRAJ: Solute-solvent hbond test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NAstruct_8OG CPPTRAJ: RMS fit with no coordinates modification test. - CPPTRAJ: CHARMM PSF write + CPPTRAJ: CHAMBER topology read/strip test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Project - CPPTRAJ: Cluster command test, read NetCDF pairwise distances. + CPPTRAJ: Start argument offset +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Unwrap All 3 comparisons passed. + + CPPTRAJ: NA test (8OG) + CPPTRAJ: Projection + CPPTRAJ: Unwrap non-orthogonal test + +All 2 comparisons passed. - CPPTRAJ: Atomic fluctuations test [:2-12 byatom]. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Unwrap +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Watershell - CPPTRAJ: Hbond, no intramolecular hydrogen bonds test + CPPTRAJ: Watershell Test, non-orthorhombic imaging. - CPPTRAJ: Diffusion test, nonorthogonal box + CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. - CPPTRAJ: Unwrap non-orthogonal test + CPPTRAJ: Modes analysis, RMS fluctuations +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AnalysisRunAvg +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volmap - CPPTRAJ: FtuFabI Assignment test + CPPTRAJ: Analysis Running Average - CPPTRAJ: Compressed broken trajectory test + CPPTRAJ: VMD VolMap Algorithm test -All 4 comparisons passed. + CPPTRAJ: Atom map charmm->amber atom order, by residue + CPPTRAJ: 2D RMSD with reference mask test. - CPPTRAJ: 2D RMSD test, no fitting. + CPPTRAJ: Secstruct (DSSP): SS assign output test - CPPTRAJ: Data file group by name test - CPPTRAJ: Multi frame strip command test. + CPPTRAJ: Momentum/velocity vector test. + CPPTRAJ: Hbond, no intramolecular hydrogen bonds test -All 9 comparisons passed. + CPPTRAJ: Center point test. + CPPTRAJ: Read CHARMM restart + CPPTRAJ: Closest command test, using mask center and solvent mask - CPPTRAJ: CHARMM COORdinates test - CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj + CPPTRAJ: Nonorthorhombic coordinate imaging test - CPPTRAJ: Center point test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Analyze_Modes + CPPTRAJ: CRD Replica Trajectory Run: Generating 384.30 traj ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AnalysisRunAvg - -All 3 comparisons passed. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SPAM + CPPTRAJ: SPAM Test - CPPTRAJ: Analysis Running Average +All 4 comparisons passed. -All 3 comparisons passed. All 1 comparisons passed. - CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Watershell - CPPTRAJ: Grid test +All 3 comparisons passed. - CPPTRAJ: Modes analysis, RMS fluctuations - CPPTRAJ: Watershell Test, non-orthorhombic imaging. +All 4 comparisons passed. - CPPTRAJ: Atomic fluctuations test [bymask :3,4,5]. -All 6 comparisons passed. +All 11 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SPAM -All 1 comparisons passed. +All 2 comparisons passed. - CPPTRAJ: SPAM Test +All 1 comparisons passed. - CPPTRAJ: Cluster command test, write ASCII pairwise distances. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volmap - CPPTRAJ: CRD Replica Trajectory Run with remdout +All 5 comparisons passed. - CPPTRAJ: Test vector center with magnitude -All 6 comparisons passed. +All 1 comparisons passed. - CPPTRAJ: Strip topology with PDB info +All 2 comparisons passed. - CPPTRAJ: VMD VolMap Algorithm test -All 5 comparisons passed. +All 9 comparisons passed. - CPPTRAJ: STFC Diffusion Test +All 3 comparisons passed. + ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LIE - - CPPTRAJ: LIE test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Density ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidOrder - - CPPTRAJ: Data file group by aspect test - - CPPTRAJ: Lipid Order Parameter Test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Density - - CPPTRAJ: Density along axis tests - - CPPTRAJ: Modes analysis, displacements - - CPPTRAJ: RMS fit to previous test - - - CPPTRAJ: Unwrap orthogonal test - CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. - -All 2 comparisons passed. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PairDist + CPPTRAJ: LIE test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CharmmParams - - CPPTRAJ: Cluster command test, read ASCII pairwise distances. - - CPPTRAJ: Test updating topology with Charmm parameters (single residue) +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PairDist +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicCorr -All 2 comparisons passed. +All 3 comparisons passed. - CPPTRAJ: Closest command test, using mask center + CPPTRAJ: Lipid Order Parameter Test. CPPTRAJ: PairDist Test. -All 10 comparisons passed. - - CPPTRAJ: Hbond, specified solute masks - + CPPTRAJ: Density along axis tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReadData +******************************************************************************** +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_systemVF +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Box -All 11 comparisons passed. + CPPTRAJ: Atomic Correlation test + + CPPTRAJ: GIST water-water interaction test + + CPPTRAJ: AutoCorr test. + CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomTypeSelect CPPTRAJ: Read vector data test (no origins, origins) + VMD VolMap Algorithm longer tests is a long test and long tests disabled. Use 'long' to run. + Skipped test: VMD VolMap Algorithm longer tests - CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM + CPPTRAJ: Box Test (Add box info) -All 8 comparisons passed. +All 2 comparisons passed. +1 comparisons skipped. - CPPTRAJ: Momentum/velocity vector test. + CPPTRAJ: Selection by atom type test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GIST +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AvgRef +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Crank_Stat - CPPTRAJ: GIST water-water interaction test + CPPTRAJ: RMSD Test with averaged reference coordinates. - CPPTRAJ: OpenDX Grid read test + CPPTRAJ: Crankshaft test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateCrd - CPPTRAJ: STFC Diffusion Test with individual distances + CPPTRAJ: COORDS data set creation and CRDFLUCT test. + +All 15 comparisons passed. - CPPTRAJ: Modes analysis, dipole correlation ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomicCorr +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoImage - CPPTRAJ: Atomic Correlation test + CPPTRAJ: AutoImage test (split DNA duplex) ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_systemVF +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Parallel - CPPTRAJ: Outtraj Test with maxmin. + CPPTRAJ: Parallel tests. -All 6 comparisons passed. +All 1 comparisons passed. - CPPTRAJ: Amber NetCDF trajectory with Velocity/Force test +All 1 comparisons passed. - CPPTRAJ: RMS: imaging after unit cell rotation ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoCorr +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LoadCrd - CPPTRAJ: Atomicfluct test with ADP output + CPPTRAJ: Force vector test. - CPPTRAJ: AutoCorr test. -All 9 comparisons passed. + CPPTRAJ: Atomic fluctuations test [start 10 stop 30 offset 2 byres bfactor]. -All 2 comparisons passed. + CPPTRAJ: CRD Replica Trajectory Run: Generating 492.20 traj + CPPTRAJ: Unwrap orthogonal test + CPPTRAJ: Randomize (around, overlap) - 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. CPPTRAJ: Structure Check with PBC + CPPTRAJ: 2D RMSD test, no fitting. + CPPTRAJ: Data file group by name test -All 2 comparisons passed. - -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Box -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve - - CPPTRAJ: Read vector data set (origins, no origins) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AtomTypeSelect - CPPTRAJ: Box Test (Add box info) + CPPTRAJ: Grid test + CPPTRAJ: Radial test, orthogonal and no imaging - CPPTRAJ: Hbond, no angle cutoff test + CPPTRAJ: Modes analysis, displacements - CPPTRAJ: Cluster, nosieve + CPPTRAJ: Cluster command test, write ASCII pairwise distances. - CPPTRAJ: Selection by atom type test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AvgRef + CPPTRAJ: STFC Diffusion Test - CPPTRAJ: Closest command test, using mask center and solvent mask + CPPTRAJ: Closest command test, solvent mask, water oxygen only - CPPTRAJ: RMSD Test with averaged reference coordinates. + CPPTRAJ: LCPO test with GAFF atom types - CPPTRAJ: Partial Surface calculation test + CPPTRAJ: CHARMM PSF write - CPPTRAJ: Force vector test. - CPPTRAJ: STFC Diffusion Test with COM + CPPTRAJ: FtuFabI Assignment test + CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar -All 1 comparisons passed. + CPPTRAJ: SPAM Pure Solvent Test + CPPTRAJ: RMS fit to previous test All 1 comparisons passed. -All 12 comparisons passed. + CPPTRAJ: LoadCrd test. +All 3 comparisons passed. -All 15 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MultiVector + CPPTRAJ: Multivector test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Lifetime - CPPTRAJ: Grid with specified center test. + CPPTRAJ: Lifetime test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Crank_Stat +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FFT -All 6 comparisons passed. + CPPTRAJ: FFT test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LoadCrd -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Parallel -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AutoImage + CPPTRAJ: Read vector data set (origins, no origins) - CPPTRAJ: Parallel tests. + CPPTRAJ: Box test (remove box info) - CPPTRAJ: LoadCrd test. + CPPTRAJ: Generate matrix with trajectory start/stop/offset - CPPTRAJ: Crankshaft test + CPPTRAJ: Hbond, specified solute masks - CPPTRAJ: AutoImage test (split DNA duplex) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateCrd +All 6 comparisons passed. - CPPTRAJ: Read Amber output test -All 4 comparisons passed. +All 10 comparisons passed. - CPPTRAJ: COORDS data set creation and CRDFLUCT test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MultiVector +All 3 comparisons passed. + All 1 comparisons passed. - CPPTRAJ: Hbond, Bridge nointramol test +All 14 comparisons passed. - CPPTRAJ: Multivector test - CPPTRAJ: Pairdist test, orthogonal imaging. +All 9 comparisons passed. + ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Lifetime +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Timecorr +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SymmRmsd +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CrossCorr - CPPTRAJ: Multi-frame density along axis test + CPPTRAJ: Timecorr test. -All 1 comparisons passed. + CPPTRAJ: CrossCorr test + CPPTRAJ: SymmRmsd - CPPTRAJ: Lifetime test. +All 2 comparisons passed. -All 14 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FFT - - - CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multidihedral ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Timecorr +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ensemble_MREMD +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MakeStructure - CPPTRAJ: FFT test. + CPPTRAJ: Multidihedral test - CPPTRAJ: STFC Diffusion Test with second mask + CPPTRAJ: M-REMD sort test. - CPPTRAJ: Timecorr test. + CPPTRAJ: Basic makestructure test - CPPTRAJ: Box test (remove box info) +All 5 comparisons passed. - CPPTRAJ: Generate matrix with trajectory start/stop/offset +******************************************************************************** +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 6 comparisons passed. - CPPTRAJ: SPAM Pure Solvent Test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CrossCorr +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Integrate - CPPTRAJ: Cluster, sieve5 +******************************************************************************** + CPPTRAJ: Integration test. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidSCD - CPPTRAJ: Closest command test, solvent mask, water oxygen only + CPPTRAJ: Basic lipid order parameter test - CPPTRAJ: CrossCorr test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SymmRmsd +All 1 comparisons passed. - CPPTRAJ: Modes analysis, pseudo trajectory creation test - CPPTRAJ: SymmRmsd + CPPTRAJ: ASP symmetry-corrected RMSD test - CPPTRAJ: Radial test, orthogonal and no imaging -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LipidSCD + CPPTRAJ: CRD Replica Trajectory Run: Generating 630.50 traj - CPPTRAJ: LoadTraj test. -All 3 comparisons passed. + CPPTRAJ: Multi-frame density along axis test + CPPTRAJ: Cluster command test, read ASCII pairwise distances. - CPPTRAJ: Basic lipid order parameter test + CPPTRAJ: Box test (Modify box length) + CPPTRAJ: Atomicfluct test with ADP output - CPPTRAJ: COORDS data set creation with velocities test + CPPTRAJ: Modes analysis, dipole correlation -All 1 comparisons passed. + CPPTRAJ: RMS: imaging after unit cell rotation + CPPTRAJ: Pairdist test, orthogonal imaging. - CPPTRAJ: Read CHARMM output test + CPPTRAJ: COORDS data set creation with velocities test - CPPTRAJ: Grid with box center offset test. + CPPTRAJ: OpenDX Grid read test -All 3 comparisons passed. + CPPTRAJ: CHARMM COORdinates test + CPPTRAJ: Data file group by aspect test - CPPTRAJ: Generate matrix with action stop/start/offset + CPPTRAJ: Read Amber output test - CPPTRAJ: Box test (Modify box length) -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MakeStructure + CPPTRAJ: Lifetime test with data set caching. CPPTRAJ: Parallel test with trajectory offset - CPPTRAJ: Basic makestructure test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multidihedral + CPPTRAJ: Generate matrix with action stop/start/offset -All 1 comparisons passed. + CPPTRAJ: Hbond, no angle cutoff test + CPPTRAJ: LoadTraj test. - CPPTRAJ: Multidihedral test + CPPTRAJ: Nonorthorhombic coordinate imaging test with familiar and COM - CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test + CPPTRAJ: STFC Diffusion Test with individual distances ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ensemble_MREMD +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts - CPPTRAJ: LoadTraj from trajin test. + CPPTRAJ: NativeContacts test. - CPPTRAJ: ASP symmetry-corrected RMSD test + CPPTRAJ: Multidihedral Nucleotide CHI test - CPPTRAJ: M-REMD sort test. +All 1 comparisons passed. - CPPTRAJ: Lifetime test with data set caching. - CPPTRAJ: 3D data read/write test + CPPTRAJ: Makestructure test with reference. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rotate - +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckChiral - CPPTRAJ: Rotation (and inverse) of coords from matrices -All 5 comparisons passed. +All 9 comparisons passed. All 1 comparisons passed. -All 7 comparisons passed. +All 12 comparisons passed. + + CPPTRAJ: Check chirality test + +All 6 comparisons passed. All 15 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_NativeContacts -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Integrate - CPPTRAJ: Total system density test - CPPTRAJ: NativeContacts test. +All 7 comparisons passed. - CPPTRAJ: Integration test. - CPPTRAJ: Grid with mask center offset test. -All 9 comparisons passed. + CPPTRAJ: GLU symmetry-corrected RMSD test + CPPTRAJ: CRD Replica Trajectory Run with remdout -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CheckChiral + CPPTRAJ: Rotate with defined axis + + CPPTRAJ: LoadTraj from trajin test. + +All 3 comparisons passed. ******************************************************************************** - CPPTRAJ: Check chirality test TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Energy ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LESsplit +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PermuteDihedrals - CPPTRAJ: Simple energy tests +All 5 comparisons passed. - CPPTRAJ: Box test (auto orthogonal box, no radii) +All 2 comparisons passed. - CPPTRAJ: Cluster, nosieve savepairdist - CPPTRAJ: LES split/average test All 6 comparisons passed. - CPPTRAJ: GLU symmetry-corrected RMSD test - - CPPTRAJ: LoadCrd append from multiple files test - - CPPTRAJ: Standard 3D data write test - - CPPTRAJ: Multidihedral Nucleotide CHI test - -All 13 comparisons passed. + CPPTRAJ: Simple energy tests +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Sieve + CPPTRAJ: PermuteDihedrals interval -120, phi psi ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PermuteDihedrals +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CharmmParams ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CCP4 - CPPTRAJ: PermuteDihedrals interval -120, phi psi - - CPPTRAJ: CCP4 read/write and DX conversion test. - - CPPTRAJ: Makestructure test with reference. - -All 2 comparisons passed. + CPPTRAJ: Cluster, nosieve + CPPTRAJ: Test updating topology with Charmm parameters (single residue) ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihCovar - -All 1 comparisons passed. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LESsplit +All 6 comparisons passed. - CPPTRAJ: Dihedral Covariance Matrix Test - CPPTRAJ: Box test (auto orthogonal box, VDW radii) + CPPTRAJ: CCP4 read/write and DX conversion test. - CPPTRAJ: Rotate with defined axis + CPPTRAJ: LES split/average test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihCovar ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CurveFit - - CPPTRAJ: TYR symmetry-corrected RMSD test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetAverage - CPPTRAJ: Randomize (around, overlap) +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VectorMath + CPPTRAJ: Dihedral Covariance Matrix Test + + CPPTRAJ: Curve fitting test. CPPTRAJ: Data set averaging and averaging over all sets test. - CPPTRAJ: Curve fitting test. + CPPTRAJ: Vector dot/cross product test - CPPTRAJ: Multidihedral protein dihedrals test - CPPTRAJ: Standard 3D data read test + CPPTRAJ: AutoImage test, use anchor mask + CPPTRAJ: Modes analysis, pseudo trajectory creation test -All 4 comparisons passed. + CPPTRAJ: STFC Diffusion Test with COM + CPPTRAJ: Randomize (around) CPPTRAJ: New Lipid Order Parameter Test, DOPC. -All 7 comparisons passed. + CPPTRAJ: Box test (auto orthogonal box, no radii) +******************************************************************************** + CPPTRAJ: Atomicfluct test with PDB B-factor/occupancy output. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander -All 5 comparisons passed. + CPPTRAJ: TYR symmetry-corrected RMSD test + CPPTRAJ: Hbond, Bridge nointramol test - CPPTRAJ: M-REMD actions test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VectorMath -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander + CPPTRAJ: Read CHARMM output test - CPPTRAJ: Vector dot/cross product test + CPPTRAJ: Grid with specified center test. + + CPPTRAJ: Total system density test + + CPPTRAJ: Multidihedral protein dihedrals test SANDER energy tests (long) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. - - CPPTRAJ: Non-orthogonal grid test. SANDER energy tests (long) is a long test and long tests disabled. Use 'long' to run. SKIP: SANDER energy tests (long) - CPPTRAJ: Cluster, nosieve loadpairdist +All 8 comparisons passed. - CPPTRAJ: Lifetime average and cumulative average test. - - CPPTRAJ: PermuteDihedrals, random rotations All 2 comparisons passed. -All 7 comparisons passed. - +All 1 comparisons passed. - CPPTRAJ: TRAJ data set creation and CRDFLUCT test. + CPPTRAJ: Lifetime average and cumulative average test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Temperature +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander_Short - CPPTRAJ: Multidihedral cyclic molecule test + CPPTRAJ: M-REMD actions test. - CPPTRAJ: Temperature test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Esander_Short +g++ -o a.out main.o NameType.o CpptrajStdio.o Energy via sander API short tests (GB/PME) requires SANDER API from AmberTools. Cpptraj was compiled without SANDER API from AmberTools support. SKIP: Energy via sander API short tests (GB/PME) +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Spline +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Temperature + + CPPTRAJ: Spline test + +All 8 comparisons passed. + + + CPPTRAJ: Temperature test. + +All 7 comparisons passed. + All 2 comparisons passed. -All 3 comparisons passed. + CPPTRAJ: Multidihedral cyclic molecule test + CPPTRAJ: PermuteDihedrals, random rotations - CPPTRAJ: Longer symmetry-corrected RMSD test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Spline + CPPTRAJ: TRAJ data set creation and CRDFLUCT test. - CPPTRAJ: Curve fitting multi-exponential tests. + CPPTRAJ: 3D data read/write test - CPPTRAJ: Spline test + CPPTRAJ: NativeContacts test, save non-native contacts, residue time series - CPPTRAJ: Standard 3D data read/append test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_KDE +All 2 comparisons passed. -All 7 comparisons passed. + CPPTRAJ: Pairdist test, nonorthogonal imaging. + +All 2 comparisons passed. - CPPTRAJ: LCPO test with GAFF atom types + + CPPTRAJ: LoadCrd append from multiple files test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_KDE CPPTRAJ: KDE test. + + CPPTRAJ: Curve fitting multi-exponential tests. + + CPPTRAJ: Cluster, sieve5 ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PDB +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CIF ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Wavelet ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CIF +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PDB - CPPTRAJ: PDB format read/write test + CPPTRAJ: Modes analysis, RMSIP and eigenvalue fraction test - CPPTRAJ: Wavelet analysis test + CPPTRAJ: Longer symmetry-corrected RMSD test. CPPTRAJ: CIF read test -All 2 comparisons passed. + CPPTRAJ: Wavelet analysis test + CPPTRAJ: PDB format read/write test -All 16 comparisons passed. +All 1 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelocityAutoCorr All 6 comparisons passed. + ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Align +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelFrc + CPPTRAJ: Velocity autocorrelation test -All 12 comparisons passed. + CPPTRAJ: Test combining coordinates, velocities, and forces. +All 4 comparisons passed. - CPPTRAJ: Temperature with SHAKE on hydrogens. - CPPTRAJ: Align Tests. +All 7 comparisons passed. +******************************************************************************** -All 3 comparisons passed. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Align +All 13 comparisons passed. -All 4 comparisons passed. +All 12 comparisons passed. -All 1 comparisons passed. + CPPTRAJ: Align Tests. +make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' - CPPTRAJ: TRAJ data set creation with velocities test. +All 2 comparisons passed. - CPPTRAJ: M-REMD ensemble outtraj test. +All 4 comparisons passed. -All 1 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_RotateDihedral -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetCmd - -All 8 comparisons passed. - All 3 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' - CPPTRAJ: Data Set commands test + Unit test passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DataSetCmd - CPPTRAJ: Cluster, sieve5 savepairdist CPPTRAJ: Rotate dihedral to target value. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelocityAutoCorr All 4 comparisons passed. - CPPTRAJ: Velocity autocorrelation test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_VelFrc + CPPTRAJ: Data Set commands test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remap ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Filter - - CPPTRAJ: Remap Test -******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CompareTop - CPPTRAJ: Basic filter test + CPPTRAJ: Box test (auto orthogonal box, VDW radii) - CPPTRAJ: Compare topology test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TopInfo + CPPTRAJ: Watershell Test, orthorhombic imaging. - CPPTRAJ: Test combining coordinates, velocities, and forces. + CPPTRAJ: Grid with box center offset test. + + CPPTRAJ: Remap Test + + CPPTRAJ: STFC Diffusion Test with second mask CPPTRAJ: Test kinetic energy calculation - CPPTRAJ: Standard 3D data, sparse + CPPTRAJ: Temperature with SHAKE on hydrogens. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CombineCrd +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TopInfo + + CPPTRAJ: Standard 3D data write test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Filter ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTrr CPPTRAJ: TRR force/velocity read -> NetCDF write test - - CPPTRAJ: Topology info print test. - - CPPTRAJ: Temperature with SHAKE on all atoms. - - CPPTRAJ: Combine COORDS test. - - CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test - - CPPTRAJ: NativeContacts test, save non-native contacts, residue time series - -All 1 comparisons passed. - - - CPPTRAJ: M-REMD no sort, running average test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Ewald - CPPTRAJ: AutoImage test, use anchor mask - CPPTRAJ: Direct sum test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CombineCrd - CPPTRAJ: Test using velocities as coordinates. + CPPTRAJ: Basic filter test - CPPTRAJ: Rotate dihedral by increment + CPPTRAJ: Topology info print test. - CPPTRAJ: Test total energy calculation + CPPTRAJ: Combine COORDS test. + + CPPTRAJ: Compare topology test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_TI - - CPPTRAJ: Nonorthogonal grid standard write/read tests. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds CPPTRAJ: TI analysis test. -All 1 comparisons passed. + CPPTRAJ: Test using velocities as coordinates. + CPPTRAJ: TRAJ data set creation with velocities test. - CPPTRAJ: Curve fitting, custom output range. + CPPTRAJ: M-REMD ensemble outtraj test. - CPPTRAJ: Generate offset traj from PDB -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixImagedBonds +All 8 comparisons passed. - CPPTRAJ: Temperature calc with extra points. - CPPTRAJ: Combine COORDS test with box info. + CPPTRAJ: Fix imaged bonds test (Ortho.) - CPPTRAJ: COORDS data set append test +All 6 comparisons passed. - CPPTRAJ: Align, unit cell rotation/imaging test. - CPPTRAJ: Fix imaged bonds test (Ortho.) + CPPTRAJ: Rotate dihedral by increment - CPPTRAJ: PQR file write with various radii + CPPTRAJ: NativeContacts test, orthorhombic imaging. - CPPTRAJ: Test partial energy calculation +All 7 comparisons passed. - CPPTRAJ: Wavelet WAFEX test - CPPTRAJ: Rotate dihedral in TRAJ data set + CPPTRAJ: Temperature with SHAKE on all atoms. - CPPTRAJ: M-REMD, generate RMS data + CPPTRAJ: Curve fitting, custom output range. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Distance - CPPTRAJ: Test writing velocities (MDVEL) + CPPTRAJ: Cluster, nosieve savepairdist - CPPTRAJ: Data filter test. +All 1 comparisons passed. - CPPTRAJ: Grid generation from 'bounds' test. -All 10 comparisons passed. + CPPTRAJ: Distance tests + CPPTRAJ: Combine COORDS test with box info. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volume -All 6 comparisons passed. + CPPTRAJ: Volume tests +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SetVelocity +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remlog + CPPTRAJ: Standard 3D data read test -All 3 comparisons passed. + CPPTRAJ: Set Velocity test + CPPTRAJ: Replica log read/analyze test. - CPPTRAJ: KDE with Kullback-Leibler divergence test + CPPTRAJ: Test writing velocities (MDVEL) - CPPTRAJ: Generate offset traj from CIF + CPPTRAJ: Grid with mask center offset test. -All 5 comparisons passed. + CPPTRAJ: Align, unit cell rotation/imaging test. +All 1 comparisons passed. -All 2 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Distance + CPPTRAJ: Test total energy calculation - CPPTRAJ: Distance tests +All 3 comparisons passed. - CPPTRAJ: NativeContacts test, orthorhombic imaging. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multicurve - CPPTRAJ: Multicurve test +All 5 comparisons passed. -All 2 comparisons passed. + CPPTRAJ: Rotate dihedral in TRAJ data set -All 3 comparisons passed. +All 6 comparisons passed. - CPPTRAJ: COORDS test storing frame metadata + CPPTRAJ: Temperature calc with extra points. - CPPTRAJ: M-REMD, meltcurve analysis -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Volume + CPPTRAJ: M-REMD no sort, running average test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Remlog - - CPPTRAJ: Volume tests +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AreaPerMol - CPPTRAJ: Filter matrix test. -******************************************************************************** + CPPTRAJ: Area per molecule test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_AreaPerMol TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DistBasedMask +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CalcState - CPPTRAJ: Replica log read/analyze test. + CPPTRAJ: KDE with Kullback-Leibler divergence test - CPPTRAJ: Test using forces as coordinates. + CPPTRAJ: Orthogonal imaged distance +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Multicurve CPPTRAJ: Distance-based atom mask tests (atom, residue) - CPPTRAJ: Area per molecule test - - CPPTRAJ: PDB filter alternate atom location IDs test - -All 6 comparisons passed. - + CPPTRAJ: Calcstate test ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SetVelocity +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Calc + CPPTRAJ: Multicurve test - CPPTRAJ: Orthogonal imaged distance CPPTRAJ: Fix imaged bonds test (Non-ortho.) - CPPTRAJ: Set Velocity test -All 17 comparisons passed. + CPPTRAJ: Structure Check with Around + CPPTRAJ: Data filter test. + CPPTRAJ: Calc test -All 4 comparisons passed. + CPPTRAJ: Scale velocity test + CPPTRAJ: COORDS data set append test -All 1 comparisons passed. + CPPTRAJ: Generate offset traj from PDB +All 10 comparisons passed. - CPPTRAJ: TRR force/velocity read -> TRR write test - CPPTRAJ: Hbond with imaging + CPPTRAJ: Standard 3D data read/append test -All 5 comparisons passed. + CPPTRAJ: Wavelet WAFEX test + CPPTRAJ: PQR file write with various radii - CPPTRAJ: Split coords and recombine test. + CPPTRAJ: Test partial energy calculation + +All 3 comparisons passed. - CPPTRAJ: Cluster, sieve5 loadpairdist -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Calc -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CalcState -All 13 comparisons passed. + CPPTRAJ: Non-orthogonal grid test. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Change + CPPTRAJ: Test using forces as coordinates. - CPPTRAJ: Calcstate test +All 2 comparisons passed. - CPPTRAJ: Test writing forces (MDFRC) CPPTRAJ: Change atom and residue name tests - -All 5 comparisons passed. - ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CreateReservoir -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixAtomOrder -All 8 comparisons passed. + CPPTRAJ: Create RREMD NetCDF reservoir test +All 1 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LowestCurve +All 1 comparisons passed. - CPPTRAJ: Calc test - CPPTRAJ: Out of order molecules test +All 7 comparisons passed. - CPPTRAJ: LowestCurve test - CPPTRAJ: Create RREMD NetCDF reservoir test +All 3 comparisons passed. -All 2 comparisons passed. + + CPPTRAJ: Calc test with data sets + + CPPTRAJ: Split coords and recombine test. + CPPTRAJ: M-REMD, generate RMS data +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_FixAtomOrder + + CPPTRAJ: Non-orthogonal imaged distance + + CPPTRAJ: Out of order molecules test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_MinImage ******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LowestCurve +******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Regress - CPPTRAJ: Minimum Image test. - -All 1 comparisons passed. + CPPTRAJ: LowestCurve test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rst + CPPTRAJ: Linear regression test. - CPPTRAJ: Non-orthogonal imaged distance +All 4 comparisons passed. - CPPTRAJ: Distance-based atom mask tests (molecule) - CPPTRAJ: Linear regression test. +All 4 comparisons passed. -All 3 comparisons passed. + CPPTRAJ: Generate offset traj from CIF - CPPTRAJ: Scale velocity test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Rst + CPPTRAJ: Minimum Image test. -******************************************************************************** - CPPTRAJ: Hbond, orthogonal imaging -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pairwise + CPPTRAJ: Distance-based atom mask tests (molecule) -All 7 comparisons passed. + CPPTRAJ: Generate restraints (rst) test + CPPTRAJ: COORDS test storing frame metadata - CPPTRAJ: Generate restraints (rst) test - CPPTRAJ: Pairwise tests +All 2 comparisons passed. + CPPTRAJ: TRR force/velocity read -> TRR write test - CPPTRAJ: Change chain ID test - CPPTRAJ: Structure Check with Around + CPPTRAJ: Test writing forces (MDFRC) - CPPTRAJ: CRD => TRR + CPPTRAJ: Change chain ID test -All 2 comparisons passed. + CPPTRAJ: Filter matrix test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Solvent -******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ParmBox + CPPTRAJ: PDB filter alternate atom location IDs test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Translate -All 4 comparisons passed. +All 5 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Pairwise CPPTRAJ: Parmbox test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Solvent - CPPTRAJ: Test solvent command with closest - - CPPTRAJ: Translate test - -All 2 comparisons passed. + CPPTRAJ: Pairwise tests -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ReplicateCell +All 6 comparisons passed. - CPPTRAJ: Replicate cell test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_ScaleDihedralK - CPPTRAJ: Scale dihedral force constant test -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PhiPsi +All 16 comparisons passed. -All 3 comparisons passed. + CPPTRAJ: Test solvent command with closest - CPPTRAJ: Phipsi test All 1 comparisons passed. +All 2 comparisons passed. - CPPTRAJ: Topology info with reference coords test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Translate - CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. +All 17 comparisons passed. - CPPTRAJ: Change chain ID of COORDS set test - CPPTRAJ: Pairdist test, nonorthogonal imaging. + CPPTRAJ: Translate test - CPPTRAJ: TRAJ test storing frame metadata +All 3 comparisons passed. - CPPTRAJ: Adding PDB info to topology +******************************************************************************** +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: Calc test with data sets + CPPTRAJ: Replicate cell test + + CPPTRAJ: Scale dihedral force constant test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Control +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_PhiPsi -All 1 comparisons passed. - -All 1 comparisons passed. + CPPTRAJ: Phipsi test + CPPTRAJ: Loop tests ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_InfraredSpec - - CPPTRAJ: Loop tests - - CPPTRAJ: Infrared spectrum calculation test - All 1 comparisons passed. All 6 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cphstats -All 3 comparisons passed. - - -All 23 comparisons passed. + CPPTRAJ: Infrared spectrum calculation test + CPPTRAJ: Explicit pH REMD ensemble data read / sort All 3 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cphstats -******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CmdLine - CPPTRAJ: Explicit pH REMD ensemble data read / sort +All 5 comparisons passed. -All 1 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XYZformat + CPPTRAJ: Command line trajectory args test, part 1 All 1 comparisons passed. - CPPTRAJ: Command line trajectory args test, part 1 -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XYZformat - CPPTRAJ: XYZ format write -All 17 comparisons passed. +All 3 comparisons passed. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Hausdorff -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CatCrd - CPPTRAJ: Scale dihedral force constant with 'useall' -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XtalSymm +All 1 comparisons passed. + + +All 2 comparisons passed. + + +All 1 comparisons passed. + + + CPPTRAJ: Simple Hausdorff distance test. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Time +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_CatCrd CPPTRAJ: Concatenate COORDS data set test All 1 comparisons passed. +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_XtalSymm - CPPTRAJ: Simple Hausdorff distance test. +All 1 comparisons passed. - CPPTRAJ: Add time to restart test CPPTRAJ: XtalSymm Reference -All 12 comparisons passed. +All 1 comparisons passed. ******************************************************************************** +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Time TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_DihedralRMS - - CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Slope ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_SplitCoords +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Slope -All 1 comparisons passed. - - -All 3 comparisons passed. + CPPTRAJ: Add time to restart test + CPPTRAJ: Dihedral RMSD tests (first, reference, reference traj.) - CPPTRAJ: SplitCoords test CPPTRAJ: Finite difference test. + CPPTRAJ: SplitCoords test ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Diagmatrix - CPPTRAJ: MW covariance matrix thermo analysis test + + CPPTRAJ: Adding PDB info to topology + + CPPTRAJ: Scale dihedral force constant with 'useall' + CPPTRAJ: Standard 3D data, sparse + + CPPTRAJ: Hbond with imaging + + CPPTRAJ: Test math functions + + CPPTRAJ: TRAJ test storing frame metadata + + + CPPTRAJ: Test writing combined coords/velocity/force NetCDF restart. ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Emin - CPPTRAJ: Basic energy minimization test. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Graft -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau - CPPTRAJ: Graft test + CPPTRAJ: CRD => TRR + CPPTRAJ: M-REMD, meltcurve analysis + CPPTRAJ: Topology info with reference coords test - CPPTRAJ: Evalulate plateau test + CPPTRAJ: Change chain ID of COORDS set test CPPTRAJ: Pairwise test, partial system - CPPTRAJ: Test math functions - - CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. + CPPTRAJ: Non-orthogonal grid centered on bin center and wrapped test -All 10 comparisons passed. + CPPTRAJ: MW covariance matrix thermo analysis test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_EvalPlateau + CPPTRAJ: Evalulate plateau test All 2 comparisons passed. - CPPTRAJ: Remove time from restart test +All 8 comparisons passed. - CPPTRAJ: Randomize (around) - CPPTRAJ: TRR => CRD + CPPTRAJ: Basic energy minimization test. + +All 4 comparisons passed. + CPPTRAJ: Command line test trajectory args test, part 2 +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Flatten - CPPTRAJ: Hausdorff distance of 2D rms output test. + CPPTRAJ: Flatten test. -All 1 comparisons passed. + CPPTRAJ: Test reading combined coords/velocity/force NetCDF restart. + CPPTRAJ: Dihedral RMSD test (to previous) -All 2 comparisons passed. +All 1 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Flatten All 1 comparisons passed. - CPPTRAJ: Flatten test. +All 10 comparisons passed. + +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Graft ******************************************************************************** TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Random - CPPTRAJ: Constant pH stats test - - CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs +All 2 comparisons passed. - CPPTRAJ: Cluster, nosieve pairwisecache none - CPPTRAJ: Test set command + CPPTRAJ: Graft test + CPPTRAJ: Test Marsaglia, PCG32, and Xoshiro128++ RNGs All 1 comparisons passed. -All 1 comparisons passed. - CPPTRAJ: Atom XYZ format read, test 1 +All 17 comparisons passed. - CPPTRAJ: Dihedral RMSD test (to previous) - -All 8 comparisons passed. +All 1 comparisons passed. -All 4 comparisons passed. +All 3 comparisons passed. All 1 comparisons passed. - CPPTRAJ: Energy minimization with angle term test. +All 6 comparisons passed. -All 1 comparisons passed. +All 12 comparisons passed. -All 6 comparisons passed. +All 8 comparisons passed. - CPPTRAJ: Add time to trajectory test All 2 comparisons passed. - CPPTRAJ: PCG32 RNG test. - All 1 comparisons passed. - CPPTRAJ: Command line wildcard test, part 1 -g++ -o a.out main.o NameType.o CpptrajStdio.o - -All 10 comparisons passed. + CPPTRAJ: Energy minimization with angle term test. + CPPTRAJ: Randomize (overlap) - CPPTRAJ: Dihedral RMS fluctuation test. - CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. + CPPTRAJ: Nonorthogonal grid standard write/read tests. + CPPTRAJ: Grid generation from 'bounds' test. - CPPTRAJ: Sorted implicit constant pH stats test + CPPTRAJ: Ewald test (NaCl crystal) - CPPTRAJ: Atom XYZ format read, test 2 + CPPTRAJ: Watershell Test, no imaging. -All 8 comparisons passed. + CPPTRAJ: Remove time from restart test + CPPTRAJ: Test set command - CPPTRAJ: Test Stdlib RNG + CPPTRAJ: Atom XYZ format read, test 1 -All 5 comparisons passed. + CPPTRAJ: Hbond, orthogonal imaging + CPPTRAJ: Constant pH stats test - CPPTRAJ: Command line wildcard test, part 2 - CPPTRAJ: Test reading comma-separated list of strings + CPPTRAJ: Hausdorff distance of 2D rms output test. +All 1 comparisons passed. - CPPTRAJ: Energy minimization with nonbond term test. - CPPTRAJ: Test Mersenne Twister RNG + CPPTRAJ: Dihedral RMS fluctuation test. +g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o - CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats +All 1 comparisons passed. - CPPTRAJ: Hausdorff distance of 2D rms output test. All 5 comparisons passed. -All 2 comparisons passed. +All 10 comparisons passed. - CPPTRAJ: Atom XYZ format read, test 3 - CPPTRAJ: Test nested loops and variables in loops + CPPTRAJ: Ewald test (trunc. oct) - CPPTRAJ: Modify time info test. -All 4 comparisons passed. + CPPTRAJ: PCG32 RNG test. + CPPTRAJ: Add time to trajectory test + CPPTRAJ: Energy minimization with dihedral and 1-4 terms test. + CPPTRAJ: Sorted implicit constant pH stats test - CPPTRAJ: Ewald test (NaCl crystal) + CPPTRAJ: Cluster, nosieve loadpairdist - CPPTRAJ: Atom XYZ format read, test 4 + CPPTRAJ: Atom XYZ format read, test 2 -All 4 comparisons passed. + CPPTRAJ: Command line wildcard test, part 1 + CPPTRAJ: Test reading comma-separated list of strings - CPPTRAJ: Test loop over data set blocks + CPPTRAJ: TRR => CRD - CPPTRAJ: Unsorted pH read/write test +All 5 comparisons passed. - CPPTRAJ: CRD(1-5) => TRR - CPPTRAJ: Cluster, sieve5 pairwisecache none +All 23 comparisons passed. - CPPTRAJ: Ewald test (trunc. oct) -make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/NameType' - CPPTRAJ: Atom XYZ format read, test 5 + CPPTRAJ: Command line wildcard test, part 2 -All 16 comparisons passed. + CPPTRAJ: Implicit pH REMD ensemble data read / sort / stats - 'ZN' 'HA2' 'HA' 'HA' 'CT11' -Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeName' -Warning: Name truncation detected: Name='ThisIsA' vs Original='ThisIsALargeString' +All 13 comparisons passed. + +make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' Unit test passed. +make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' +make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' - CPPTRAJ: Test for filename wildcards and oversets + CPPTRAJ: Test nested loops and variables in loops -All 3 comparisons passed. + CPPTRAJ: Energy minimization with nonbond term test. + CPPTRAJ: Atom XYZ format read, test 3 - CPPTRAJ: Atom XYZ format read, test 6 - CPPTRAJ: Cluster, random + CPPTRAJ: Test Stdlib RNG + CPPTRAJ: Pairdist test, 2 masks. - CPPTRAJ: CRD(6-10) => TRR + CPPTRAJ: Hausdorff distance of 2D rms output test. -All 13 comparisons passed. +All 2 comparisons passed. - CPPTRAJ: OpenMM basic energy minimization tests (bonds) + CPPTRAJ: Randomize (no restrictions) - CPPTRAJ: XtalSymm Reimaging by Atom + CPPTRAJ: Unsorted pH read/write test All 4 comparisons passed. -All 6 comparisons passed. - +All 3 comparisons passed. - CPPTRAJ: OpenMM basic energy minimization tests (angles) -All 28 comparisons passed. +All 16 comparisons passed. - CPPTRAJ: TRR (appended) => CRD -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve +All 4 comparisons passed. - CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). - CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) +All 3 comparisons passed. -All 1 comparisons passed. +All 5 comparisons passed. - CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) - CPPTRAJ: Read specific columns test. + CPPTRAJ: OpenMM basic energy minimization tests (bonds) - CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). + CPPTRAJ: Modify time info test. - CPPTRAJ: Watershell Test, orthorhombic imaging. + CPPTRAJ: Atom XYZ format read, test 4 - CPPTRAJ: Write non-square matrix - CPPTRAJ: GMX: CRD with offset CPPTRAJ: Ewald test (partial system, trunc. oct) + CPPTRAJ: GIST test, orthogonal cell + CPPTRAJ: CRD(1-5) => TRR - CPPTRAJ: Read non-square matrix + CPPTRAJ: Test Mersenne Twister RNG - CPPTRAJ: Read square matrix - CPPTRAJ: GMX: TRR with offset - CPPTRAJ: Randomize (overlap) + CPPTRAJ: Cluster, sieve5 savepairdist + CPPTRAJ: XtalSymm Reimaging by Atom + CPPTRAJ: Test loop over data set blocks -All 15 comparisons passed. +All 4 comparisons passed. All 4 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 + +All 5 comparisons passed. Ewald test (ortho), 10 frames is a long test and long tests disabled. Use 'long' to run. + Skipped test: Ewald test (ortho), 10 frames All 4 comparisons passed. 2 comparisons skipped. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LibPME - CPPTRAJ: Clustering, One DataSet + CPPTRAJ: Test for filename wildcards and oversets - CPPTRAJ: Particle mesh Ewald test (NaCl crystal) + CPPTRAJ: Atom XYZ format read, test 5 -All 5 comparisons passed. + CPPTRAJ: OpenMM basic energy minimization tests (angles) + CPPTRAJ: CRD(6-10) => TRR ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_LibPME - CPPTRAJ: XTC read test + CPPTRAJ: Particle mesh Ewald test (NaCl crystal) + +All 13 comparisons passed. - CPPTRAJ: Clustering, Two DataSets CPPTRAJ: Particle mesh Ewald test (trunc. oct) - CPPTRAJ: Watershell Test, no imaging. - CPPTRAJ: Pairdist test, 2 masks. + CPPTRAJ: Atom XYZ format read, test 6 + CPPTRAJ: OpenMM basic energy minimization tests (dihedrals) - CPPTRAJ: Randomize (no restrictions) +All 6 comparisons passed. - CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) -All 5 comparisons passed. + CPPTRAJ: Read specific columns test. + CPPTRAJ: OpenMM basic energy minimization tests (nonbonds) -All 4 comparisons passed. + CPPTRAJ: TRR (appended) => CRD + CPPTRAJ: Write non-square matrix - CPPTRAJ: Clustering, dihedral DataSet + CPPTRAJ: GMX: CRD with offset - CPPTRAJ: CRD => XTC + CPPTRAJ: Cluster, sieve5 loadpairdist + + CPPTRAJ: OpenMM basic energy minimization tests (Tz2 PME) + + CPPTRAJ: Read non-square matrix + + CPPTRAJ: Particle mesh Ewald test (ortho) All 5 comparisons passed. -All 3 comparisons passed. + CPPTRAJ: Cluster, nosieve pairwisecache none + CPPTRAJ: Read square matrix - CPPTRAJ: Clustering, two dihedral DataSets + CPPTRAJ: GMX: TRR with offset - CPPTRAJ: GIST test, orthogonal cell +All 15 comparisons passed. - CPPTRAJ: Clustering, dihedral DataSet, K-means - CPPTRAJ: XTC => CRD +All 5 comparisons passed. - CPPTRAJ: Particle mesh Ewald test (ortho) +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsXtc - CPPTRAJ: Clustering, two dihedral DataSets, K-means + CPPTRAJ: XTC read test + CPPTRAJ: Cluster, sieve5 pairwisecache none CPPTRAJ: Particle mesh Ewald test (ortho, with mask) - CPPTRAJ: CRD(1-5) => XTC -g++ -o a.out main.o ArgList.o CpptrajStdio.o StringRoutines.o -make[5]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests/ArgList' - - Unit test passed. -make[4]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' -make[3]: Leaving directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/unitTests' + CPPTRAJ: CRD => XTC + CPPTRAJ: Cluster, random CPPTRAJ: PME test (partial system, trunc. oct) - CPPTRAJ: XtalSymm Reimaging by Molecule - - CPPTRAJ: CRD(6-10) => XTC -All 8 comparisons passed. +All 28 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN - - CPPTRAJ: DBSCAN test - - CPPTRAJ: DBSCAN automatic parameter determination test. +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_RandomSieve -All 5 comparisons passed. + CPPTRAJ: Cluster test with random sieve (Save Pairwise Distances). + CPPTRAJ: XTC => CRD -All 9 comparisons passed. + CPPTRAJ: XtalSymm Reimaging by Molecule + CPPTRAJ: Cluster test with random sieve (Load Pairwise Distances). 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 @@ -3607,54 +3610,64 @@ CPPTRAJ: LJ PME test. + CPPTRAJ: CRD(1-5) => XTC + CPPTRAJ: LJ PME kappa sweep test, 0.25 - CPPTRAJ: DBSCAN kdist map test +All 4 comparisons passed. - CPPTRAJ: XTC (appended) => CRD +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DataSet - CPPTRAJ: DBSCAN with sieve + CPPTRAJ: Clustering, One DataSet - CPPTRAJ: LJ PME kappa sweep test, 0.35 + CPPTRAJ: CRD(6-10) => XTC -All 4 comparisons passed. + CPPTRAJ: Clustering, Two DataSets -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans + CPPTRAJ: LJ PME kappa sweep test, 0.35 - CPPTRAJ: Cpptraj Kmeans + CPPTRAJ: Clustering, dihedral DataSet - CPPTRAJ: Cpptraj Kmeans random + CPPTRAJ: XTC (appended) => CRD + + CPPTRAJ: Clustering, two dihedral DataSets + CPPTRAJ: Clustering, dihedral DataSet, K-means CPPTRAJ: LJ PME kappa sweep test, 0.45 - CPPTRAJ: GMX: CRD with offset - CPPTRAJ: LJ PME kappa sweep test, 0.5 + CPPTRAJ: Clustering, two dihedral DataSets, K-means -All 6 comparisons passed. + CPPTRAJ: GMX: CRD with offset + +All 8 comparisons passed. ******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_SymmRMSD +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_DBSCAN - CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) + CPPTRAJ: DBSCAN test -All 3 comparisons passed. + CPPTRAJ: LJ PME kappa sweep test, 0.5 +All 9 comparisons passed. - CPPTRAJ: LJ with switch function test + + CPPTRAJ: DBSCAN automatic parameter determination test. CPPTRAJ: GMX: XTC with offset -All 5 comparisons passed. + CPPTRAJ: DBSCAN kdist map test + + CPPTRAJ: LJ with switch function test + CPPTRAJ: DBSCAN with sieve All 5 comparisons passed. -******************************************************************************** -TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites - CPPTRAJ: Cluster command test, coordinate writes. +All 4 comparisons passed. + All 4 comparisons passed. @@ -3662,11 +3675,36 @@ TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_GromacsTNG CPPTRAJ: TNG read test +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_Kmeans - CPPTRAJ: Cluster command test, coordinate writes using info file. + CPPTRAJ: Cpptraj Kmeans + + CPPTRAJ: Cpptraj Kmeans random CPPTRAJ: GIST test, nonorthogonal cell +All 6 comparisons passed. + +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_SymmRMSD + + CPPTRAJ: Clustering with symmetry-corrected RMSD metric (also 2D SRMSD) + + CPPTRAJ: TNG read test (with offset) + +All 5 comparisons passed. + +******************************************************************************** +TEST: /build/reproducible-path/cpptraj-5.1.0+dfsg/test/Test_Cluster_TrajWrites + + CPPTRAJ: Cluster command test, coordinate writes. + + CPPTRAJ: Cluster command test, coordinate writes using info file. + +All 6 comparisons passed. + + All 8 comparisons passed. ******************************************************************************** @@ -3674,7 +3712,8 @@ CPPTRAJ: Density peaks clustering test - CPPTRAJ: TNG read test (with offset) +All 3 comparisons passed. + All 3 comparisons passed. @@ -3683,9 +3722,6 @@ CPPTRAJ: Clustering with specified # reps -All 6 comparisons passed. - - All 2 comparisons passed. @@ -3707,7 +3743,7 @@ 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 186123352 Aug 6 22:29 ../bin/cpptraj +-rwxr-xr-x 1 pbuilder2 pbuilder2 186123352 Sep 9 04:55 ../bin/cpptraj ===================== TEST SUMMARY ====================== 853 out of 859 comparisons OK (0 failed, 0 warnings, 6 skipped). 480 out of 480 program executions completed. @@ -3719,7 +3755,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/cpptraj/ - make -j40 install DESTDIR=/build/reproducible-path/cpptraj-5.1.0\+dfsg/debian/cpptraj AM_UPDATE_INFO_DIR=no + make -j42 install DESTDIR=/build/reproducible-path/cpptraj-5.1.0\+dfsg/debian/cpptraj AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg' cd src && make install make[2]: Entering directory '/build/reproducible-path/cpptraj-5.1.0+dfsg/src' @@ -3764,12 +3800,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/503249/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/503249/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/2415790 and its subdirectories -I: Current time: Wed Aug 6 10:30:05 -12 2025 -I: pbuilder-time-stamp: 1754519405 +I: removing directory /srv/workspace/pbuilder/503249 and its subdirectories +I: Current time: Wed Sep 9 18:56:07 +14 2026 +I: pbuilder-time-stamp: 1788929767 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/cpptraj_5.1.0+dfsg-4.diff: 84.9% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/cpptraj_5.1.0+dfsg-4.diff.gz b2/build.log: 82.9% -- replaced with stdout Compressing the 1st log... b1/build.log: 83.1% -- replaced with stdout Wed Aug 6 22:33:09 UTC 2025 I: diffoscope 303 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_cpptraj_unstable_amd64_1754519589 + touch /var/log/reproducible-builds/diffoscope_stamp_cpptraj_unstable_amd64_1754519589 + RESULT=0 + systemd-run '--description=diffoscope on cpptraj/5.1.0+dfsg-4 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_19-64290 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4 --run-session -c jenkins-reproducible-unstable-diffoscope-fead0c32-cf9d-4ca7-b6e3-bdbd461df086 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/dbd-tmp-mF07AjI ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/cpptraj_5.1.0+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/cpptraj_5.1.0+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/cpptraj_5.1.0+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/b1/cpptraj_5.1.0+dfsg-4_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/b2/cpptraj_5.1.0+dfsg-4_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_19-64290.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/cpptraj_5.1.0+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/cpptraj_5.1.0+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/cpptraj_5.1.0+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/b1/cpptraj_5.1.0+dfsg-4_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.dE0NwvQ4/b2/cpptraj_5.1.0+dfsg-4_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 160ms CPU time consumed: 162ms _ _ ___ _ __ _ __ | |_ _ __ __ _ (_) / __| '_ \| '_ \| __| '__/ _` || | | (__| |_) | |_) | |_| | | (_| || | \___| .__/| .__/ \__|_| \__,_|/ | |_| |_| |__/ Wed Aug 6 22:33:09 UTC 2025 I: diffoscope 303 found no differences in the changes files, and a .buildinfo file also exists. Wed Aug 6 22:33:09 UTC 2025 I: cpptraj from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-08-06 22:33:10] INFO: Starting at 2025-08-06 22:33:10.314901 [2025-08-06 22:33:10] INFO: Generating the pages of 1 package(s) [2025-08-06 22:33:10] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/cpptraj didn't produce a buildlog, even though it has been built. [2025-08-06 22:33:10] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/cpptraj_5.1.0+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/cpptraj_5.1.0+dfsg-4.diff.gz is missing [2025-08-06 22:33:10] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/cpptraj_5.1.0+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/cpptraj_5.1.0+dfsg-4.diff.gz is missing [2025-08-06 22:33:10] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/cpptraj_5.1.0+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/cpptraj_5.1.0+dfsg-4.diff.gz is missing [2025-08-06 22:33:10] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/cpptraj_5.1.0+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/cpptraj_5.1.0+dfsg-4.diff.gz is missing [2025-08-06 22:33:10] INFO: Finished at 2025-08-06 22:33:10.421981, took: 0:00:00.107083 Wed Aug 6 22:33:10 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/cpptraj.html Wed Aug 6 22:33:10 UTC 2025 I: Removing signed cpptraj_5.1.0+dfsg-4_amd64.buildinfo.asc files: removed './b1/cpptraj_5.1.0+dfsg-4_amd64.buildinfo.asc' removed './b2/cpptraj_5.1.0+dfsg-4_amd64.buildinfo.asc' 1754519590 amd64 unstable cpptraj Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/cpptraj_5.1.0+dfsg-4.rbuild.log: 82.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/cpptraj_5.1.0+dfsg-4.rbuild.log.gz [2025-08-06 22:33:10] INFO: Starting at 2025-08-06 22:33:10.681336 [2025-08-06 22:33:10] INFO: Generating the pages of 1 package(s) [2025-08-06 22:33:10] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/cpptraj_5.1.0+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/cpptraj_5.1.0+dfsg-4.diff.gz is missing [2025-08-06 22:33:10] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/cpptraj_5.1.0+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/cpptraj_5.1.0+dfsg-4.diff.gz is missing [2025-08-06 22:33:10] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/arm64/cpptraj_5.1.0+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/arm64/cpptraj_5.1.0+dfsg-4.diff.gz is missing [2025-08-06 22:33:10] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/trixie/armhf/cpptraj_5.1.0+dfsg-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/armhf/cpptraj_5.1.0+dfsg-4.diff.gz is missing [2025-08-06 22:33:10] INFO: Finished at 2025-08-06 22:33:10.785085, took: 0:00:00.103751 All cleanup done. Wed Aug 6 22:33:10 UTC 2025 - total duration: 0h 6m 27s. Wed Aug 6 22:33:10 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-Lg1EwLIc, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 6min 28.265s CPU time consumed: 5.494s