Mon Nov 11 00:05:51 UTC 2024 I: starting to build libpdb-redo/unstable/armhf on jenkins on '2024-11-11 00:05' Mon Nov 11 00:05:51 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_33/17485/console.log Mon Nov 11 00:05:51 UTC 2024 I: Downloading source for unstable/libpdb-redo=3.1.5-5 --2024-11-11 00:05:51-- http://deb.debian.org/debian/pool/main/libp/libpdb-redo/libpdb-redo_3.1.5-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2296 (2.2K) [text/prs.lines.tag] Saving to: ‘libpdb-redo_3.1.5-5.dsc’ 0K .. 100% 267M=0s 2024-11-11 00:05:51 (267 MB/s) - ‘libpdb-redo_3.1.5-5.dsc’ saved [2296/2296] Mon Nov 11 00:05:52 UTC 2024 I: libpdb-redo_3.1.5-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libpdb-redo Binary: libpdb-redo-dev, libpdb-redo3 Architecture: any Version: 3.1.5-5 Maintainer: Debian Med Packaging Team Uploaders: Maarten L. Hekkelman Homepage: https://github.com/PDB-REDO/libpdb-redo Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/libpdb-redo Vcs-Git: https://salsa.debian.org/med-team/libpdb-redo.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@, mrc Build-Depends: debhelper-compat (= 13), libcifpp-dev (>= 7), cmake, libnewuoa-dev (>= 0.1.2), pkgconf, libgsl-dev, libboost-dev, libboost-regex-dev, libeigen3-dev, libclipper-dev, zlib1g-dev, libccp4-dev (>= 6.5.1-5) Package-List: libpdb-redo-dev deb libdevel optional arch=any libpdb-redo3 deb libs optional arch=any Checksums-Sha1: 63effd6eeaeac273a6fe5aa6ed83e5ea3cbeaf03 870508 libpdb-redo_3.1.5.orig.tar.gz 50ffb8a1fbfd78dd891e101e13b5886d46dae776 4300 libpdb-redo_3.1.5-5.debian.tar.xz Checksums-Sha256: bb9bdadea952c9057ab3649ccfe6e7383bb6cb5cfa1f9bdf6a5fd2f4faf83667 870508 libpdb-redo_3.1.5.orig.tar.gz 77c038d2e0a9c574652de0f771418c7e5ddf2a7edacc5dc7b549e2e8006f80d7 4300 libpdb-redo_3.1.5-5.debian.tar.xz Files: c0b761daafe29b26c96e2b08fdb44e00 870508 libpdb-redo_3.1.5.orig.tar.gz 6e1e0d65ccf0891d22037cd01bc8053b 4300 libpdb-redo_3.1.5-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJKBAEBCgA0FiEEpytoJCJrtAfiS56AWHUD7Hrn7c4FAmckAbAWHG1hYXJ0ZW5A aGVra2VsbWFuLmNvbQAKCRBYdQPseuftzi6rD/9EPVISn50KRSiKbch98+eKQrR4 7jdoOgzAqQx3cUGrTQi+eUcckpWRVNLEmqe0F+iBixq0sAPz0DNwWted5hw3FuvN te/5AL6SbJFj04K3wb++xuEtwtP05ZlCHS8g2LyeQf94dCtbY843Zzz4xArvGI3C QlwVmNsuptR4mMqPMPQ/5RkqVRevn9JLA5frW0CtvP5izb6VNKQz3OH/LNlpy5OB EqMwOj0AIkw2RHvA0QYW15YXNX1hD5EilnsHQyI8xiHFuRZC/Rg0s4KWyrbFZsR1 soAizzyQE8bV5Eps4HvoQLCSGzoqbfHo3AO46lnW9w2hUvYMfKsdbANB501ja0EW sZ4UBOwvrjYvq115+MCde5P01I6s7i+1R7+ZPYgijVjxB8vd9XHT83dA7BqqYszi ecH2VNmKlFOLIowW6nRthDjH0G81UMAJ1bRnAGTD75yPalrXRRWG1MZymGQX4zOC 8KwTch7YsEq1xw69llKkSEJmkObsPydwkcoovJZbwLyKgaJLJCZUcdjBYaEC2+2u K1v8hHAyvenqG9dBlqTGAxLpu3AjnfgLhBZGiUlpA+cfhjftdCGPhcBI04rzGh2w O/DYghiSDf0ufqXENn9zbHwucC4VrVhu2HLgx1LyDdq70u6b7OhUL/e0hmgqX69z Anmo/mNiN+k8d8n/zw== =5N5u -----END PGP SIGNATURE----- Mon Nov 11 00:05:52 UTC 2024 I: Checking whether the package is not for us Mon Nov 11 00:05:52 UTC 2024 I: Starting 1st build on remote node virt32z-armhf-rb.debian.net. Mon Nov 11 00:05:52 UTC 2024 I: Preparing to do remote build '1' on virt32z-armhf-rb.debian.net. Mon Nov 11 00:13:04 UTC 2024 I: Deleting $TMPDIR on virt32z-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Nov 10 12:05:59 -12 2024 I: pbuilder-time-stamp: 1731283559 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 [libpdb-redo_3.1.5-5.dsc] I: copying [./libpdb-redo_3.1.5.orig.tar.gz] I: copying [./libpdb-redo_3.1.5-5.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Oct 31 22:16:16 2024 gpgv: using RSA key A72B6824226BB407E24B9E80587503EC7AE7EDCE gpgv: issuer "maarten@hekkelman.com" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libpdb-redo_3.1.5-5.dsc: no acceptable signature found dpkg-source: info: extracting libpdb-redo in libpdb-redo-3.1.5 dpkg-source: info: unpacking libpdb-redo_3.1.5.orig.tar.gz dpkg-source: info: unpacking libpdb-redo_3.1.5-5.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1211/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='6be6612fc4084f9195a7c4cbfa06ed18' 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='1211' 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.hkC4U0o2/pbuilderrc_Nbqi --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.hkC4U0o2/b1 --logfile b1/build.log libpdb-redo_3.1.5-5.dsc' SUDO_GID='110' SUDO_UID='103' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32z 6.1.0-27-armmp-lpae #1 SMP Debian 6.1.115-1 (2024-11-01) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1211/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: armhf 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), libcifpp-dev (>= 7), cmake, libnewuoa-dev (>= 0.1.2), pkgconf, libgsl-dev, libboost-dev, libboost-regex-dev, libeigen3-dev, libclipper-dev, zlib1g-dev, libccp4-dev (>= 6.5.1-5) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19689 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 libcifpp-dev (>= 7); however: Package libcifpp-dev is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libnewuoa-dev (>= 0.1.2); however: Package libnewuoa-dev is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-regex-dev; however: Package libboost-regex-dev is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libclipper-dev; however: Package libclipper-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libccp4-dev (>= 6.5.1-5); however: Package libccp4-dev 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} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} fftw-dev{a} fftw2{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-dev{a} libboost-regex-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost1.83-dev{a} libbrotli1{a} libccp4-data{a} libccp4-dev{a} libccp4c0t64{a} libccp4f0t64{a} libcifpp-data{a} libcifpp-dev{a} libcifpp7{a} libclipper-dev{a} libclipper2{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libeigen3-dev{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libgssapi-krb5-2{a} libhwloc15{a} libicu-dev{a} libicu72{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libmmdb2-0{a} libmmdb2-dev{a} libmpich12{a} libnewuoa-dev{a} libnewuoa0{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{a} sfftw-dev{a} sfftw2{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libhwloc-plugins libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libssl3 linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 88 newly installed, 0 to remove and 0 not upgraded. Need to get 61.7 MB of archives. After unpacking 370 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf libproc2-0 armhf 2:4.0.4-6 [56.0 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf procps armhf 2:4.0.4-6 [864 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-5 [1091 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-10 [88.8 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-2 [723 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf cmake-data all 3.30.5-1 [2223 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5+b1 [9088 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.1 [604 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf libarchive13t64 armhf 3.7.4-1.1 [306 kB] Get: 22 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b5 [296 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.1-1+b1 [22.3 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 27 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8 [18.2 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8 [50.2 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf libldap-2.5-0 armhf 2.5.18+dfsg-3+b1 [163 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB] Get: 35 http://deb.debian.org/debian unstable/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB] Get: 36 http://deb.debian.org/debian unstable/main armhf libcurl4t64 armhf 8.11.0-1 [303 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB] Get: 38 http://deb.debian.org/debian unstable/main armhf libjsoncpp26 armhf 1.9.6-2 [70.0 kB] Get: 39 http://deb.debian.org/debian unstable/main armhf librhash1 armhf 1.4.5-1 [143 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf libuv1t64 armhf 1.48.0-7 [134 kB] Get: 41 http://deb.debian.org/debian unstable/main armhf cmake armhf 3.30.5-1 [5365 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-8 [517 kB] Get: 44 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 47 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 48 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 53 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB] Get: 54 http://deb.debian.org/debian unstable/main armhf libgfortran5 armhf 14.2.0-8 [263 kB] Get: 55 http://deb.debian.org/debian unstable/main armhf libhwloc15 armhf 2.11.2-1 [134 kB] Get: 56 http://deb.debian.org/debian unstable/main armhf libmpich12 armhf 4.2.0-14 [1498 kB] Get: 57 http://deb.debian.org/debian unstable/main armhf fftw2 armhf 2.1.5-7 [188 kB] Get: 58 http://deb.debian.org/debian unstable/main armhf fftw-dev armhf 2.1.5-7 [218 kB] Get: 59 http://deb.debian.org/debian unstable/main armhf icu-devtools armhf 72.1-5+b1 [187 kB] Get: 60 http://deb.debian.org/debian unstable/main armhf libboost1.83-dev armhf 1.83.0-3.2 [10.6 MB] Get: 61 http://deb.debian.org/debian unstable/main armhf libboost-dev armhf 1.83.0.2+b2 [3832 B] Get: 62 http://deb.debian.org/debian unstable/main armhf libboost-regex1.83.0 armhf 1.83.0-3.2 [307 kB] Get: 63 http://deb.debian.org/debian unstable/main armhf libicu-dev armhf 72.1-5+b1 [10.1 MB] Get: 64 http://deb.debian.org/debian unstable/main armhf libboost-regex1.83-dev armhf 1.83.0-3.2 [335 kB] Get: 65 http://deb.debian.org/debian unstable/main armhf libboost-regex-dev armhf 1.83.0.2+b2 [3856 B] Get: 66 http://deb.debian.org/debian unstable/main armhf libccp4-data all 8.0.0-4 [62.7 kB] Get: 67 http://deb.debian.org/debian unstable/main armhf libccp4c0t64 armhf 8.0.0-4 [76.2 kB] Get: 68 http://deb.debian.org/debian unstable/main armhf libmmdb2-0 armhf 2.0.22-1+b2 [280 kB] Get: 69 http://deb.debian.org/debian unstable/main armhf libccp4f0t64 armhf 8.0.0-4 [195 kB] Get: 70 http://deb.debian.org/debian unstable/main armhf libccp4-dev armhf 8.0.0-4 [43.0 kB] Get: 71 http://deb.debian.org/debian unstable/main armhf libcifpp-data all 7.0.7-3 [484 kB] Get: 72 http://deb.debian.org/debian unstable/main armhf libcifpp7 armhf 7.0.7-3 [855 kB] Get: 73 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] Get: 74 http://deb.debian.org/debian unstable/main armhf libcifpp-dev armhf 7.0.7-3 [111 kB] Get: 75 http://deb.debian.org/debian unstable/main armhf sfftw2 armhf 2.1.5-7 [190 kB] Get: 76 http://deb.debian.org/debian unstable/main armhf libclipper2 armhf 2.1.20201109-2+b3 [1106 kB] Get: 77 http://deb.debian.org/debian unstable/main armhf libmmdb2-dev armhf 2.0.22-1+b2 [92.9 kB] Get: 78 http://deb.debian.org/debian unstable/main armhf sfftw-dev armhf 2.1.5-7 [221 kB] Get: 79 http://deb.debian.org/debian unstable/main armhf libclipper-dev armhf 2.1.20201109-2+b3 [82.4 kB] Get: 80 http://deb.debian.org/debian unstable/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB] Get: 81 http://deb.debian.org/debian unstable/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB] Get: 82 http://deb.debian.org/debian unstable/main armhf pkgconf armhf 1.8.1-4 [26.1 kB] Get: 83 http://deb.debian.org/debian unstable/main armhf libeigen3-dev all 3.4.0-4 [1041 kB] Get: 84 http://deb.debian.org/debian unstable/main armhf libgslcblas0 armhf 2.8+dfsg-5 [85.5 kB] Get: 85 http://deb.debian.org/debian unstable/main armhf libgsl28 armhf 2.8+dfsg-5 [812 kB] Get: 86 http://deb.debian.org/debian unstable/main armhf libgsl-dev armhf 2.8+dfsg-5 [1030 kB] Get: 87 http://deb.debian.org/debian unstable/main armhf libnewuoa0 armhf 0.1.2-1 [15.4 kB] Get: 88 http://deb.debian.org/debian unstable/main armhf libnewuoa-dev armhf 0.1.2-1 [7504 B] Fetched 61.7 MB in 1s (74.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:armhf. (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 ... 19689 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.4-6_armhf.deb ... Unpacking libproc2-0:armhf (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../01-procps_2%3a4.0.4-6_armhf.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.24_all.deb ... 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Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.40.2-10_armhf.deb ... Unpacking bsdextrautils (2.40.2-10) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../10-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.13.0-1_armhf.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package cmake-data. Preparing to unpack .../17-cmake-data_3.30.5-1_all.deb ... Unpacking cmake-data (3.30.5-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../18-libicu72_72.1-5+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-5+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../19-libxml2_2.12.7+dfsg+really2.9.14-0.1_armhf.deb ... Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package libarchive13t64:armhf. Preparing to unpack .../20-libarchive13t64_3.7.4-1.1_armhf.deb ... Unpacking libarchive13t64:armhf (3.7.4-1.1) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../21-libbrotli1_1.1.0-2+b5_armhf.deb ... Unpacking libbrotli1:armhf (1.1.0-2+b5) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../22-libkrb5support0_1.21.3-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.21.3-3) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../23-libcom-err2_1.47.1-1+b1_armhf.deb ... Unpacking libcom-err2:armhf (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../24-libk5crypto3_1.21.3-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.21.3-3) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../25-libkeyutils1_1.6.3-4_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-4) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../26-libkrb5-3_1.21.3-3_armhf.deb ... Unpacking libkrb5-3:armhf (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:armhf. 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Unpacking libpsl5t64:armhf (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../33-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:armhf. Preparing to unpack .../34-libssh2-1t64_1.11.1-1_armhf.deb ... Unpacking libssh2-1t64:armhf (1.11.1-1) ... Selecting previously unselected package libcurl4t64:armhf. Preparing to unpack .../35-libcurl4t64_8.11.0-1_armhf.deb ... Unpacking libcurl4t64:armhf (8.11.0-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../36-libexpat1_2.6.4-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.4-1) ... Selecting previously unselected package libjsoncpp26:armhf. Preparing to unpack .../37-libjsoncpp26_1.9.6-2_armhf.deb ... Unpacking libjsoncpp26:armhf (1.9.6-2) ... Selecting previously unselected package librhash1:armhf. Preparing to unpack .../38-librhash1_1.4.5-1_armhf.deb ... Unpacking librhash1:armhf (1.4.5-1) ... Selecting previously unselected package libuv1t64:armhf. Preparing to unpack .../39-libuv1t64_1.48.0-7_armhf.deb ... Unpacking libuv1t64:armhf (1.48.0-7) ... Selecting previously unselected package cmake. Preparing to unpack .../40-cmake_3.30.5-1_armhf.deb ... Unpacking cmake (3.30.5-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../41-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../42-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../43-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../44-libarchive-zip-perl_1.68-1_all.deb ... 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Preparing to unpack .../50-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 .../51-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../52-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../53-libgfortran5_14.2.0-8_armhf.deb ... Unpacking libgfortran5:armhf (14.2.0-8) ... Selecting previously unselected package libhwloc15:armhf. Preparing to unpack .../54-libhwloc15_2.11.2-1_armhf.deb ... Unpacking libhwloc15:armhf (2.11.2-1) ... Selecting previously unselected package libmpich12:armhf. Preparing to unpack .../55-libmpich12_4.2.0-14_armhf.deb ... Unpacking libmpich12:armhf (4.2.0-14) ... Selecting previously unselected package fftw2. 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Unpacking libcifpp-dev:armhf (7.0.7-3) ... Selecting previously unselected package sfftw2. Preparing to unpack .../74-sfftw2_2.1.5-7_armhf.deb ... Unpacking sfftw2 (2.1.5-7) ... Selecting previously unselected package libclipper2:armhf. Preparing to unpack .../75-libclipper2_2.1.20201109-2+b3_armhf.deb ... Unpacking libclipper2:armhf (2.1.20201109-2+b3) ... Selecting previously unselected package libmmdb2-dev. Preparing to unpack .../76-libmmdb2-dev_2.0.22-1+b2_armhf.deb ... Unpacking libmmdb2-dev (2.0.22-1+b2) ... Selecting previously unselected package sfftw-dev. Preparing to unpack .../77-sfftw-dev_2.1.5-7_armhf.deb ... Unpacking sfftw-dev (2.1.5-7) ... Selecting previously unselected package libclipper-dev:armhf. Preparing to unpack .../78-libclipper-dev_2.1.20201109-2+b3_armhf.deb ... Unpacking libclipper-dev:armhf (2.1.20201109-2+b3) ... Selecting previously unselected package libpkgconf3:armhf. Preparing to unpack .../79-libpkgconf3_1.8.1-4_armhf.deb ... Unpacking libpkgconf3:armhf (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../80-pkgconf-bin_1.8.1-4_armhf.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:armhf. Preparing to unpack .../81-pkgconf_1.8.1-4_armhf.deb ... Unpacking pkgconf:armhf (1.8.1-4) ... Selecting previously unselected package libeigen3-dev. Preparing to unpack .../82-libeigen3-dev_3.4.0-4_all.deb ... Unpacking libeigen3-dev (3.4.0-4) ... Selecting previously unselected package libgslcblas0:armhf. Preparing to unpack .../83-libgslcblas0_2.8+dfsg-5_armhf.deb ... Unpacking libgslcblas0:armhf (2.8+dfsg-5) ... Selecting previously unselected package libgsl28:armhf. Preparing to unpack .../84-libgsl28_2.8+dfsg-5_armhf.deb ... Unpacking libgsl28:armhf (2.8+dfsg-5) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../85-libgsl-dev_2.8+dfsg-5_armhf.deb ... Unpacking libgsl-dev (2.8+dfsg-5) ... Selecting previously unselected package libnewuoa0. Preparing to unpack .../86-libnewuoa0_0.1.2-1_armhf.deb ... Unpacking libnewuoa0 (0.1.2-1) ... Selecting previously unselected package libnewuoa-dev. Preparing to unpack .../87-libnewuoa-dev_0.1.2-1_armhf.deb ... Unpacking libnewuoa-dev (0.1.2-1) ... Setting up libexpat1:armhf (2.6.4-1) ... Setting up libpipeline1:armhf (1.5.8-1) ... Setting up libkeyutils1:armhf (1.6.3-4) ... Setting up libboost1.83-dev:armhf (1.83.0-3.2) ... Setting up libicu72:armhf (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-10) ... Setting up libgslcblas0:armhf (2.8+dfsg-5) ... Setting up libmmdb2-0:armhf (2.0.22-1+b2) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libboost-regex1.83.0:armhf (1.83.0-3.2) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:armhf (1.1.0-2+b5) ... Setting up libuv1t64:armhf (1.48.0-7) ... Setting up libmagic1t64:armhf (1:5.45-3+b1) ... Setting up libpsl5t64:armhf (0.21.2-1.1+b1) ... Setting up libnghttp2-14:armhf (1.64.0-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:armhf (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libccp4-data (8.0.0-4) ... Setting up libnewuoa0 (0.1.2-1) ... Setting up libelf1t64:armhf (0.192-4) ... Setting up libkrb5support0:armhf (1.21.3-3) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:armhf (1.8.1-4) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libjsoncpp26:armhf (1.9.6-2) ... Setting up libproc2-0:armhf (2:4.0.4-6) ... Setting up libhwloc15:armhf (2.11.2-1) ... Setting up libmmdb2-dev (2.0.22-1+b2) ... Setting up autopoint (0.22.5-2) ... Setting up icu-devtools (72.1-5+b1) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:armhf (1.21.3-3) ... Setting up libcifpp-data (7.0.7-3) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-8) ... Setting up libgfortran5:armhf (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b2) ... Setting up libmpich12:armhf (4.2.0-14) ... Setting up sensible-utils (0.0.24) ... Setting up libccp4c0t64:armhf (8.0.0-4) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up cmake-data (3.30.5-1) ... Setting up librhash1:armhf (1.4.5-1) ... Setting up libkrb5-3:armhf (1.21.3-3) ... Setting up libboost-dev:armhf (1.83.0.2+b2) ... Setting up libssh2-1t64:armhf (1.11.1-1) ... Setting up libgsl28:armhf (2.8+dfsg-5) ... Setting up libicu-dev:armhf (72.1-5+b1) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libgsl-dev (2.8+dfsg-5) ... Setting up libtool (2.4.7-8) ... Setting up libnewuoa-dev (0.1.2-1) ... Setting up sfftw2 (2.1.5-7) ... Setting up libcifpp7:armhf (7.0.7-3) ... Setting up libccp4f0t64:armhf (8.0.0-4) ... Setting up libldap-2.5-0:armhf (2.5.18+dfsg-3+b1) ... Setting up pkgconf:armhf (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up fftw2 (2.1.5-7) ... Setting up sfftw-dev (2.1.5-7) ... Setting up libeigen3-dev (3.4.0-4) ... Setting up libgssapi-krb5-2:armhf (1.21.3-3) ... Setting up libboost-regex1.83-dev:armhf (1.83.0-3.2) ... Setting up libclipper2:armhf (2.1.20201109-2+b3) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up fftw-dev (2.1.5-7) ... Setting up libboost-regex-dev:armhf (1.83.0.2+b2) ... Setting up libarchive13t64:armhf (3.7.4-1.1) ... Setting up libcurl4t64:armhf (8.11.0-1) ... Setting up libccp4-dev:armhf (8.0.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libclipper-dev:armhf (2.1.20201109-2+b3) ... Setting up libcifpp-dev:armhf (7.0.7-3) ... Setting up cmake (3.30.5-1) ... Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/libpdb-redo-3.1.5/ && 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 > ../libpdb-redo_3.1.5-5_source.changes dpkg-buildpackage: info: source package libpdb-redo dpkg-buildpackage: info: source version 3.1.5-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Maarten L. Hekkelman dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean 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/libpdb-redo-3.1.5' dh_auto_configure -- -DBUILD_SHARED_LIBS=ON -DPDB_REDO_BUILD_TESTS=ON -DBUILD_MINIMIZER=OFF cd obj-arm-linux-gnueabihf && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DBUILD_SHARED_LIBS=ON -DPDB_REDO_BUILD_TESTS=ON -DBUILD_MINIMIZER=OFF .. -- The CXX compiler identification is GNU 14.2.0 -- The C compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Looking for ccp4/ccp4_general.h - /usr/include -- Found CCP4: /usr/lib/arm-linux-gnueabihf/libccp4c.so -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for clipper/clipper.h - /usr/include -- Found CCP4: /usr/lib/arm-linux-gnueabihf/libclipper-core.so -- FFTW2 libraries - /usr/lib/libsfftw.so -- - /usr/lib/libsrfftw.so -- FFTW2 header directory - /usr/include -- Performing Test _LINKING_WITH_CLIPPER_CORE -- Performing Test _LINKING_WITH_CLIPPER_CORE - Success -- Looking for clipper/clipper-ccp4.h - /usr/include -- Found CCP4: /usr/lib/arm-linux-gnueabihf/libclipper-ccp4.so -- Looking for clipper/clipper-contrib.h - /usr/include -- Found CCP4: /usr/lib/arm-linux-gnueabihf/libclipper-contrib.so -- CCP4 include directory: /usr/include -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.3.1") -- Git hash not found -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Looking for ccp4/ccp4_general.h - /usr/include -- Found CCP4: /usr/lib/arm-linux-gnueabihf/libccp4c.so -- Looking for clipper/clipper.h - /usr/include -- Found CCP4: /usr/lib/arm-linux-gnueabihf/libclipper-core.so -- FFTW2 libraries - /usr/lib/libsfftw.so -- - /usr/lib/libsrfftw.so -- FFTW2 header directory - /usr/include -- Looking for clipper/clipper-ccp4.h - /usr/include -- Found CCP4: /usr/lib/arm-linux-gnueabihf/libclipper-ccp4.so -- Looking for clipper/clipper-contrib.h - /usr/include -- Found CCP4: /usr/lib/arm-linux-gnueabihf/libclipper-contrib.so -- CCP4 include directory: /usr/include -- Configuring done (6.7s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED PDB_REDO_BUILD_TESTS -- Build files have been written to: /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf make[1]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5' dh_auto_build cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/libpdb-redo-3.1.5 -B/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf/CMakeFiles /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' make -f CMakeFiles/pdb-redo.dir/build.make CMakeFiles/pdb-redo.dir/depend make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' cd /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libpdb-redo-3.1.5 /build/reproducible-path/libpdb-redo-3.1.5 /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf/CMakeFiles/pdb-redo.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' make -f CMakeFiles/pdb-redo.dir/build.make CMakeFiles/pdb-redo.dir/build make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' [ 5%] Building CXX object CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o -MF CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/src/AtomShape.cpp [ 11%] Building CXX object CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o [ 17%] Building CXX object CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o -MF CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/src/BondMap.cpp /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o -MF CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/src/ClipperWrapper.cpp [ 23%] Building CXX object CMakeFiles/pdb-redo.dir/src/Compound.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Compound.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Compound.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Compound.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/src/Compound.cpp [ 29%] Building CXX object CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o -MF CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/src/DistanceMap.cpp [ 35%] Building CXX object CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o -MF CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/src/MapMaker.cpp [ 41%] Building CXX object CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/src/Ramachandran.cpp /build/reproducible-path/libpdb-redo-3.1.5/src/MapMaker.cpp: In member function ‘void pdb_redo::MapMaker::fixMTZ() [with FTYPE = float]’: /build/reproducible-path/libpdb-redo-3.1.5/src/MapMaker.cpp:1135:22: note: parameter passing for argument of type ‘clipper::datatypes::F_phi’ when C++17 is enabled changed to match C++14 in GCC 10.1 1135 | auto mFo = mFbData[ih] - mFdData[ih]; | ^~~ [ 47%] Building CXX object CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o -MF CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/src/ResolutionCalculator.cpp [ 52%] Building CXX object CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o -MF CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/src/SkipList.cpp In file included from /usr/include/c++/14/vector:72, from /usr/include/clipper/ccp4/ccp4_utils.h:49, from /usr/include/clipper/clipper-ccp4.h:7, from /build/reproducible-path/libpdb-redo-3.1.5/src/MapMaker.cpp:31: /usr/include/c++/14/bits/vector.tcc: In member function ‘constexpr void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/14/bits/vector.tcc:700:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 700 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/vector:66: In member function ‘constexpr void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void clipper::Array2d::resize(const int&, const int&, const T&) [with T = double]’ at /usr/include/clipper/core/clipper_types.h:379:40, inlined from ‘clipper::Matrix::Matrix(const int&, const int&, T) [with T = double]’ at /usr/include/clipper/core/clipper_types.h:406:27, inlined from ‘clipper::BasisFn_base::Fderiv::Fderiv(const int&)’ at /usr/include/clipper/core/resol_fn.h:80:43, inlined from ‘clipper::BasisFn_base::BasisFn_base(const int&)’ at /usr/include/clipper/core/resol_fn.h:86:46, inlined from ‘clipper::BasisFn_spline::BasisFn_spline(const clipper::HKL_data_base&, const int&, clipper::ftype)’ at /usr/include/clipper/core/resol_basisfn.h:136:120, inlined from ‘void pdb_redo::MapMaker::printStats() [with FTYPE = float]’ at /build/reproducible-path/libpdb-redo-3.1.5/src/MapMaker.cpp:1177:26: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘constexpr void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘void clipper::Array2d::resize(const int&, const int&, const T&) [with T = double]’ at /usr/include/clipper/core/clipper_types.h:379:40, inlined from ‘clipper::Matrix::Matrix(const int&, const int&, T) [with T = double]’ at /usr/include/clipper/core/clipper_types.h:406:27, inlined from ‘clipper::BasisFn_base::Fderiv::Fderiv(const int&)’ at /usr/include/clipper/core/resol_fn.h:80:43, inlined from ‘clipper::BasisFn_base::BasisFn_base(const int&)’ at /usr/include/clipper/core/resol_fn.h:86:46, inlined from ‘clipper::BasisFn_spline::BasisFn_spline(const clipper::HKL_data_base&, const int&, clipper::ftype)’ at /usr/include/clipper/core/resol_basisfn.h:136:120, inlined from ‘void pdb_redo::MapMaker::printStats() [with FTYPE = double]’ at /build/reproducible-path/libpdb-redo-3.1.5/src/MapMaker.cpp:1177:26: /usr/include/c++/14/bits/stl_vector.h:1037:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1037 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 58%] Building CXX object CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/src/Statistics.cpp [ 64%] Building CXX object CMakeFiles/pdb-redo.dir/src/TLS.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/TLS.cpp.o -MF CMakeFiles/pdb-redo.dir/src/TLS.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/TLS.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/src/TLS.cpp In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/libpdb-redo-3.1.5/src/Statistics.cpp:27: /usr/include/c++/14/bits/stl_pair.h: In instantiation of ‘constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double; _T2 = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]’: /build/reproducible-path/libpdb-redo-3.1.5/src/Statistics.cpp:542:41: required from here 542 | mRmsScaled[zsc.first] = std::make_pair(qa * mRMSDensityFd, qb * mRMSDensityFd); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ In file included from /usr/include/c++/14/regex:52, from /usr/include/cif++/condition.hpp:35, from /usr/include/cif++/category.hpp:31, from /usr/include/cif++/datablock.hpp:29, from /usr/include/cif++/file.hpp:31, from /usr/include/cif++.hpp:30, from /build/reproducible-path/libpdb-redo-3.1.5/src/Statistics.cpp:30: /usr/include/c++/14/bits/stl_algo.h: In function ‘constexpr void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1876 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 70%] Building CXX object CMakeFiles/pdb-redo.dir/src/Version.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Version.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Version.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Version.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/src/Version.cpp In file included from /usr/include/c++/14/set:62, from /usr/include/cif++/text.hpp:35, from /usr/include/cif++/item.hpp:31, from /usr/include/cif++/row.hpp:29, from /usr/include/cif++/condition.hpp:29: /usr/include/c++/14/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = clipper::Coord_grid; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = pdb_redo::StatsCollector::cmpGPt; _Alloc = std::allocator >]’: /usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, pdb_redo::StatsCollector::cmpGPt, std::allocator > >::const_iterator’ changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/regex:56: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = clipper::Coord_grid; _Tp = double; _Compare = pdb_redo::StatsCollector::cmpGPt; _Alloc = std::allocator >]’, inlined from ‘void pdb_redo::StatsCollector::collectSums(std::vector&, GridPtDataMap&) const’ at /build/reproducible-path/libpdb-redo-3.1.5/src/Statistics.cpp:1022:36: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, pdb_redo::StatsCollector::cmpGPt, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = clipper::Coord_grid; _Tp = double; _Compare = pdb_redo::StatsCollector::cmpGPt; _Alloc = std::allocator >]’, inlined from ‘pdb_redo::StatsCollector::sumDensity(std::vector&, GridPtDataMap&, std::map, std::vector >&) const::’ at /build/reproducible-path/libpdb-redo-3.1.5/src/Statistics.cpp:987:32, inlined from ‘void pdb_redo::iterateGrid(const clipper::Coord_orth&, float, const clipper::Xmap&, F&&) [with F = StatsCollector::sumDensity(std::vector&, GridPtDataMap&, std::map, std::vector >&) const::; FTYPE = float]’ at /build/reproducible-path/libpdb-redo-3.1.5/include/pdb-redo/Statistics.hpp:75:9, inlined from ‘void pdb_redo::StatsCollector::sumDensity(std::vector&, GridPtDataMap&, std::map, std::vector >&) const’ at /build/reproducible-path/libpdb-redo-3.1.5/src/Statistics.cpp:974:14: /usr/include/c++/14/bits/stl_map.h:513:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, pdb_redo::StatsCollector::cmpGPt, std::allocator > >::const_iterator’ changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In function ‘constexpr void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, inlined from ‘constexpr void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4771:18, inlined from ‘void pdb_redo::StatsCollector::initialize()’ at /build/reproducible-path/libpdb-redo-3.1.5/src/Statistics.cpp:480:7: /usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1905 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1906 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1907 | __comp); | ~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 [ 76%] Linking CXX shared library libpdb-redo.so /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb-redo.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libpdb-redo.so.3.1 -o libpdb-redo.so.3.1.5 "CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o" "CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o" "CMakeFiles/pdb-redo.dir/src/ClipperWrapper.cpp.o" "CMakeFiles/pdb-redo.dir/src/Compound.cpp.o" "CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o" "CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o" "CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o" "CMakeFiles/pdb-redo.dir/src/ResolutionCalculator.cpp.o" "CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o" "CMakeFiles/pdb-redo.dir/src/Statistics.cpp.o" "CMakeFiles/pdb-redo.dir/src/TLS.cpp.o" "CMakeFiles/pdb-redo.dir/src/Version.cpp.o" /usr/lib/arm-linux-gnueabihf/libcifpp.so.7.0.7 /usr/lib/arm-linux-gnueabihf/libnewuoa.so.0.1.2 /usr/lib/arm-linux-gnueabihf/libclipper-ccp4.so /usr/lib/arm-linux-gnueabihf/libclipper-contrib.so /usr/lib/arm-linux-gnueabihf/libclipper-core.so /usr/lib/arm-linux-gnueabihf/libccp4c.so /usr/lib/arm-linux-gnueabihf/libz.so /usr/bin/cmake -E cmake_symlink_library libpdb-redo.so.3.1.5 libpdb-redo.so.3.1 libpdb-redo.so make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' [ 76%] Built target pdb-redo make -f CMakeFiles/pdb-redo-unit-test.dir/build.make CMakeFiles/pdb-redo-unit-test.dir/depend make -f examples/CMakeFiles/pdb-redo-example.dir/build.make examples/CMakeFiles/pdb-redo-example.dir/depend make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' cd /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libpdb-redo-3.1.5 /build/reproducible-path/libpdb-redo-3.1.5 /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf/CMakeFiles/pdb-redo-unit-test.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' cd /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libpdb-redo-3.1.5 /build/reproducible-path/libpdb-redo-3.1.5/examples /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf/examples /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf/examples/CMakeFiles/pdb-redo-example.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' make -f CMakeFiles/pdb-redo-unit-test.dir/build.make CMakeFiles/pdb-redo-unit-test.dir/build make -f examples/CMakeFiles/pdb-redo-example.dir/build.make examples/CMakeFiles/pdb-redo-example.dir/build make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' [ 82%] Building CXX object examples/CMakeFiles/pdb-redo-example.dir/example.cpp.o cd /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf/examples && /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -I/build/reproducible-path/libpdb-redo-3.1.5/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -MD -MT examples/CMakeFiles/pdb-redo-example.dir/example.cpp.o -MF CMakeFiles/pdb-redo-example.dir/example.cpp.o.d -o CMakeFiles/pdb-redo-example.dir/example.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/examples/example.cpp [ 88%] Building CXX object CMakeFiles/pdb-redo-unit-test.dir/test/pdb-redo-unit-test.cpp.o /usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -I/build/reproducible-path/libpdb-redo-3.1.5/include -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -MD -MT CMakeFiles/pdb-redo-unit-test.dir/test/pdb-redo-unit-test.cpp.o -MF CMakeFiles/pdb-redo-unit-test.dir/test/pdb-redo-unit-test.cpp.o.d -o CMakeFiles/pdb-redo-unit-test.dir/test/pdb-redo-unit-test.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/test/pdb-redo-unit-test.cpp [ 94%] Linking CXX executable pdb-redo-example cd /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb-redo-example.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wl,-z,relro -Wl,-z,now "CMakeFiles/pdb-redo-example.dir/example.cpp.o" -o pdb-redo-example -Wl,-rpath,/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf ../libpdb-redo.so.3.1.5 /usr/lib/arm-linux-gnueabihf/libcifpp.so.7.0.7 /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libnewuoa.so.0.1.2 /usr/lib/arm-linux-gnueabihf/libclipper-ccp4.so /usr/lib/arm-linux-gnueabihf/libclipper-contrib.so /usr/lib/arm-linux-gnueabihf/libclipper-core.so /usr/lib/arm-linux-gnueabihf/libccp4c.so make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' [ 94%] Built target pdb-redo-example [100%] Linking CXX executable pdb-redo-unit-test /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb-redo-unit-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wl,-z,relro -Wl,-z,now "CMakeFiles/pdb-redo-unit-test.dir/test/pdb-redo-unit-test.cpp.o" -o pdb-redo-unit-test -Wl,-rpath,/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf libpdb-redo.so.3.1.5 /usr/lib/arm-linux-gnueabihf/libcifpp.so.7.0.7 /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libnewuoa.so.0.1.2 /usr/lib/arm-linux-gnueabihf/libclipper-ccp4.so /usr/lib/arm-linux-gnueabihf/libclipper-contrib.so /usr/lib/arm-linux-gnueabihf/libclipper-core.so /usr/lib/arm-linux-gnueabihf/libccp4c.so make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' [100%] Built target pdb-redo-unit-test make[2]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' dh_auto_test cd obj-arm-linux-gnueabihf && make -j3 test ARGS\+=--verbose ARGS\+=-j3 make[1]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j3 UpdateCTestConfiguration from :/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf/DartConfiguration.tcl Parse Config file:/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf/DartConfiguration.tcl Parse Config file:/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf/DartConfiguration.tcl Test project /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: pdb-redo-unit-test 1: Test command: /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf/pdb-redo-unit-test "--" "/build/reproducible-path/libpdb-redo-3.1.5/test" 1: Working Directory: /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf 1: Test timeout computed to be: 1500 test 2 Start 2: pdb-redo-example 2: Test command: /build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf/examples/pdb-redo-example 2: Working Directory: /build/reproducible-path/libpdb-redo-3.1.5/examples 2: Test timeout computed to be: 1500 2: 2: Configuration error: 2: 2: The attempt to retrieve compound information for "PRO" failed. 2: 2: This information is searched for in a CCD file called components.cif or 2: components.cif.gz which should be located in one of the following directories: 2: 2: "/var/cache/libcifpp" 2: "/usr/share/libcifpp" 2: 2: (Note that you can add a directory to the search paths by setting the 2: LIBCIFPP_DATA_DIR environmental variable) 2: 2: On Linux an optional cron script might have been installed that automatically updates 2: components.cif and mmCIF dictionary files. This script only works when the file 2: libcifpp.conf contains an uncommented line with the text: 2: 2: update=true 2: 2: If you do not have a working cron script, you can manually update the files 2: in /var/cache/libcifpp using the following commands: 2: 2: curl -o /var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif 2: curl -o /var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic 2: curl -o /var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic 2: 2: No compound factory objects are created since none of the data sources is found. 2: Missing compound bond info for ALA 2: Missing compound bond info for ARG 2: Missing compound bond info for ASN 2: Missing compound bond info for ASP 2: Missing compound bond info for CYS 2: Missing compound bond info for GLN 2: Missing compound bond info for GLU 2: Missing compound bond info for GLY 2: Missing compound bond info for ILE 2: Missing compound bond info for LEU 2: Missing compound bond info for LYS 2: Missing compound bond info for MET 2: Missing compound bond info for PHE 2: Missing compound bond info for PRO 2: Missing compound bond info for REA 2: Missing compound bond info for SER 2: Missing compound bond info for THR 2: Missing compound bond info for TRP 2: Missing compound bond info for TYR 2: Missing compound bond info for VAL 2: Missing information for compound 'PRO' 2: Missing bond information for compound PRO 2: Missing information for compound 'ASN' 2: Missing bond information for compound ASN 2: Missing information for compound 'PHE' 2: Missing bond information for compound PHE 2: Missing information for compound 'SER' 2: Missing bond information for compound SER 2: Missing information for compound 'GLY' 2: Missing bond information for compound GLY 2: Missing information for compound 'TRP' 2: Missing bond information for compound TRP 2: Missing information for compound 'LYS' 2: Missing bond information for compound LYS 2: Missing information for compound 'ILE' 2: Missing bond information for compound ILE 2: Missing information for compound 'ARG' 2: Missing bond information for compound ARG 2: Missing information for compound 'GLU' 2: Missing bond information for compound GLU 2: Missing information for compound 'LEU' 2: Missing bond information for compound LEU 2: Missing information for compound 'VAL' 2: Missing bond information for compound VAL 2: Missing information for compound 'MET' 2: Missing bond information for compound MET 2: Missing information for compound 'ALA' 2: Missing bond information for compound ALA 2: Missing information for compound 'GLN' 2: Missing bond information for compound GLN 2: Missing information for compound 'ASP' 2: Missing bond information for compound ASP 2: Missing information for compound 'THR' 2: Missing bond information for compound THR 2: Missing information for compound 'TYR' 2: Missing bond information for compound TYR 2: Missing information for compound 'CYS' 2: Missing bond information for compound CYS 2: Missing information for compound 'REA' 2: Missing bond information for compound REA 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: nan 2: 0.962323 2: 0.961218 2: 1.2 2: 0.804563 2: 0.956281 2: 1.16442 2: 1.17157 2: 0.736907 2: 0.98891 2: 0.63726 2: 0.899501 2: 1.13951 2: 1.10304 2: 0.993256 2: 0.843706 2: 1.2 2: 0.394465 2: 0.622517 2: 1.13009 2: 0.811815 2: 1.12736 2: 1.04113 2: 1.15404 2: 0.966251 2: 0.264242 2: 0.896923 2: 0.947966 2: 0.759697 2: 0.714666 2: 0 2: 0 2: 0.58491 2: 0.883804 2: 0.6127 2: 0 2: 1.2 2: 0.816853 2: 1.2 2: 0.863403 2: 0.930392 2: 1.2 2: 0 2: 1.17888 2: 0.883952 2: 0.696931 2: 0.306483 2: 1.05932 2: 1.16462 2: 0.985143 2: 1.14584 2: 0.625949 2: 0.499085 2: 0.997431 2: 0.896065 2: 0.897962 2: 0 2: 1.2 2: 0.534169 2: 0.365134 2: 0.794768 2: 0.74366 2: 0.800937 2: 1.08071 2: 1.16712 2: 0.63442 2: 0.969202 2: 1.2 2: 0.984084 2: 0.359675 2: 0.780296 2: 0.601323 2: 0 2: 0.437712 2: 1.00255 2: 0.966266 2: 0.967664 2: 1.01481 2: 0.61683 2: 0.542967 2: 0.278281 2: 0.801292 2: 0 2: 0.611326 2: 0.396568 2: 0.641594 2: 0.460736 2: 0.794802 2: 0.0962642 2: 0.856458 2: 0.115798 2: 1.06967 2: 0.580771 2: 0.93537 2: 1.1918 2: 0.235196 2: 0.511667 2: 0.550865 2: 0.329081 2: 1.18026 2: 0.943706 1/2 Test #2: pdb-redo-example ................. Passed 1.73 sec 1: Running 7 test cases... 1: Reading map from "/build/reproducible-path/libpdb-redo-3.1.5/test/../examples/1cbs_map.mtz" 1: with labels: FB: FWT,PHWT 1: with labels: FD: DELFWT,PHDELWT 1: with labels: FA: FAN,PHAN 1: with labels: FO: FP,SIGFP 1: with labels: FC: FC_ALL,PHIC_ALL 1: Read Xmaps with sampling rate: 1.5 1: stored resolution: 1.79991 1: calculated reshi = 1.80009 reslo = 7.99918 1: spacegroup: P 21 21 21 1: cell: Cell ( 45.65, 47.56, 77.61, 90, 90, 90) 1: grid: Nuvw = ( 80, 80, 132) 1: R-factor : 0.180853 1: Free R-factor : 0.184876 1: Loading component LYS... done 1: Loading component ILE... done 1: Loading component ARG... done 1: Loading component GLU... done 1: Loading component LEU... done 1: Loading component VAL... done 1: Loading component MET... done 1: Loading component ALA... done 1: Loading component GLN... done 1: Loading component ASP... done 1: Loading component THR... done 1: Loading component TYR... done 1: Loading component CYS... done 1: Loading component REA... done 1: Loading component HOH... 1: Configuration error: 1: 1: The attempt to retrieve compound information for "HOH" failed. 1: 1: This information is searched for in a CCD file called components.cif or 1: components.cif.gz which should be located in one of the following directories: 1: 1: "/var/cache/libcifpp" 1: "/usr/share/libcifpp" 1: 1: (Note that you can add a directory to the search paths by setting the 1: LIBCIFPP_DATA_DIR environmental variable) 1: 1: On Linux an optional cron script might have been installed that automatically updates 1: components.cif and mmCIF dictionary files. This script only works when the file 1: libcifpp.conf contains an uncommented line with the text: 1: 1: update=true 1: 1: If you do not have a working cron script, you can manually update the files 1: in /var/cache/libcifpp using the following commands: 1: 1: curl -o /var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif 1: curl -o /var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic 1: curl -o /var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic 1: 1: The current order of compound factory objects is: 1: 1: CCD components file: "/build/reproducible-path/libpdb-redo-3.1.5/test/minimal-components.cif" 1: done 1: 1: Intercept & gradient before LS: -0.076201 (0.000425224) 0.1134 (0.00066587) 1: 1: Rescale SD(delta-rho) using Q-Q plot for asym A: 1: ====================================================== 1: Input & updated SD(delta-rho): 0.123854 ; 0.137899 1: 1: 1: Intercept & gradient before LS: 0.112013 (0.00322152) -0.0975523 (0.00506053) 1: 1: Rescale SD(delta-rho) using Q-Q plot for asym B: 1: ====================================================== 1: Input & updated SD(delta-rho): 0.123854 ; 0.111772 1: 1: 1: Intercept & gradient before LS: -0.038699 (0.00144741) -0.0997851 (0.00226694) 1: 1: Rescale SD(delta-rho) using Q-Q plot for asym C: 1: ====================================================== 1: Input & updated SD(delta-rho): 0.123854 ; 0.111495 1: 1: Calculating radii with B Factor 24.9788 1: Radius for atom with type N is 1.03582 1: Radius for atom with type C is 1.04896 1: Radius for atom with type O is 1.02401 1: Radius for atom with type S is 1.01993 1: skipping water in bond map calculation 1: Loading component HOH... done 1: Unknown compound: HOH 1: Missing compound information for HOH 1: The asym ID's of ndb_poly_seq_scheme and pdbx_poly_seq_scheme are not equal, dropping ndb_poly_seq_scheme 1: Reading map from "/build/reproducible-path/libpdb-redo-3.1.5/test/../examples/1cbs_map.mtz" 1: with labels: FB: FWT,PHWT 1: with labels: FD: DELFWT,PHDELWT 1: with labels: FA: FAN,PHAN 1: with labels: FO: FP,SIGFP 1: with labels: FC: FC_ALL,PHIC_ALL 1: Read Xmaps with sampling rate: 0.75 1: stored resolution: 1.79991 1: calculated reshi = 1.80009 reslo = 7.99918 1: spacegroup: P 21 21 21 1: cell: Cell ( 45.65, 47.56, 77.61, 90, 90, 90) 1: grid: Nuvw = ( 40, 40, 72) 1: R-factor : 0.180853 1: Free R-factor : 0.184876 1: Loading component U_K... done 1: 1: Intercept & gradient before LS: -0.0615663 (0.000573911) 0.0873704 (0.000898727) 1: 1: Rescale SD(delta-rho) using Q-Q plot for asym A: 1: ====================================================== 1: Input & updated SD(delta-rho): 0.11509 ; 0.125146 1: 1: 1: Intercept & gradient before LS: 0.0679982 (0.0146148) -0.0420235 (0.0228119) 1: 1: Rescale SD(delta-rho) using Q-Q plot for asym B: 1: ====================================================== 1: Input & updated SD(delta-rho): 0.11509 ; 0.110254 1: 1: 1: Intercept & gradient before LS: -0.00860157 (0.000800546) -0.185508 (0.00125356) 1: 1: Rescale SD(delta-rho) using Q-Q plot for asym C: 1: ====================================================== 1: Input & updated SD(delta-rho): 0.11509 ; 0.09374 1: 1: Calculating radii with B Factor 24.9788 1: Radius for atom with type N is 1.03582 1: Radius for atom with type C is 1.04896 1: Radius for atom with type O is 1.02401 1: Radius for atom with type S is 1.01993 1: skipping water in bond map calculation 1: Missing compound bond info for U_K 1: Missing information for compound 'U_K' 1: Missing bond information for compound U_K 1: Loading component HOH... done 1: Unknown compound: HOH 1: Missing compound information for HOH 1: The asym ID's of ndb_poly_seq_scheme and pdbx_poly_seq_scheme are not equal, dropping ndb_poly_seq_scheme 1: skipping water in bond map calculation 1: skipping water in bond map calculation 1: 1: *** No errors detected 1:  2/2 Test #1: pdb-redo-unit-test ............... Passed 7.61 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 7.62 sec make[1]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/reproducible-path/libpdb-redo-3.1.5/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/libpdb-redo-3.1.5 -B/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/arm-linux-gnueabihf/libpdb-redo.so.3.1.5 -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/arm-linux-gnueabihf/libpdb-redo.so.3.1 -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/arm-linux-gnueabihf/libpdb-redo.so -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/pdb-redo/pdb-redoTargets.cmake -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/pdb-redo/pdb-redoTargets-none.cmake -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/SkipList.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Restraints.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/DistanceMap.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/TLS.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Version.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Minimizer.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Ramachandran.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/AtomShape.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/ResolutionCalculator.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Compound.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/exports.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Statistics.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/BondMap.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/MapMaker.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/ClipperWrapper.hpp -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/pdb-redo/pdb-redoConfig.cmake -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/arm-linux-gnueabihf/cmake/pdb-redo/pdb-redoConfigVersion.cmake -- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/libpdb-redo.pc make[1]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-arm-linux-gnueabihf' dh_install dh_installdocs dh_installchangelogs dh_installexamples 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 libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libpdb-redo3/usr/lib/arm-linux-gnueabihf/libpdb-redo.so.3.1.5 found in none of the libraries dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libpdb-redo-dev' in '../libpdb-redo-dev_3.1.5-5_armhf.deb'. dpkg-deb: building package 'libpdb-redo3' in '../libpdb-redo3_3.1.5-5_armhf.deb'. dpkg-deb: building package 'libpdb-redo3-dbgsym' in '../libpdb-redo3-dbgsym_3.1.5-5_armhf.deb'. dpkg-genbuildinfo --build=binary -O../libpdb-redo_3.1.5-5_armhf.buildinfo dpkg-genchanges --build=binary -O../libpdb-redo_3.1.5-5_armhf.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/1211 and its subdirectories I: Current time: Sun Nov 10 12:12:47 -12 2024 I: pbuilder-time-stamp: 1731283967 Mon Nov 11 00:13:08 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt64c-armhf-rb.debian.net. Mon Nov 11 00:13:08 UTC 2024 I: Preparing to do remote build '2' on virt64c-armhf-rb.debian.net. Mon Nov 11 00:19:18 UTC 2024 I: Deleting $TMPDIR on virt64c-armhf-rb.debian.net. Mon Nov 11 00:19:21 UTC 2024 I: libpdb-redo_3.1.5-5_armhf.changes: Format: 1.8 Date: Thu, 31 Oct 2024 23:10:45 +0100 Source: libpdb-redo Binary: libpdb-redo-dev libpdb-redo3 libpdb-redo3-dbgsym Architecture: armhf Version: 3.1.5-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Maarten L. Hekkelman Description: libpdb-redo-dev - Development files for libpdb-redo libpdb-redo3 - Library file for libpdb-redo Closes: 1086519 Changes: libpdb-redo (3.1.5-5) unstable; urgency=medium . * Remove incorrect dependency, Closes: #1086519 Checksums-Sha1: 840118aee1fd078355f2d50d56ccc1932fc09aed 627428 libpdb-redo-dev_3.1.5-5_armhf.deb 9ed767f9bf88117616b4a6c34d94037cc1fa8337 6276196 libpdb-redo3-dbgsym_3.1.5-5_armhf.deb e3a8b7c5a58a0d1a8573636ee66f7e94c2393ee3 272056 libpdb-redo3_3.1.5-5_armhf.deb 3c05ab8793a0dbc4d0a3844deb114e7732fb0a93 7112 libpdb-redo_3.1.5-5_armhf.buildinfo Checksums-Sha256: 0d2ad23a0f4f4e61a7bfad82fa0203e7a380cdf836e1f68f18b8beed38e673cd 627428 libpdb-redo-dev_3.1.5-5_armhf.deb 7eddc440ddf9c90a963a32a0203596fffd5b68b2fc6e7be82167da9b1d9142a1 6276196 libpdb-redo3-dbgsym_3.1.5-5_armhf.deb 5ea152100fdd9ca843e229e9b9c106fc7b3b7de354dca3025729d9a91e8ce387 272056 libpdb-redo3_3.1.5-5_armhf.deb b8090c20f3a75bdc3fed15126ebf0f8555995968a7fae259f45700836af9675b 7112 libpdb-redo_3.1.5-5_armhf.buildinfo Files: 9ccba95c06c8036549502644fd49fdcc 627428 libdevel optional libpdb-redo-dev_3.1.5-5_armhf.deb 5d51b6f90f648c0fcf55d3e52906c416 6276196 debug optional libpdb-redo3-dbgsym_3.1.5-5_armhf.deb 5ac4a4ff48df22f96c61d6e6c13bcd22 272056 libs optional libpdb-redo3_3.1.5-5_armhf.deb 20c0156dfb4283075de8ef36917191fe 7112 libs optional libpdb-redo_3.1.5-5_armhf.buildinfo Mon Nov 11 00:19:22 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_33-17485.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.hkC4U0o2/libpdb-redo_3.1.5-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.hkC4U0o2/libpdb-redo_3.1.5-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.hkC4U0o2/libpdb-redo_3.1.5-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.hkC4U0o2/b1/libpdb-redo_3.1.5-5_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.hkC4U0o2/b2/libpdb-redo_3.1.5-5_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.451s) 0.451s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.092s) 0.092s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 785ms CPU time consumed: 785ms Mon Nov 11 00:19:23 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Mon Nov 11 00:19:23 UTC 2024 I: libpdb-redo from unstable built successfully and reproducibly on armhf. Mon Nov 11 00:19:24 UTC 2024 I: Submitting .buildinfo files to external archives: Mon Nov 11 00:19:24 UTC 2024 I: Submitting 8.0K b1/libpdb-redo_3.1.5-5_armhf.buildinfo.asc Mon Nov 11 00:19:25 UTC 2024 I: Submitting 8.0K b2/libpdb-redo_3.1.5-5_armhf.buildinfo.asc Mon Nov 11 00:19:26 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Nov 11 00:19:26 UTC 2024 I: Done submitting .buildinfo files. Mon Nov 11 00:19:26 UTC 2024 I: Removing signed libpdb-redo_3.1.5-5_armhf.buildinfo.asc files: removed './b1/libpdb-redo_3.1.5-5_armhf.buildinfo.asc' removed './b2/libpdb-redo_3.1.5-5_armhf.buildinfo.asc'