I: pbuilder: network access will be disabled during build I: Current time: Mon Jan 12 15:20:56 +14 2026 I: pbuilder-time-stamp: 1768180856 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [gemmi_0.6.5+ds-2.dsc] I: copying [./gemmi_0.6.5+ds.orig.tar.xz] I: copying [./gemmi_0.6.5+ds-2.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Jul 9 09:03:26 2024 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./gemmi_0.6.5+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting gemmi in gemmi-0.6.5+ds dpkg-source: info: unpacking gemmi_0.6.5+ds.orig.tar.xz dpkg-source: info: unpacking gemmi_0.6.5+ds-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-system-tao-pegtl.patch dpkg-source: info: applying use-system-doctest.patch dpkg-source: info: applying tao-pegtl-3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3648558/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 Jan 12 01:21 /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/3648558/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3648558/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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(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=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=4c914f64f721483daf58962a3ede7e5b 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=3648558 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.UYKLhwIp/pbuilderrc_8UUN --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UYKLhwIp/b2 --logfile b2/build.log gemmi_0.6.5+ds-2.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 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3648558/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: cmake, debhelper-compat (= 13), dh-python, doctest-dev, help2man, libstb-dev, python3-dev, python3-numpy, python3-pybind11 (>= 2.6.0), python3-pytest, tao-pegtl-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19967 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 cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on doctest-dev; however: Package doctest-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on libstb-dev; however: Package libstb-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11 (>= 2.6.0); however: Package python3-pybind11 is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on tao-pegtl-dev; however: Package tao-pegtl-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-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-python{a} dh-strip-nondeterminism{a} doctest-dev{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.5-0{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnsl2{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libstb-dev{a} libstb0t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} procps{a} pybind11-dev{a} python3{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pybind11{a} python3-pytest{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tao-pegtl-dev{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libeigen3-dev libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-pygments wget 0 packages upgraded, 106 newly installed, 0 to remove and 0 not upgraded. Need to get 64.6 MB of archives. After unpacking 273 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.8-1 [815 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.8-1 [2163 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-4 [256 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2~rc1-2 [23.8 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 13 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.8-1 [1970 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.8-1 [677 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-12 [92.0 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.30.5-1 [2223 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.30.5-1 [11.4 MB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 64 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 76 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 75.2.0-1 [731 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20241024 [109 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 doctest-dev all 2.4.11-1 [216 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libpython3.12t64 amd64 3.12.8-1 [2151 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libpython3.12-dev amd64 3.12.8-1 [5136 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.12.6-1 [9952 B] Get: 95 http://deb.debian.org/debian trixie/main amd64 libstb0t64 amd64 0.0~git20240715.f7f20f39fe4f+ds-1 [220 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libstb-dev amd64 0.0~git20240715.f7f20f39fe4f+ds-1 [654 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 pybind11-dev all 2.13.6-1 [204 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 python3.12-dev amd64 3.12.8-1 [505 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.12.6-1 [26.1 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 101 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 python3-pybind11 all 2.13.6-1 [215 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 8.3.3-1 [249 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] Fetched 64.6 MB in 14s (4488 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. 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Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up dh-python (6.20241024) ... Processing triggers for libc-bin (2.40-4) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3648558/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/3648558/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/gemmi-0.6.5+ds/ && 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 > ../gemmi_0.6.5+ds-2_source.changes dpkg-buildpackage: info: source package gemmi dpkg-buildpackage: info: source version 0.6.5+ds-2 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 --buildsystem cmake --with python3 dh_auto_clean -O--buildsystem=cmake debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds' rm -rf .pytest_cache examples/__pycache__ tests/__pycache__ make[1]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds' dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary dh binary --buildsystem cmake --with python3 dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds' dh_auto_configure -- -DBUILD_SHARED_LIBS=OFF -DUSE_PYTHON=ON cd obj-x86_64-linux-gnu && 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/x86_64-linux-gnu -DBUILD_SHARED_LIBS=OFF -DUSE_PYTHON=ON .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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 -- 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 -- Gemmi version 0.6.5 -- Build type: None -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Benchmarks not configured. -- The python module will be built. -- Found Python: /usr/bin/python3 (found version "3.12.8") found components: Interpreter Development.Module -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/lib/python3/dist-packages/pybind11/include (found version "2.13.6") -- Found pybind11 2.13.6: /usr/lib/python3/dist-packages/pybind11/include;/usr/include/python3.12 -- Configuring done (1.6s) -- 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 -- Build files have been written to: /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds' dh_auto_build -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' /usr/bin/cmake 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-I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/mmcif.cpp [ 16%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/json.cpp.o [ 18%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast 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-I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/riding_h.cpp /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/read_cif.cpp [ 22%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o [ 27%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o [ 27%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o [ 27%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/resinfo.cpp /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/xds_ascii.cpp [ 29%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/sprintf.cpp /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/to_mmcif.cpp [ 29%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/to_pdb.cpp /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/topo.cpp /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/monlib.cpp /build/reproducible-path/gemmi-0.6.5+ds/src/sprintf.cpp:30:86: note: '#pragma message: Using system stb_sprintf.h, not the bundled one. It may not work.' 30 | # pragma message("Using system stb_sprintf.h, not the bundled one. It may not work.") | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/src/gz.cpp:15: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/prog/options.cpp:8: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/src/mtz.cpp:3: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, from /build/reproducible-path/gemmi-0.6.5+ds/src/json.cpp:3: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:11, from /build/reproducible-path/gemmi-0.6.5+ds/src/xds_ascii.cpp:3: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz2cif.hpp:14, from /build/reproducible-path/gemmi-0.6.5+ds/src/mtz2cif.cpp:3: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/intensit.hpp:14, from /build/reproducible-path/gemmi-0.6.5+ds/src/intensit.cpp:3: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, from /build/reproducible-path/gemmi-0.6.5+ds/src/read_cif.cpp:5: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mmread.hpp:12, from /build/reproducible-path/gemmi-0.6.5+ds/src/mmread_gz.cpp:4: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [ 29%] Built target options In file included from /usr/include/c++/14/bits/stl_tree.h:63, from /usr/include/c++/14/map:62, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/topo.hpp:8, from /build/reproducible-path/gemmi-0.6.5+ds/src/topo.cpp:3: In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = gemmi::Topo::Rule; _Up = gemmi::Topo::Rule; bool _IsMove = true]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = true; _II = gemmi::Topo::Rule*; _OI = gemmi::Topo::Rule*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = true; _II = gemmi::Topo::Rule*; _OI = gemmi::Topo::Rule*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = true; _II = __gnu_cxx::__normal_iterator >; _OI = gemmi::Topo::Rule*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, inlined from '_OI std::copy(_II, _II, _OI) [with _II = move_iterator<__gnu_cxx::__normal_iterator > >; _OI = gemmi::Topo::Rule*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<__gnu_cxx::__normal_iterator > >; _ForwardIterator = gemmi::Topo::Rule*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator<__gnu_cxx::__normal_iterator > >; _ForwardIterator = gemmi::Topo::Rule*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = move_iterator<__gnu_cxx::__normal_iterator > >; _ForwardIterator = gemmi::Topo::Rule*; _Tp = gemmi::Topo::Rule]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = std::move_iterator<__gnu_cxx::__normal_iterator > >; _Tp = gemmi::Topo::Rule; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1022:38, inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::move_iterator<__gnu_cxx::__normal_iterator > >; = void; _Tp = gemmi::Topo::Rule; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, inlined from 'void gemmi::vector_move_extend(std::vector&, std::vector&&) [with T = Topo::Rule]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/util.hpp:260:15, inlined from 'void gemmi::Topo::apply_all_restraints(const gemmi::MonLib&)' at /build/reproducible-path/gemmi-0.6.5+ds/src/topo.cpp:608:27: /usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 17 and 9223372036854775792 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/bits/stl_tree.h:64: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = gemmi::Topo::Rule]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = gemmi::Topo::Rule]' at /usr/include/c++/14/bits/alloc_traits.h:509:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = gemmi::Topo::Rule; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = std::move_iterator<__gnu_cxx::__normal_iterator > >; _Tp = gemmi::Topo::Rule; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1013:40, inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::move_iterator<__gnu_cxx::__normal_iterator > >; = void; _Tp = gemmi::Topo::Rule; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, inlined from 'void gemmi::vector_move_extend(std::vector&, std::vector&&) [with T = Topo::Rule]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/util.hpp:260:15, inlined from 'void gemmi::Topo::apply_all_restraints(const gemmi::MonLib&)' at /build/reproducible-path/gemmi-0.6.5+ds/src/topo.cpp:608:27: /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [16, 9223372036854775792] allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 31%] Linking CXX static library libgemmi_cpp.a /usr/bin/cmake -P CMakeFiles/gemmi_cpp.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/gemmi_cpp.dir/link.txt --verbose=1 /usr/bin/ar qc libgemmi_cpp.a CMakeFiles/gemmi_cpp.dir/src/align.cpp.o CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o CMakeFiles/gemmi_cpp.dir/src/json.cpp.o CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o /usr/bin/ranlib libgemmi_cpp.a make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [ 31%] Built target gemmi_cpp make -f CMakeFiles/gemmi_prog.dir/build.make CMakeFiles/gemmi_prog.dir/depend make -f CMakeFiles/gemmi_py.dir/build.make CMakeFiles/gemmi_py.dir/depend make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_py.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/gemmi_py.dir/build.make CMakeFiles/gemmi_py.dir/build make -f CMakeFiles/gemmi_prog.dir/build.make CMakeFiles/gemmi_prog.dir/build make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [ 35%] Building CXX object CMakeFiles/gemmi_py.dir/python/mol.cpp.o [ 35%] Building CXX object CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o [ 35%] Building CXX object CMakeFiles/gemmi_py.dir/python/align.cpp.o [ 35%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/align.cpp.o [ 37%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o [ 37%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o [ 39%] Building CXX object CMakeFiles/gemmi_py.dir/python/cif.cpp.o [ 41%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o [ 43%] Building CXX object CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o [ 43%] Building CXX object CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 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CMakeFiles/gemmi_py.dir/python/write.cpp.o [ 81%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o [ 81%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.12 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/write.cpp.o -MF CMakeFiles/gemmi_py.dir/python/write.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/write.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/write.cpp /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/merge.cpp /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mask.cpp [ 83%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mondiff.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, from /build/reproducible-path/gemmi-0.6.5+ds/prog/map.cpp:6: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, from /build/reproducible-path/gemmi-0.6.5+ds/prog/mask.cpp:5: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/prog/ecalc.cpp:5: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cif2mtz.hpp:15, from /build/reproducible-path/gemmi-0.6.5+ds/prog/cif2mtz.cpp:10: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/prog/mapcoef.cpp:11: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/python/mtz.cpp:3: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, from /build/reproducible-path/gemmi-0.6.5+ds/python/ccp4.cpp:3: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz2cif.hpp:14, from /build/reproducible-path/gemmi-0.6.5+ds/prog/merge.cpp:12: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 83%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/monlib_opt.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cif2mtz.hpp:15, from /build/reproducible-path/gemmi-0.6.5+ds/python/hkl.cpp:9: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/prog/map2sf.cpp:10: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/pdb.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/python/read.cpp:7: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 85%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -Wno-psabi -MD -MT CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz.cpp [ 85%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz2cif.cpp [ 87%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/reindex.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz.cpp:8: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz2cif.hpp:14, from /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz2cif.cpp:8: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/prog/reindex.cpp:9: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 87%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/residues.cpp [ 89%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/rmsz.cpp [ 91%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/sf2map.cpp [ 91%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp [ 93%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/sg.cpp [ 93%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/tags.cpp [ 95%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/validate.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, from /build/reproducible-path/gemmi-0.6.5+ds/prog/sf2map.cpp:6: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 95%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/validate_mon.cpp [ 97%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/wcn.cpp [100%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/xds2mtz.cpp In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19, from /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:9: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:11, from /build/reproducible-path/gemmi-0.6.5+ds/prog/xds2mtz.cpp:8: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/prog/wcn.cpp:10: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [100%] Linking CXX shared module gemmi.cpython-312-x86_64-linux-gnu.so /usr/bin/cmake -E cmake_link_script CMakeFiles/gemmi_py.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong 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CMakeFiles/gemmi_py.dir/python/sym.cpp.o CMakeFiles/gemmi_py.dir/python/topo.cpp.o CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o CMakeFiles/gemmi_py.dir/python/write.cpp.o CMakeFiles/gemmi_cpp.dir/src/align.cpp.o CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o CMakeFiles/gemmi_cpp.dir/src/intensit.cpp.o CMakeFiles/gemmi_cpp.dir/src/json.cpp.o CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o /usr/lib/x86_64-linux-gnu/libz.so [100%] Linking CXX executable gemmi /usr/bin/cmake -E cmake_link_script CMakeFiles/gemmi_prog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/gemmi_prog.dir/prog/align.cpp.o CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o CMakeFiles/gemmi_prog.dir/prog/h.cpp.o CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o CMakeFiles/gemmi_prog.dir/prog/main.cpp.o CMakeFiles/gemmi_prog.dir/prog/map.cpp.o CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o CMakeFiles/options.dir/prog/options.cpp.o -o gemmi libgemmi_cpp.a /usr/lib/x86_64-linux-gnu/libz.so make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [100%] Built target gemmi_prog lto-wrapper: warning: using serial compilation of 118 LTRANS jobs lto-wrapper: note: see the '-flto' option documentation for more information /usr/include/c++/14/bits/stl_heap.h: In function '__adjust_heap.isra': /usr/include/c++/14/bits/stl_heap.h:224: note: the ABI of passing structure with 'complex float' member has changed in GCC 4.4 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, /usr/bin/strip /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/gemmi.cpython-312-x86_64-linux-gnu.so make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [100%] Built target 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[ 2%] Building CXX object CMakeFiles/hello.dir/examples/hello.cpp.o [ 4%] Building CXX object CMakeFiles/cpptest.dir/tests/cif.cpp.o [ 4%] Building CXX object CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o [ 4%] Building CXX object CMakeFiles/cpptest.dir/tests/main.cpp.o [ 6%] Building CXX object CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o [ 6%] Building CXX object CMakeFiles/doc_example.dir/docs/code/elem.cpp.o [ 8%] Building CXX object CMakeFiles/doc_example.dir/docs/code/cell.cpp.o /usr/bin/c++ -DUSE_STD_SNPRINTF=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/cpptest.dir/tests/cif.cpp.o -MF 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compiler generated dependencies of target options make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build Consolidate compiler generated dependencies of target gemmi_cpp make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/gemmi_cpp.dir/build.make CMakeFiles/gemmi_cpp.dir/build make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/options.dir/build'. make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/gemmi_cpp.dir/build'. make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [ 12%] Built target options [ 41%] Built target gemmi_cpp make -f CMakeFiles/doc_maybegz.dir/build.make CMakeFiles/doc_maybegz.dir/depend make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/depend make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/depend make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/depend make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/doc_maybegz.dir/DependInfo.cmake "--color=" make -f CMakeFiles/gemmi_prog.dir/build.make CMakeFiles/gemmi_prog.dir/depend make[5]: Entering directory 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Dependencies file "CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/build Dependencies file "CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". make -f CMakeFiles/doc_maybegz.dir/build.make CMakeFiles/doc_maybegz.dir/build make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' Dependencies file "CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/build make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/build Dependencies file "CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' Dependencies file "CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' Dependencies file "CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/h.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/main.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/map.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". 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[ 41%] Building CXX object CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o [ 43%] Building CXX object CMakeFiles/test_disulf.dir/tests/disulf.cpp.o [ 45%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o [ 45%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o [ 45%] Building CXX object CMakeFiles/check_conn.dir/examples/check_conn.cpp.o /usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -MF CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o.d -o CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/newmtz.cpp /usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -MF CMakeFiles/test_disulf.dir/tests/disulf.cpp.o.d -o CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/tests/disulf.cpp /usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/maybegz.cpp /usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -MF CMakeFiles/check_conn.dir/examples/check_conn.cpp.o.d -o CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/examples/check_conn.cpp /usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/mutate.cpp Consolidate compiler generated dependencies of target gemmi_prog make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/gemmi_prog.dir/build.make CMakeFiles/gemmi_prog.dir/build make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/gemmi_prog.dir/build'. make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [ 87%] Built target gemmi_prog make -f CMakeFiles/print-version.dir/build.make CMakeFiles/print-version.dir/depend make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/print-version.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/print-version.dir/build.make CMakeFiles/print-version.dir/build make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [ 87%] gemmi --version cd /build/reproducible-path/gemmi-0.6.5+ds && /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/gemmi --version gemmi 0.6.5 make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [ 87%] Built target print-version In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23, from /build/reproducible-path/gemmi-0.6.5+ds/docs/code/newmtz.cpp:1: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mmread.hpp:12, from /build/reproducible-path/gemmi-0.6.5+ds/docs/code/maybegz.cpp:2: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10, from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mmread.hpp:12, from /build/reproducible-path/gemmi-0.6.5+ds/tests/disulf.cpp:11: /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes] 37 | typedef std::unique_ptr fileptr_t; | ^ [ 89%] Linking CXX executable doc_example /usr/bin/cmake -E cmake_link_script CMakeFiles/doc_example.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/doc_example.dir/docs/code/sym.cpp.o CMakeFiles/doc_example.dir/docs/code/elem.cpp.o CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o CMakeFiles/doc_example.dir/docs/code/cell.cpp.o CMakeFiles/doc_example.dir/src/resinfo.cpp.o -o doc_example make[5]: Leaving directory 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-ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -o check_conn libgemmi_cpp.a /usr/lib/x86_64-linux-gnu/libz.so make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [ 95%] Built target check_conn [ 95%] Linking CXX executable cpptest /usr/bin/cmake -E cmake_link_script CMakeFiles/cpptest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/cpptest.dir/tests/main.cpp.o CMakeFiles/cpptest.dir/tests/cif.cpp.o -o cpptest make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [ 95%] Built target cpptest [ 97%] Linking CXX executable doc_maybegz /usr/bin/cmake -E cmake_link_script CMakeFiles/doc_maybegz.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/doc_maybegz.dir/docs/code/maybegz.cpp.o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -o doc_maybegz libgemmi_cpp.a /usr/lib/x86_64-linux-gnu/libz.so make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [ 97%] Built target doc_maybegz [100%] Linking CXX executable test_disulf /usr/bin/cmake -E cmake_link_script CMakeFiles/test_disulf.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -o test_disulf libgemmi_cpp.a /usr/lib/x86_64-linux-gnu/libz.so make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [100%] Built target test_disulf make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/depend make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' cd /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/check.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/build make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' /usr/bin/ctest -C None Test project /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu Start 1: cpptest 1/1 Test #1: cpptest .......................... Passed 0.00 sec 100% tests passed, 0 tests failed out of 1 Total Test time (real) = 0.00 sec make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' [100%] Built target check make[4]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make[2]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' PYTHONPATH=$(find . -name 'obj-*') pytest-3 -k 'not test_sfcalc_' ........................................................................ [ 38%] .............................s.................s......sssssssssssssss... [ 76%] ............................................. [100%] =========================== short test summary info ============================ SKIPPED [1] tests/test_mol.py:535: BioPython not installed. SKIPPED [1] tests/test_monlib.py:110: $CLIBD_MON not defined. SKIPPED [1] tests/test_prog.py:131: Program gemmi not found. SKIPPED [1] tests/test_prog.py:140: Program gemmi not found. SKIPPED [1] tests/test_prog.py:149: Program gemmi not found. SKIPPED [1] tests/test_prog.py:47: Program gemmi not found. SKIPPED [1] tests/test_prog.py:55: Program gemmi not found. SKIPPED [1] tests/test_prog.py:62: Program gemmi not found. SKIPPED [1] tests/test_prog.py:68: Program gemmi not found. SKIPPED [1] tests/test_prog.py:74: Program gemmi not found. SKIPPED [1] tests/test_prog.py:80: Program gemmi not found. SKIPPED [1] tests/test_seq.py:127: BioPython not installed. SKIPPED [1] tests/test_seq.py:132: BioPython not installed. SKIPPED [1] tests/test_seq.py:139: BioPython not installed. SKIPPED [1] tests/test_seq.py:146: BioPython not installed. SKIPPED [1] tests/test_seq.py:105: BioPython not installed. SKIPPED [1] tests/test_seq.py:114: BioPython not installed. 172 passed, 17 skipped, 2 deselected in 1.00s make[1]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/gemmi-0.6.5\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/gemmi-0.6.5+ds -B/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/bin/gemmi -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqid.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fourier.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/smcif.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/intensit.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pirfasta.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fail.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cellred.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/contact.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fprime.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/neighbor.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_json.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cif.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/qcp.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/polyheur.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_mmcif.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pdb.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/calculate.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/chemcomp.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/neutron92.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/scaling.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/chemcomp_xyz.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/bond_idx.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/binner.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/refln.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/dencalc.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/model.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/modify.hpp -- Installing: 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/build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mtz2cif.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/assembly.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/util.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/eig3.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/crd.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/json.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmdb.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pdb_id.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/asudata.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/atof.hpp -- Installing: 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/build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/read_cif.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/monlib.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/sprintf.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/iterator.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/grid.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/addends.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_pdb.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/blob.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/span.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/floodfill.hpp -- Installing: 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/build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/utf.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cifdoc.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/xds_ascii.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/pocketfft_hdronly.h -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/fast_float.h -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/tinydir.h -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/riding_h.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/interop.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ecalc.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/read_map.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/numb.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqalign.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fstream.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/version.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/resinfo.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/twin.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/select.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/solmask.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_cif.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/atox.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmread.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqtools.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mtz.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/align.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmcif_impl.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/it92.hpp -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/x86_64-linux-gnu/libgemmi_cpp.a -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/gemmi/gemmi-targets.cmake -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/gemmi/gemmi-targets-none.cmake -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/gemmi/gemmi-config.cmake -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/gemmi/gemmi-config-version.cmake -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi.cpython-312-x86_64-linux-gnu.so -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/ccd_gi.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/matthews.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/monomers.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/weight.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/mtz_i_sigi.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/long_geom.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/mtrix_iso.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/rama_plot.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/rama_gather.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/map2mtz.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/sub_ccd.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/ccd_subgraph.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/refln-stats.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/maskdiff.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/merge_mtz_mmcif.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/from_json.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/multiproc.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/patterson_slice.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/col_order.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/aafreq.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/simple_search.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/maskcheck.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/cif_i_sigi.py -- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/hello.py make[1]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu' dh_install -O--buildsystem=cmake dh_installdocs -O--buildsystem=cmake dh_installchangelogs -O--buildsystem=cmake debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds' help2man 'tail -n +9 docs/gemmi-help.txt' \ --version-string 0.6.5+ds --name 'CLI for GEMMI library' \ --no-info --help-option '' > debian/gemmi.1 sed -i 's/.TH GEMMI-HELP.TXT/.TH gemmi/' debian/gemmi.1 sed -i 's/gemmi-help.txt/gemmi/' debian/gemmi.1 dh_installman make[1]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds' dh_python3 -O--buildsystem=cmake dh_installsystemduser -O--buildsystem=cmake dh_perl -O--buildsystem=cmake dh_link -O--buildsystem=cmake dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake dh_fixperms -O--buildsystem=cmake dh_missing -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dwz: debian/python3-gemmi/usr/lib/python3/dist-packages/gemmi.cpython-312-x86_64-linux-gnu.so: .debug_info section not present dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dpkg-gencontrol: warning: Provides field of package python3-gemmi: substitution variable ${python3:Provides} used, but is not defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'gemmi' in '../gemmi_0.6.5+ds-2_amd64.deb'. dpkg-deb: building package 'gemmi-dev' in '../gemmi-dev_0.6.5+ds-2_amd64.deb'. dpkg-deb: building package 'gemmi-dbgsym' in '../gemmi-dbgsym_0.6.5+ds-2_amd64.deb'. dpkg-deb: building package 'python3-gemmi' in '../python3-gemmi_0.6.5+ds-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gemmi_0.6.5+ds-2_amd64.buildinfo dpkg-genchanges --build=binary -O../gemmi_0.6.5+ds-2_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/3648558/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3648558/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/3648558 and its subdirectories I: Current time: Mon Jan 12 15:31:07 +14 2026 I: pbuilder-time-stamp: 1768181467