I: pbuilder: network access will be disabled during build I: Current time: Tue Jul 7 08:40:28 +14 2026 I: pbuilder-time-stamp: 1783363228 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-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_0.7.1+ds-1~exp1.dsc] I: copying [./gemmi_0.7.1+ds.orig.tar.xz] I: copying [./gemmi_0.7.1+ds-1~exp1.debian.tar.xz] I: Extracting source error: the following required arguments were not provided: --keyring Usage: sqv --keyring --cleartext --output For more information, try '--help'. dpkg-source: warning: cannot verify inline signature for ./gemmi_0.7.1+ds-1~exp1.dsc: no acceptable signature found dpkg-source: info: extracting gemmi in gemmi-0.7.1+ds dpkg-source: info: unpacking gemmi_0.7.1+ds.orig.tar.xz dpkg-source: info: unpacking gemmi_0.7.1+ds-1~exp1.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/2258084/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-arm64. 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 Jul 6 18:40 /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/2258084/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2258084/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=experimental EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=e378dde8b2484384a15dd27bf1d260c1 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=2258084 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.Sr7NPWZ7/pbuilderrc_Avb6 --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Sr7NPWZ7/b2 --logfile b2/build.log gemmi_0.7.1+ds-1~exp1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2258084/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: cmake, debhelper-compat (= 13), dh-sequence-python3, doctest-dev, help2man, libstb-dev, pybuild-plugin-pyproject, python3-dev, python3-nanobind, 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 ... 19964 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-sequence-python3; however: Package dh-sequence-python3 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 pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-nanobind; however: Package python3-nanobind 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} libeigen3-dev{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgnutls30t64{a} libgssapi-krb5-2{a} libidn2-0{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap2{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5t64{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libstb-dev{a} libstb0t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} nanobind-dev{a} netbase{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} pybind11-dev{a} pybuild-plugin-pyproject{a} python3{a} python3-build{a} python3-dev{a} python3-iniconfig{a} python3-installer{a} python3-minimal{a} python3-nanobind{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pluggy{a} python3-pybind11{a} python3-pyproject-hooks{a} python3-pytest{a} python3-wheel{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} robin-map-dev{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 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-pygments wget 0 packages upgraded, 112 newly installed, 0 to remove and 0 not upgraded. Need to get 53.3 MB of archives. After unpacking 225 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.3-4 [854 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.1-1 [93.3 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.3-4 [2000 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.3-1 [27.2 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025b-3 [260 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.8-2 [21.3 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.3-4 [1890 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.3-4 [751 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.3-1 [10.2 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.3-1 [28.2 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1 [136 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.1-2 [104 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-19 [361 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:2.2.4+ds-1 [3604 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-8 [63.0 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-8 [873 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-8 [1131 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-5 [93.8 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.6-2 [2268 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-1 [629 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-3 [323 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1+b1 [24.2 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 46 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-2 [107 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1.1 [71.4 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.8.0-1 [63.2 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.14.0-1 [359 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.6-1 [131 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.50.0-2 [148 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.6-2 [9906 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 72 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250414 [116 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 doctest-dev all 2.4.11-1 [216 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 pkg-config arm64 1.8.1-4 [14.0 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libeigen3-dev all 3.4.0-5 [1034 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.7.1-1 [145 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libpython3.13 arm64 3.13.3-4 [1974 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libpython3.13-dev arm64 3.13.3-4 [4694 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.13.3-1 [10.4 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libstb0t64 arm64 0.0~git20241109.5c20573+ds-1 [199 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libstb-dev arm64 0.0~git20241109.5c20573+ds-1 [637 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 robin-map-dev all 1.3.0-1 [29.8 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 nanobind-dev all 2.5.0-1 [165 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 pybind11-dev all 2.13.6-2 [205 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 25.0-1 [56.6 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 python3-wheel all 0.46.1-2 [21.7 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 python3-build all 1.2.2-2 [36.1 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 pybuild-plugin-pyproject all 6.20250414 [11.8 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 python3.13-dev arm64 3.13.3-4 [504 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.13.3-1 [26.1 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 108 http://deb.debian.org/debian unstable/main arm64 python3-nanobind all 2.5.0-1 [41.8 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 python3-pybind11 all 2.13.6-2 [215 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 python3-pytest all 8.3.5-2 [250 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] Fetched 53.3 MB in 0s (218 MB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19964 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.3-4_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.3-4) ... 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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/2258084/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for experimental I: user script /srv/workspace/pbuilder/2258084/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/gemmi-0.7.1+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_0.7.1+ds-1~exp1_source.changes dpkg-buildpackage: info: source package gemmi dpkg-buildpackage: info: source version 0.7.1+ds-1~exp1 dpkg-buildpackage: info: source distribution experimental dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem cmake dh_auto_clean -O--buildsystem=cmake dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary dh binary --buildsystem cmake 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-0.7.1+ds' dh_auto_configure -- -DBUILD_SHARED_LIBS=OFF -DUSE_PYTHON=ON cd obj-aarch64-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/aarch64-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 0.7.1 -- Build type: None -- Found ZLIB: /usr/lib/aarch64-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 "3.13.3") found components: Interpreter Development.Module -- Found nanobind 2.5.0: /usr/share/nanobind -- Configuring done (3.1s) -- 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-0.7.1+ds/obj-aarch64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds' dh_auto_build -O--buildsystem=cmake cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/gemmi-0.7.1+ds -B/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make -f CMakeFiles/gemmi_cpp.dir/build.make CMakeFiles/gemmi_cpp.dir/depend make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/depend make -f CMakeFiles/nanobind-static.dir/build.make CMakeFiles/nanobind-static.dir/depend make[3]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' cd /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.7.1+ds /build/reproducible-path/gemmi-0.7.1+ds /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu/CMakeFiles/options.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' cd /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_static_property.cpp.o -MF CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_static_property.cpp.o.d -o CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_static_property.cpp.o -c /usr/share/nanobind/src/nb_static_property.cpp /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/calculate.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/src/calculate.cpp /usr/bin/c++ -I/usr/include/python3.13 -I/usr/share/nanobind/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fno-strict-aliasing -MD -MT CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_ft.cpp.o -MF CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_ft.cpp.o.d -o CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_ft.cpp.o -c /usr/share/nanobind/src/nb_ft.cpp [ 13%] Building CXX object CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/common.cpp.o /usr/bin/c++ -I/usr/include/python3.13 -I/usr/share/nanobind/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fno-strict-aliasing -MD -MT CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/common.cpp.o -MF CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/common.cpp.o.d -o CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/common.cpp.o -c /usr/share/nanobind/src/common.cpp In file included from /build/reproducible-path/gemmi-0.7.1+ds/src/calculate.cpp:3: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Atom]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:86:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 86 | template<> inline std::pair calculate_b_iso_range(const Atom& atom) { | ^ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_aniso_range(const Model&)': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:76: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^ [ 15%] Building CXX object CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/error.cpp.o /usr/bin/c++ -I/usr/include/python3.13 -I/usr/share/nanobind/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fno-strict-aliasing -MD -MT CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/error.cpp.o -MF CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/error.cpp.o.d -o CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/error.cpp.o -c /usr/share/nanobind/src/error.cpp [ 15%] Building CXX object CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/trampoline.cpp.o /usr/bin/c++ -I/usr/include/python3.13 -I/usr/share/nanobind/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fno-strict-aliasing -MD -MT CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/trampoline.cpp.o -MF CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/trampoline.cpp.o.d -o CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/trampoline.cpp.o -c /usr/share/nanobind/src/trampoline.cpp [ 16%] Building CXX object CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/implicit.cpp.o /usr/bin/c++ -I/usr/include/python3.13 -I/usr/share/nanobind/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fno-strict-aliasing -MD -MT CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/implicit.cpp.o -MF CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/implicit.cpp.o.d -o CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/implicit.cpp.o -c /usr/share/nanobind/src/implicit.cpp [ 16%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o [ 18%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/ddl.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/src/ddl.cpp /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/crd.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/crd.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/src/crd.cpp [ 20%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/eig3.cpp.o /usr/bin/c++ -DGEMMI_BUILD 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CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/src/mmcif.cpp [ 26%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/mmread_gz.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/src/mmread_gz.cpp make[3]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' [ 26%] Built target options [ 26%] Building CXX 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-Wformat -Werror=format-security -mbranch-protection=standard -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/mtz.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/src/mtz.cpp [ 28%] Linking CXX static library libnanobind-static.a /usr/bin/cmake -P CMakeFiles/nanobind-static.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/nanobind-static.dir/link.txt --verbose=1 [ 28%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast 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file included from /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/topo.hpp:14, from /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/crd.hpp:8, from /build/reproducible-path/gemmi-0.7.1+ds/src/crd.cpp:3: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Atom]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:86:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 86 | template<> inline std::pair calculate_b_iso_range(const Atom& atom) { | ^ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_aniso_range(const Model&)': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:76: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^ [ 30%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/polyheur.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/polyheur.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/src/polyheur.cpp In file included from /build/reproducible-path/gemmi-0.7.1+ds/src/monlib.cpp:4: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Atom]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:86:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 86 | template<> inline std::pair calculate_b_iso_range(const Atom& atom) { | ^ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_aniso_range(const Model&)': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:76: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^ [ 32%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/src/read_cif.cpp [ 32%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/src/resinfo.cpp [ 33%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/src/riding_h.cpp [ 33%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/select.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/select.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/select.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/select.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/src/select.cpp [ 35%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/src/sprintf.cpp /build/reproducible-path/gemmi-0.7.1+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-0.7.1+ds/include/gemmi/topo.hpp:14, from /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/riding_h.hpp:9, from /build/reproducible-path/gemmi-0.7.1+ds/src/riding_h.cpp:3: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Atom]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:86:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 86 | template<> inline std::pair calculate_b_iso_range(const Atom& atom) { | ^ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_aniso_range(const Model&)': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:76: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^ [ 35%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/symmetry.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/symmetry.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/symmetry.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/symmetry.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/src/symmetry.cpp [ 37%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_json.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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_json.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/to_json.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/to_json.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/src/to_json.cpp [ 37%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/src/to_mmcif.cpp [ 39%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/src/to_pdb.cpp [ 39%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/src/topo.cpp [ 41%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/src/xds_ascii.cpp In file included from /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/topo.hpp:14, from /build/reproducible-path/gemmi-0.7.1+ds/src/topo.cpp:3: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Atom]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:86:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 86 | template<> inline std::pair calculate_b_iso_range(const Atom& atom) { | ^ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_aniso_range(const Model&)': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:76: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^ [ 41%] 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/ccp4.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/fprime.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/monlib.cpp.o CMakeFiles/gemmi_cpp.dir/src/mtz.cpp.o CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o CMakeFiles/gemmi_cpp.dir/src/pdb.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/select.cpp.o CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o CMakeFiles/gemmi_cpp.dir/src/symmetry.cpp.o CMakeFiles/gemmi_cpp.dir/src/to_json.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/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-0.7.1+ds/obj-aarch64-linux-gnu' [ 41%] 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-0.7.1+ds/obj-aarch64-linux-gnu' cd /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.7.1+ds /build/reproducible-path/gemmi-0.7.1+ds /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' cd /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.7.1+ds /build/reproducible-path/gemmi-0.7.1+ds /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu 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-DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/prog/blobs.cpp [ 47%] Building CXX object CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/usr/include/python3.13 -I/usr/share/nanobind/include -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o -MF CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/python/gemmi.cpp [ 47%] Building CXX object CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/align.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/align.cpp.o.d -o 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-ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_py.dir/python/elem.cpp.o -MF CMakeFiles/gemmi_py.dir/python/elem.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/elem.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/python/elem.cpp [ 54%] Building CXX object CMakeFiles/gemmi_py.dir/python/grid.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/usr/include/python3.13 -I/usr/share/nanobind/include -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_py.dir/python/grid.cpp.o -MF CMakeFiles/gemmi_py.dir/python/grid.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/grid.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/python/grid.cpp In file included from /build/reproducible-path/gemmi-0.7.1+ds/prog/blobs.cpp:13: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Atom]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:86:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 86 | template<> inline std::pair calculate_b_iso_range(const Atom& atom) { | ^ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_aniso_range(const Model&)': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:76: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^ [ 54%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/prog/contact.cpp [ 56%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/prog/contents.cpp In file included from /build/reproducible-path/gemmi-0.7.1+ds/prog/contents.cpp:15: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Atom]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:86:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 86 | template<> inline std::pair calculate_b_iso_range(const Atom& atom) { | ^ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_aniso_range(const Model&)': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:76: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^ [ 58%] Building CXX object CMakeFiles/gemmi_py.dir/python/hkl.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/usr/include/python3.13 -I/usr/share/nanobind/include -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden 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CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/prog/convert.cpp [ 60%] Building CXX object CMakeFiles/gemmi_py.dir/python/mol.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/usr/include/python3.13 -I/usr/share/nanobind/include -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_py.dir/python/mol.cpp.o -MF CMakeFiles/gemmi_py.dir/python/mol.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/mol.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/python/mol.cpp [ 62%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/prog/crd.cpp [ 62%] Building CXX object CMakeFiles/gemmi_py.dir/python/monlib.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/usr/include/python3.13 -I/usr/share/nanobind/include -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_py.dir/python/monlib.cpp.o -MF CMakeFiles/gemmi_py.dir/python/monlib.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/monlib.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/python/monlib.cpp [ 62%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/prog/ecalc.cpp In file included from /build/reproducible-path/gemmi-0.7.1+ds/prog/convert.cpp:16: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Atom]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:86:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 86 | template<> inline std::pair calculate_b_iso_range(const Atom& atom) { | ^ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_aniso_range(const Model&)': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:76: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^ In file included from /build/reproducible-path/gemmi-0.7.1+ds/python/mol.cpp:4: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Atom]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:86:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 86 | template<> inline std::pair calculate_b_iso_range(const Atom& atom) { | ^ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_aniso_range(const Model&)': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:76: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^ In file included from /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/topo.hpp:14, from /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/crd.hpp:8, from /build/reproducible-path/gemmi-0.7.1+ds/prog/crd.cpp:6: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Atom]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:86:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 86 | template<> inline std::pair calculate_b_iso_range(const Atom& atom) { | ^ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_aniso_range(const Model&)': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:76: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^ [ 64%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/prog/fprime.cpp /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In instantiation of 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Model]': /build/reproducible-path/gemmi-0.7.1+ds/python/mol.cpp:283:9: required from here 224 | pyModel | ~~~~~~~ 225 | .def(nb::init()) | ~~~~~~~~~~~~~~~~~~~~~ 226 | .def_rw("num", &Model::num) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 227 | .def("__len__", [](const Model& self) { return self.chains.size(); }) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 228 | .def("__iter__", [](Model& self) { return usual_iterator(self, self.chains); }, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 229 | nb::keep_alive<0, 1>()) | ~~~~~~~~~~~~~~~~~~~~~~~ 230 | .def("__getitem__", &get_child, nb::arg("index"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 231 | nb::rv_policy::reference_internal) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 232 | .def("__getitem__", [](Model& self, const std::string& name) -> Chain& { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 | return *impl::find_iter(self.chains, name); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 | }, nb::arg("name"), nb::rv_policy::reference_internal) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 | .def("all", (CraProxy (Model::*)()) &Model::all, nb::keep_alive<0, 1>()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 236 | .def("get_subchain", | ~~~~~~~~~~~~~~~~~~~~ 237 | (ResidueSpan (Model::*)(const std::string&)) &Model::get_subchain, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 238 | nb::arg("name"), nb::rv_policy::reference_internal) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 239 | .def("subchains", (std::vector (Model::*)()) &Model::subchains, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 | nb::call_policy()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 241 | .def("find_residue_group", &Model::find_residue_group, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 242 | nb::arg("chain"), nb::arg("seqid"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 | nb::keep_alive<0, 1>()) | ~~~~~~~~~~~~~~~~~~~~~~~ 244 | .def("sole_residue", &Model::sole_residue, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 | nb::arg("chain"), nb::arg("seqid"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 246 | nb::rv_policy::reference_internal) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 247 | .def("get_all_residue_names", &Model::get_all_residue_names) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 248 | .def("find_cra", (CRA (Model::*)(const AtomAddress&, bool)) &Model::find_cra, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 249 | nb::arg(), nb::arg("ignore_segment")=false) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 250 | .def("find_chain", | ~~~~~~~~~~~~~~~~~~ 251 | (Chain* (Model::*)(const std::string&))&Model::find_chain, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 252 | nb::arg("name"), nb::rv_policy::reference_internal) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 253 | .def("find_last_chain", &Model::find_last_chain, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 254 | nb::arg("name"), nb::rv_policy::reference_internal) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 255 | .def("add_chain", | ~~~~~~~~~~~~~~~~~ 256 | [](Model& self, const Chain& chain, int pos, bool unique_name) -> Chain& { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 257 | Chain& ref = add_child(self, chain, pos); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 258 | if (unique_name) | ~~~~~~~~~~~~~~~~ 259 | ensure_unique_chain_name(self, ref); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 260 | return ref; | ~~~~~~~~~~~ 261 | }, nb::arg("chain"), nb::arg("pos")=-1, nb::arg("unique_name")=false, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 262 | nb::rv_policy::reference_internal) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 263 | // for compatibility with older gemmi version | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 264 | .def("add_chain", [](Model& self, const std::string& name) -> Chain& { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 265 | self.chains.emplace_back(name); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 266 | return self.chains.back(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 267 | }, nb::arg("name"), nb::rv_policy::reference_internal) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 268 | .def("remove_chain", &Model::remove_chain, nb::arg("name")) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 269 | .def("__delitem__", &Model::remove_chain, nb::arg("name")) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 270 | .def("__delitem__", remove_child, nb::arg("index")) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 271 | .def("__delitem__", remove_children) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 272 | .def("remove_alternative_conformations", remove_alternative_conformations) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 273 | .def("remove_hydrogens", remove_hydrogens) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 274 | .def("remove_waters", remove_waters) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 275 | .def("remove_ligands_and_waters", remove_ligands_and_waters) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 276 | .def("has_hydrogen", &has_hydrogen) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 277 | .def("count_atom_sites", &count_atom_sites, nb::arg("sel")=nb::none()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 278 | .def("count_occupancies", &count_occupancies, nb::arg("sel")=nb::none()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 279 | .def("calculate_mass", &calculate_mass) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 280 | .def("calculate_center_of_mass", [](const Model& self) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 281 | return calculate_center_of_mass(self).get(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 282 | }) | ~~ 283 | .def("calculate_b_iso_range", &calculate_b_iso_range) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:77:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 77 | template std::pair calculate_b_iso_range(const T& obj) { | ^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/algorithm:60, from /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/model.hpp:8, from /build/reproducible-path/gemmi-0.7.1+ds/python/mol.cpp:3: /usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = const double&; _T2 = const double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': /usr/include/c++/14/bits/stl_algo.h:3441:28: required from 'constexpr std::pair<_FIter, _FIter> std::minmax(initializer_list<_Tp>) [with _Tp = double]' 3441 | return std::make_pair(*__p.first, *__p.second); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:100:31: required from here 100 | auto u = std::minmax({eig[0], eig[1], eig[2]}); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In instantiation of 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Chain]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:80:35: required from 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Model]' 80 | auto r = calculate_b_iso_range(child); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/python/mol.cpp:283:9: required from here 224 | pyModel | ~~~~~~~ 225 | .def(nb::init()) | ~~~~~~~~~~~~~~~~~~~~~ 226 | .def_rw("num", &Model::num) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 227 | .def("__len__", [](const Model& self) { return self.chains.size(); }) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 228 | .def("__iter__", [](Model& self) { return usual_iterator(self, self.chains); }, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 229 | nb::keep_alive<0, 1>()) | ~~~~~~~~~~~~~~~~~~~~~~~ 230 | .def("__getitem__", &get_child, nb::arg("index"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 231 | nb::rv_policy::reference_internal) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 232 | .def("__getitem__", [](Model& self, const std::string& name) -> Chain& { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 | return *impl::find_iter(self.chains, name); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 | }, nb::arg("name"), nb::rv_policy::reference_internal) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 | .def("all", (CraProxy (Model::*)()) &Model::all, nb::keep_alive<0, 1>()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 236 | .def("get_subchain", | ~~~~~~~~~~~~~~~~~~~~ 237 | (ResidueSpan (Model::*)(const std::string&)) &Model::get_subchain, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 238 | nb::arg("name"), nb::rv_policy::reference_internal) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 239 | .def("subchains", (std::vector (Model::*)()) &Model::subchains, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 | nb::call_policy()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 241 | .def("find_residue_group", &Model::find_residue_group, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 242 | nb::arg("chain"), nb::arg("seqid"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 | nb::keep_alive<0, 1>()) | ~~~~~~~~~~~~~~~~~~~~~~~ 244 | .def("sole_residue", &Model::sole_residue, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 | nb::arg("chain"), nb::arg("seqid"), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 246 | nb::rv_policy::reference_internal) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 247 | .def("get_all_residue_names", &Model::get_all_residue_names) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 248 | .def("find_cra", (CRA (Model::*)(const AtomAddress&, bool)) &Model::find_cra, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 249 | nb::arg(), nb::arg("ignore_segment")=false) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 250 | .def("find_chain", | ~~~~~~~~~~~~~~~~~~ 251 | (Chain* (Model::*)(const std::string&))&Model::find_chain, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 252 | nb::arg("name"), nb::rv_policy::reference_internal) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 253 | .def("find_last_chain", &Model::find_last_chain, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 254 | nb::arg("name"), nb::rv_policy::reference_internal) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 255 | .def("add_chain", | ~~~~~~~~~~~~~~~~~ 256 | [](Model& self, const Chain& chain, int pos, bool unique_name) -> Chain& { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 257 | Chain& ref = add_child(self, chain, pos); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 258 | if (unique_name) | ~~~~~~~~~~~~~~~~ 259 | ensure_unique_chain_name(self, ref); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 260 | return ref; | ~~~~~~~~~~~ 261 | }, nb::arg("chain"), nb::arg("pos")=-1, nb::arg("unique_name")=false, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 262 | nb::rv_policy::reference_internal) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 263 | // for compatibility with older gemmi version | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 264 | .def("add_chain", [](Model& self, const std::string& name) -> Chain& { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 265 | self.chains.emplace_back(name); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 266 | return self.chains.back(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 267 | }, nb::arg("name"), nb::rv_policy::reference_internal) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 268 | .def("remove_chain", &Model::remove_chain, nb::arg("name")) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 269 | .def("__delitem__", &Model::remove_chain, nb::arg("name")) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 270 | .def("__delitem__", remove_child, nb::arg("index")) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 271 | .def("__delitem__", remove_children) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 272 | .def("remove_alternative_conformations", remove_alternative_conformations) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 273 | .def("remove_hydrogens", remove_hydrogens) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 274 | .def("remove_waters", remove_waters) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 275 | .def("remove_ligands_and_waters", remove_ligands_and_waters) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 276 | .def("has_hydrogen", &has_hydrogen) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 277 | .def("count_atom_sites", &count_atom_sites, nb::arg("sel")=nb::none()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 278 | .def("count_occupancies", &count_occupancies, nb::arg("sel")=nb::none()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 279 | .def("calculate_mass", &calculate_mass) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 280 | .def("calculate_center_of_mass", [](const Model& self) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 281 | return calculate_center_of_mass(self).get(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 282 | }) | ~~ 283 | .def("calculate_b_iso_range", &calculate_b_iso_range) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:77:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 77 | template std::pair calculate_b_iso_range(const T& obj) { | ^~~~~~~~~~~~~~~~~~~~~ [ 64%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/prog/grep.cpp [ 66%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/h.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/h.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/h.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/h.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/prog/h.cpp [ 67%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/prog/json2cif.cpp In file included from /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/topo.hpp:14, from /build/reproducible-path/gemmi-0.7.1+ds/prog/h.cpp:12: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Atom]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:86:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 86 | template<> inline std::pair calculate_b_iso_range(const Atom& atom) { | ^ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_aniso_range(const Model&)': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:76: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^ [ 67%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/main.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/main.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/main.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/main.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/prog/main.cpp [ 69%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/map.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/map.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/map.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/map.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/prog/map.cpp [ 69%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/prog/map2sf.cpp /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:34: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Model]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:77:42: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 77 | template std::pair calculate_b_iso_range(const T& obj) { | ^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/share/nanobind/include/nanobind/nanobind.h:55, from /build/reproducible-path/gemmi-0.7.1+ds/python/common.h:11, from /build/reproducible-path/gemmi-0.7.1+ds/python/mol.cpp:11: /usr/share/nanobind/include/nanobind/nb_func.h: In lambda function: /usr/share/nanobind/include/nanobind/nb_func.h:275:29: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 275 | cap->func((in.template get()) | ~~~~~^~~~ [ 71%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/prog/mapcoef.cpp /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Residue]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:80:35: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 80 | auto r = calculate_b_iso_range(child); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ [ 71%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/prog/mask.cpp [ 73%] Building CXX object CMakeFiles/gemmi_py.dir/python/mtz.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/usr/include/python3.13 -I/usr/share/nanobind/include -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -Wno-psabi -MD -MT CMakeFiles/gemmi_py.dir/python/mtz.cpp.o -MF CMakeFiles/gemmi_py.dir/python/mtz.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/mtz.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/python/mtz.cpp [ 73%] Building CXX object CMakeFiles/gemmi_py.dir/python/read.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/usr/include/python3.13 -I/usr/share/nanobind/include -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_py.dir/python/read.cpp.o -MF CMakeFiles/gemmi_py.dir/python/read.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/read.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/python/read.cpp [ 75%] Building CXX object CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/usr/include/python3.13 -I/usr/share/nanobind/include -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -Wno-psabi -MD -MT CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o -MF CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/python/recgrid.cpp [ 77%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/prog/merge.cpp /usr/share/nanobind/include/nanobind/nb_func.h: In static member function 'static constexpr PyObject* nanobind::detail::func_create (*&)(const gemmi::Model&), std::pair, const gemmi::Model&, 0, nanobind::scope, nanobind::name, nanobind::is_method>(std::pair (*&)(const gemmi::Model&), std::pair (*)(const gemmi::Model&), std::index_sequence<0>, const nanobind::scope&, const nanobind::name&, const nanobind::is_method&)::::_FUN(void*, PyObject**, uint8_t*, nanobind::rv_policy, nanobind::detail::cleanup_list*)': /usr/share/nanobind/include/nanobind/nb_func.h:219:14: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 219 | f.impl = [](void *p, PyObject **args, uint8_t *args_flags, rv_policy policy, | ^ /usr/share/nanobind/include/nanobind/nb_func.h: In static member function 'static constexpr PyObject* nanobind::detail::func_create (*&)(const gemmi::Model&), std::pair, const gemmi::Model&, 0, nanobind::scope, nanobind::name, nanobind::is_method>(std::pair (*&)(const gemmi::Model&), std::pair (*)(const gemmi::Model&), std::index_sequence<0>, const nanobind::scope&, const nanobind::name&, const nanobind::is_method&)::::_FUN(void*, PyObject**, uint8_t*, nanobind::rv_policy, nanobind::detail::cleanup_list*)': /usr/share/nanobind/include/nanobind/nb_func.h:219:14: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 [ 77%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/prog/mondiff.cpp [ 77%] Building CXX object CMakeFiles/gemmi_py.dir/python/scaling.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/usr/include/python3.13 -I/usr/share/nanobind/include -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_py.dir/python/scaling.cpp.o -MF CMakeFiles/gemmi_py.dir/python/scaling.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/scaling.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/python/scaling.cpp [ 79%] 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-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/prog/monlib_opt.cpp /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_aniso_range(const Model&)': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:34: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^~~~~~~~~~~~~~~~~~~~~~~ [ 79%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/prog/mtz.cpp [ 81%] Building CXX object CMakeFiles/gemmi_py.dir/python/search.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/usr/include/python3.13 -I/usr/share/nanobind/include -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_py.dir/python/search.cpp.o -MF CMakeFiles/gemmi_py.dir/python/search.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/search.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/python/search.cpp [ 83%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/prog/mtz2cif.cpp [ 83%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/prog/reindex.cpp [ 84%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/prog/residues.cpp /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Chain]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:80:35: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 80 | auto r = calculate_b_iso_range(child); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ [ 84%] Building CXX object CMakeFiles/gemmi_py.dir/python/sf.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/usr/include/python3.13 -I/usr/share/nanobind/include -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_py.dir/python/sf.cpp.o -MF CMakeFiles/gemmi_py.dir/python/sf.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/sf.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/python/sf.cpp [ 84%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/prog/rmsz.cpp In file included from /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:13, from /build/reproducible-path/gemmi-0.7.1+ds/python/sf.cpp:10: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Atom]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:86:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 86 | template<> inline std::pair calculate_b_iso_range(const Atom& atom) { | ^ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_aniso_range(const Model&)': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:76: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^ [ 86%] Building CXX object CMakeFiles/gemmi_py.dir/python/sym.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/usr/include/python3.13 -I/usr/share/nanobind/include -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_py.dir/python/sym.cpp.o -MF CMakeFiles/gemmi_py.dir/python/sym.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/sym.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/python/sym.cpp [ 88%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/set.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/set.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/set.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/set.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/prog/set.cpp In file included from /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/topo.hpp:14, from /build/reproducible-path/gemmi-0.7.1+ds/prog/rmsz.cpp:8: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Atom]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:86:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 86 | template<> inline std::pair calculate_b_iso_range(const Atom& atom) { | ^ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_aniso_range(const Model&)': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:76: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^ In file included from /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/it92.hpp:16, from /build/reproducible-path/gemmi-0.7.1+ds/python/sf.cpp:6: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair gemmi::ExpSum::calculate_with_derivative(float) const [with int N = 5]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:20:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 5; Real = float]' 20 | std::tie(y1, dy) = precal.calculate_with_derivative(x1); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:122:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 5; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]' 122 | return determine_cutoff_radius(x1, precal, (CReal)cutoff); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/python/sf.cpp:62:36: required from 'void {anonymous}::add_dencalc(nanobind::module_&, const char*) [with Table = gemmi::IT92]' 62 | return self.estimate_radius(precal, bb); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/python/sf.cpp:89:20: required from here 89 | add_dencalc(m, "DensityCalculatorX"); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/formfact.hpp:74:26: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 74 | std::pair calculate_with_derivative(float r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair<_ForwardIterator, _ForwardIterator> gemmi::ExpSum::calculate_with_derivative(Real) const [with int N = 1; Real = double]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:20:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = double]' 20 | std::tie(y1, dy) = precal.calculate_with_derivative(x1); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:122:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::Neutron92; GReal = float; CReal = double; typename Table::Coef::coef_type = double; typename Table::Coef = gemmi::GaussianCoef<0, 1, double>]' 122 | return determine_cutoff_radius(x1, precal, (CReal)cutoff); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/python/sf.cpp:62:36: required from 'void {anonymous}::add_dencalc(nanobind::module_&, const char*) [with Table = gemmi::Neutron92]' 62 | return self.estimate_radius(precal, bb); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/python/sf.cpp:91:25: required from here 91 | add_dencalc(m, "DensityCalculatorN"); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/formfact.hpp:49:24: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 49 | std::pair calculate_with_derivative(Real r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair gemmi::ExpSum::calculate_with_derivative(float) const [with int N = 1]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:20:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = float]' 20 | std::tie(y1, dy) = precal.calculate_with_derivative(x1); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:122:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]' 122 | return determine_cutoff_radius(x1, precal, (CReal)cutoff); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:135:37: required from 'void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<0, 1, float>; Table = gemmi::IT92; GReal = float]' 135 | CReal radius = estimate_radius(precal, b); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:114:32: required from 'void gemmi::DensityCalculator::add_c_contribution_to_grid(const gemmi::Atom&, float) [with Table = gemmi::IT92; GReal = float]' 114 | do_add_atom_density_to_grid(atom, GaussianCoef<0, 1, CReal>{0}, c); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/python/sf.cpp:48:40: required from 'void {anonymous}::add_dencalc(nanobind::module_&, const char*) [with Table = gemmi::IT92]' 48 | .def("add_c_contribution_to_grid", &DenCalc::add_c_contribution_to_grid) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/python/sf.cpp:89:20: required from here 89 | add_dencalc(m, "DensityCalculatorX"); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/formfact.hpp:74:26: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 74 | std::pair calculate_with_derivative(float r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp: In member function 'void gemmi::DensityCalculator::set_refmac_compatible_blur(const gemmi::Model&, bool) [with Table = gemmi::IT92; GReal = float]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:99:43: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 99 | double b_min = calculate_b_aniso_range(model).first; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ [ 88%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/prog/sf2map.cpp [ 88%] Building CXX object CMakeFiles/gemmi_py.dir/python/topo.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/usr/include/python3.13 -I/usr/share/nanobind/include -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_py.dir/python/topo.cpp.o -MF CMakeFiles/gemmi_py.dir/python/topo.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/topo.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/python/topo.cpp [ 90%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/prog/sfcalc.cpp [ 90%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/prog/sg.cpp In file included from /build/reproducible-path/gemmi-0.7.1+ds/prog/sf2map.cpp:8: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Atom]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:86:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 86 | template<> inline std::pair calculate_b_iso_range(const Atom& atom) { | ^ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_aniso_range(const Model&)': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:76: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^ [ 92%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/prog/tags.cpp In file included from /build/reproducible-path/gemmi-0.7.1+ds/prog/sfcalc.cpp:8: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Atom]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:86:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 86 | template<> inline std::pair calculate_b_iso_range(const Atom& atom) { | ^ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_aniso_range(const Model&)': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:76: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^ In file included from /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/topo.hpp:14, from /build/reproducible-path/gemmi-0.7.1+ds/python/topo.cpp:3: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Atom]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:86:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 86 | template<> inline std::pair calculate_b_iso_range(const Atom& atom) { | ^ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_aniso_range(const Model&)': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:76: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^ [ 94%] Building CXX object CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/usr/include/python3.13 -I/usr/share/nanobind/include -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o -MF CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/python/unitcell.cpp In file included from /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/it92.hpp:16, from /build/reproducible-path/gemmi-0.7.1+ds/prog/sfcalc.cpp:14: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair gemmi::ExpSum::calculate_with_derivative(float) const [with int N = 5]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:20:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 5; Real = float]' 20 | std::tie(y1, dy) = precal.calculate_with_derivative(x1); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:122:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 5; Table = gemmi::IT92; GReal = float; CReal = float; typename Table::Coef::coef_type = float; typename Table::Coef = gemmi::GaussianCoef<4, 1, float>]' 122 | return determine_cutoff_radius(x1, precal, (CReal)cutoff); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:135:37: required from 'void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<4, 1, float>; Table = gemmi::IT92; GReal = float]' 135 | CReal radius = estimate_radius(precal, b); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:108:32: required from 'void gemmi::DensityCalculator::add_atom_density_to_grid(const gemmi::Atom&) [with Table = gemmi::IT92; GReal = float]' 108 | do_add_atom_density_to_grid(atom, Table::get(el, atom.charge), addends.get(el)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:182:11: required from 'void gemmi::DensityCalculator::add_model_density_to_grid(const gemmi::Model&) [with Table = gemmi::IT92; GReal = float]' 182 | add_atom_density_to_grid(atom); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:187:5: required from 'void gemmi::DensityCalculator::put_model_density_on_grid(const gemmi::Model&) [with Table = gemmi::IT92; GReal = float]' 187 | add_model_density_to_grid(model); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/prog/sfcalc.cpp:252:36: required from 'void {anonymous}::process_with_fft(const gemmi::Structure&, gemmi::DensityCalculator&, bool, const gemmi::AsuData >*, gemmi::Scaling&, bool, const RefFile&, const gemmi::AsuData >&, const char*) [with Table = gemmi::IT92; Real = float]' 252 | dencalc.put_model_density_on_grid(st.models[0]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/prog/sfcalc.cpp:736:23: required from 'void {anonymous}::process_with_table(bool, gemmi::Structure&, const gemmi::SmallStructure&, double, bool, const OptParser&) [with Table = gemmi::IT92]' 736 | process_with_fft(st, dencalc, mott_bethe, mask_data_ptr, scaling, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 737 | p.options[Verbose], file, scale_to, map_file); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/prog/sfcalc.cpp:857:43: required from here 857 | process_with_table>(use_st, st, small, wavelength, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 858 | table == 'm', p); | ~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/formfact.hpp:74:26: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 74 | std::pair calculate_with_derivative(float r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/formfact.hpp: In instantiation of 'std::pair<_ForwardIterator, _ForwardIterator> gemmi::ExpSum::calculate_with_derivative(Real) const [with int N = 1; Real = double]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:20:54: required from 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 1; Real = double]' 20 | std::tie(y1, dy) = precal.calculate_with_derivative(x1); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:122:35: required from 'gemmi::DensityCalculator::CReal gemmi::DensityCalculator::estimate_radius(const gemmi::ExpSum&, CReal) const [with int N = 1; Table = gemmi::Neutron92; GReal = float; CReal = double; typename Table::Coef::coef_type = double; typename Table::Coef = gemmi::GaussianCoef<0, 1, double>]' 122 | return determine_cutoff_radius(x1, precal, (CReal)cutoff); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:135:37: required from 'void gemmi::DensityCalculator::do_add_atom_density_to_grid(const gemmi::Atom&, const Coef&, float) [with Coef = gemmi::GaussianCoef<0, 1, double>; Table = gemmi::Neutron92; GReal = float]' 135 | CReal radius = estimate_radius(precal, b); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:108:32: required from 'void gemmi::DensityCalculator::add_atom_density_to_grid(const gemmi::Atom&) [with Table = gemmi::Neutron92; GReal = float]' 108 | do_add_atom_density_to_grid(atom, Table::get(el, atom.charge), addends.get(el)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:182:11: required from 'void gemmi::DensityCalculator::add_model_density_to_grid(const gemmi::Model&) [with Table = gemmi::Neutron92; GReal = float]' 182 | add_atom_density_to_grid(atom); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:187:5: required from 'void gemmi::DensityCalculator::put_model_density_on_grid(const gemmi::Model&) [with Table = gemmi::Neutron92; GReal = float]' 187 | add_model_density_to_grid(model); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/prog/sfcalc.cpp:252:36: required from 'void {anonymous}::process_with_fft(const gemmi::Structure&, gemmi::DensityCalculator&, bool, const gemmi::AsuData >*, gemmi::Scaling&, bool, const RefFile&, const gemmi::AsuData >&, const char*) [with Table = gemmi::Neutron92; Real = float]' 252 | dencalc.put_model_density_on_grid(st.models[0]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/prog/sfcalc.cpp:736:23: required from 'void {anonymous}::process_with_table(bool, gemmi::Structure&, const gemmi::SmallStructure&, double, bool, const OptParser&) [with Table = gemmi::Neutron92]' 736 | process_with_fft(st, dencalc, mott_bethe, mask_data_ptr, scaling, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 737 | p.options[Verbose], file, scale_to, map_file); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/prog/sfcalc.cpp:862:49: required from here 862 | process_with_table>(use_st, st, small, 0., false, p); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/formfact.hpp:49:24: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 49 | std::pair calculate_with_derivative(Real r) const { | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/gemmi-0.7.1+ds/prog/sfcalc.cpp:19: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp: In function 'Real gemmi::determine_cutoff_radius(Real, const ExpSum&, Real) [with int N = 5; Real = float]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/dencalc.hpp:20:54: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 20 | std::tie(y1, dy) = precal.calculate_with_derivative(x1); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/gemmi-0.7.1+ds/prog/sfcalc.cpp: In function 'void {anonymous}::process_with_table(bool, gemmi::Structure&, const gemmi::SmallStructure&, double, bool, const OptParser&) [with Table = gemmi::C4322]': /build/reproducible-path/gemmi-0.7.1+ds/prog/sfcalc.cpp:663:56: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 663 | double b_min = gemmi::calculate_b_aniso_range(st.models[0]).first; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ [ 94%] Building CXX object CMakeFiles/gemmi_py.dir/python/write.cpp.o /usr/bin/c++ -Dgemmi_py_EXPORTS -I/usr/include/python3.13 -I/usr/share/nanobind/include -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -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-0.7.1+ds/python/write.cpp [ 94%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/prog/validate.cpp [ 96%] 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-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/prog/validate_mon.cpp [ 96%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/prog/wcn.cpp [ 98%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o /usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.7.1+ds/third_party -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/prog/xds2mtz.cpp In file included from /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/topo.hpp:14, from /build/reproducible-path/gemmi-0.7.1+ds/prog/validate_mon.cpp:10: /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_iso_range(const T&) [with T = Atom]': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:86:80: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 86 | template<> inline std::pair calculate_b_iso_range(const Atom& atom) { | ^ /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp: In function 'std::pair gemmi::calculate_b_aniso_range(const Model&)': /build/reproducible-path/gemmi-0.7.1+ds/include/gemmi/calculate.hpp:91:76: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | inline std::pair calculate_b_aniso_range(const Model& model) { | ^ [100%] Linking CXX shared module py/gemmi/gemmi_ext.cpython-313-aarch64-linux-gnu.so Copying gemmi/__init__.py /usr/bin/cmake -E copy /build/reproducible-path/gemmi-0.7.1+ds/python/gemmi/__init__.py py/gemmi/__init__.py /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-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast 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[ 2%] Building CXX object CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o [ 4%] Building CXX object CMakeFiles/hello.dir/examples/hello.cpp.o /usr/bin/c++ -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -MF CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o.d -o CMakeFiles/doc_example2.dir/docs/code/cif_cc.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/docs/code/cif_cc.cpp /usr/bin/c++ -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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'/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' cd /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.7.1+ds /build/reproducible-path/gemmi-0.7.1+ds /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/DependInfo.cmake "--color=" make[5]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' cd /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.7.1+ds /build/reproducible-path/gemmi-0.7.1+ds /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu 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Dependencies file "CMakeFiles/gemmi_prog.dir/prog/blobs.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". make[5]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' Dependencies file "CMakeFiles/gemmi_prog.dir/prog/cif2json.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". make -f CMakeFiles/check_conn.dir/build.make CMakeFiles/check_conn.dir/build make[5]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make -f CMakeFiles/cpptest.dir/build.make CMakeFiles/cpptest.dir/build make[5]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make[5]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' Dependencies file "CMakeFiles/gemmi_prog.dir/prog/cif2mtz.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". make -f CMakeFiles/doc_example.dir/build.make CMakeFiles/doc_example.dir/build make -f CMakeFiles/doc_newmtz.dir/build.make CMakeFiles/doc_newmtz.dir/build make -f CMakeFiles/test_disulf.dir/build.make CMakeFiles/test_disulf.dir/build make[5]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' Dependencies file "CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". make[5]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' Dependencies file "CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". make[5]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make[5]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' Dependencies file "CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". Dependencies file "CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-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-0.7.1+ds/obj-aarch64-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-0.7.1+ds/obj-aarch64-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-0.7.1+ds/obj-aarch64-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-0.7.1+ds/obj-aarch64-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-0.7.1+ds/obj-aarch64-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-0.7.1+ds/obj-aarch64-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-0.7.1+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". 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Dependencies file "CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-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-0.7.1+ds/obj-aarch64-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-0.7.1+ds/obj-aarch64-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-0.7.1+ds/obj-aarch64-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-0.7.1+ds/obj-aarch64-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-0.7.1+ds/obj-aarch64-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-0.7.1+ds/obj-aarch64-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-0.7.1+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". 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[ 41%] Building CXX object CMakeFiles/doc_example.dir/docs/code/elem.cpp.o Dependencies file "CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". /usr/bin/c++ -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -UNDEBUG -MD -MT CMakeFiles/doc_example.dir/docs/code/elem.cpp.o -MF CMakeFiles/doc_example.dir/docs/code/elem.cpp.o.d -o CMakeFiles/doc_example.dir/docs/code/elem.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/docs/code/elem.cpp Dependencies file "CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o.d" is newer than depends file "/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu/CMakeFiles/gemmi_prog.dir/compiler_depend.internal". 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[ 45%] Building CXX object CMakeFiles/test_disulf.dir/tests/disulf.cpp.o /usr/bin/c++ -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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-0.7.1+ds/tests/disulf.cpp [ 45%] Building CXX object CMakeFiles/cpptest.dir/tests/windowsh.cpp.o [ 45%] Building CXX object CMakeFiles/doc_example.dir/docs/code/sym.cpp.o [ 45%] Building CXX object CMakeFiles/check_conn.dir/examples/check_conn.cpp.o /usr/bin/c++ -I/build/reproducible-path/gemmi-0.7.1+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.7.1+ds=. 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CMakeFiles/cpptest.dir/tests/cif.cpp.o -MF CMakeFiles/cpptest.dir/tests/cif.cpp.o.d -o CMakeFiles/cpptest.dir/tests/cif.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/tests/cif.cpp Consolidate compiler generated dependencies of target gemmi_prog make[5]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make -f CMakeFiles/gemmi_prog.dir/build.make CMakeFiles/gemmi_prog.dir/build make[5]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make[5]: Nothing to be done for 'CMakeFiles/gemmi_prog.dir/build'. make[5]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' [ 89%] 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-0.7.1+ds/obj-aarch64-linux-gnu' cd /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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Checking test dependency graph end Connected to MAKE jobserver test 1 Start 1: cpptest 1: Test command: /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu/cpptest 1: Working Directory: /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu 1: Test timeout computed to be: 10000000 1: [doctest] doctest version is "2.4.11" 1: [doctest] run with "--help" for options 1: =============================================================================== 1: [doctest] test cases: 14 | 14 passed | 0 failed | 0 skipped 1: [doctest] assertions: 129 | 129 passed | 0 failed | 1: [doctest] Status: SUCCESS! 1/1 Test #1: cpptest .......................... Passed 0.01 sec 100% tests passed, 0 tests failed out of 1 Total Test time (real) = 0.01 sec make[1]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake cd obj-aarch64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/gemmi-0.7.1\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/gemmi-0.7.1+ds -B/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/bin/gemmi -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/cif.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/xds_ascii.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/xds2mtz.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/version.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/util.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/utf.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/unitcell.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/twin.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/topo.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/to_pdb.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/to_mmcif.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/to_json.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/to_cif.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/to_chemcomp.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/third_party -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/third_party/tinydir.h -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/third_party/pocketfft_hdronly.h -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/third_party/fast_float.h -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/symmetry.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/stats.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/sprintf.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/span.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/solmask.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/smcif.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/small.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/sfcalc.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/serialize.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/seqtools.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/seqid.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/seqalign.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/select.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/scaling.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/riding_h.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/resinfo.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/refln.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/reciproc.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/recgrid.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/read_cif.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/qcp.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/polyheur.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/pirfasta.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/pdb_id.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/pdb.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/numb.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/neutron92.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/neighbor.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/mtz2cif.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/mtz.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/monlib.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/modify.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/model.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/mmread_gz.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/mmread.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/mmdb.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/mmcif_impl.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/mmcif.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/metadata.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/math.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/logger.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/linkhunt.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/levmar.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/json.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/iterator.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/it92.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/interop.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/intensit.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/input.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/gz.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/grid.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/fstream.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/fprime.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/fourier.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/formfact.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/floodfill.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/fileutil.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/fail.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/enumstr.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/elem.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/eig3.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/ecalc.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/dirwalk.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/dencalc.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/ddl.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/crd.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/contact.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/cifdoc.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/cif2mtz.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/chemcomp.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/cellred.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/ccp4.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/calculate.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/c4322.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/bond_idx.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/blob.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/binner.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/bessel.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/atox.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/atof.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/asumask.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/asudata.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/assembly.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/align.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/include/gemmi/addends.hpp -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/aarch64-linux-gnu/libgemmi_cpp.a -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/aarch64-linux-gnu/cmake/gemmi/gemmi-targets.cmake -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/aarch64-linux-gnu/cmake/gemmi/gemmi-targets-none.cmake -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/aarch64-linux-gnu/cmake/gemmi/gemmi-config.cmake -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/aarch64-linux-gnu/cmake/gemmi/gemmi-config-version.cmake -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/gemmi_ext.cpython-313-aarch64-linux-gnu.so -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/weight.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/to_rdkit.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/sub_ccd.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/simple_search.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/refln-stats.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/rama_plot.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/rama_gather.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/qq-plot.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/patterson_slice.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/multiproc.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/mtz_i_sigi.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/mtrix_iso.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/monomers.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/merge_mtz_mmcif.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/matthews.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/maskdiff.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/maskcheck.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/map2mtz.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/long_geom.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/hello.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/from_json.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/col_order.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/cif_i_sigi.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/ccd_subgraph.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/ccd_gi.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/aafreq.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/__init__.py -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/py.typed -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/__init__.pyi -- Installing: /build/reproducible-path/gemmi-0.7.1+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/cif.pyi make[1]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-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-0.7.1+ds' help2man 'tail -n +9 docs/gemmi-help.txt' \ --version-string 0.7.1+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-0.7.1+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 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: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.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 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_0.7.1+ds-1~exp1_arm64.deb'. dpkg-deb: building package 'gemmi-dbgsym' in '../gemmi-dbgsym_0.7.1+ds-1~exp1_arm64.deb'. dpkg-deb: building package 'gemmi-dev' in '../gemmi-dev_0.7.1+ds-1~exp1_arm64.deb'. dpkg-deb: building package 'python3-gemmi' in '../python3-gemmi_0.7.1+ds-1~exp1_arm64.deb'. dpkg-deb: building package 'python3-gemmi-dbgsym' in '../python3-gemmi-dbgsym_0.7.1+ds-1~exp1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../gemmi_0.7.1+ds-1~exp1_arm64.buildinfo dpkg-genchanges --build=binary -O../gemmi_0.7.1+ds-1~exp1_arm64.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: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2258084/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2258084/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/2258084 and its subdirectories I: Current time: Tue Jul 7 08:43:47 +14 2026 I: pbuilder-time-stamp: 1783363427