Fri Oct 10 12:51:31 UTC 2025 I: starting to build gemmi/forky/arm64 on jenkins on '2025-10-10 12:51' Fri Oct 10 12:51:31 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_9/102660/console.log Fri Oct 10 12:51:31 UTC 2025 I: Downloading source for forky/gemmi=0.7.1+ds-2 --2025-10-10 12:51:31-- http://deb.debian.org/debian/pool/main/g/gemmi/gemmi_0.7.1%2bds-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2386 (2.3K) [text/prs.lines.tag] Saving to: ‘gemmi_0.7.1+ds-2.dsc’ 0K .. 100% 260M=0s 2025-10-10 12:51:31 (260 MB/s) - ‘gemmi_0.7.1+ds-2.dsc’ saved [2386/2386] Fri Oct 10 12:51:31 UTC 2025 I: gemmi_0.7.1+ds-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gemmi Binary: gemmi, gemmi-dev, python3-gemmi Architecture: any Version: 0.7.1+ds-2 Maintainer: Debichem Team Uploaders: Andrius Merkys , Roland Mas , Homepage: https://project-gemmi.github.io Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/debichem-team/gemmi Vcs-Git: https://salsa.debian.org/debichem-team/gemmi.git Testsuite: autopkgtest Testsuite-Triggers: python3-biopython, python3-numpy, python3-pytest Build-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 Package-List: gemmi deb science optional arch=any gemmi-dev deb libdevel optional arch=any python3-gemmi deb python optional arch=any Checksums-Sha1: 338914a2f96c701d9015561188c9ec4461e4393d 1372068 gemmi_0.7.1+ds.orig.tar.xz 0d476711accb2bb7a0eb96dafb394a8916d4e282 7544 gemmi_0.7.1+ds-2.debian.tar.xz Checksums-Sha256: dfa6d8c53370a765f63455745867f13c9e0755f15060ac20a55eaa517f68459d 1372068 gemmi_0.7.1+ds.orig.tar.xz 7cf6349d02b937ab59fe3b6f4c8d41e451b11fce3a4071bf7503dea1a9f6b193 7544 gemmi_0.7.1+ds-2.debian.tar.xz Files: ec4888e9d6e607b22bf5f78b55b1e7c5 1372068 gemmi_0.7.1+ds.orig.tar.xz 9a4d8fbd2bcbac4e4c62fdd752efda01 7544 gemmi_0.7.1+ds-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEdyKS9veshfrgQdQe5fQ/nCc08ocFAmjc6k8SHG1lcmt5c0Bk ZWJpYW4ub3JnAAoJEOX0P5wnNPKHamcP/0n9X3VoCHa+DZGfufz8nyV9r1WVrTZn 8YbWaFOAc0Rokkzl4xiA+b/XtopqtT/YHNQWpuRJqAvaTelanU7uEv0wp7RLqPbt Kbvrq4e3bYwmhNwJuKs9HEX5uylP66ewizvcYgVuZb4t0AY2ur6Z2E/ZlysqgJJc p8LkUZ4ZUdZMb3G9P58o58X9whd5QSnctOsVyHx43fwHeetlgbi1rOiJRGRuMXQh H9ffLIyleDXzuUP504mZ62snfThOKjEB5YTtOJupCFmrvFouWe9jJydPlOKsv/8F ODuEYkPHV3pdF10RSZsNG0/NeHeZDWoWKVU5G5id3LskSG0tgWQ4wcxKjnvuP7rc oZn/U/adWloDWz8VjPsSoyT0sae9LJT7pcp4Ejck1AhvN3kOJMRinjVPPF6Rbt4c mXyT6O3BmtVDFERxcexE3ng8ViQ3q1TN7OD62FnFZohkPcbuigRpAAY/9dnW9yD2 Ysyp/H6Yxl9Xf4lrMd0Ma7lR93YeRTOBWSMrVmiaNrakaFJ/9r8RIqRAFF6OdBjd lKvhozLmXcMzYMN7EnUWxmH8VxN403zCbo6xe0/hDo71w95jcADbOc6eABeSQ3GG tDtSPE8R1AhYsgFb6sxyRykZ5RvBClO8SNktlqj5lIYhm5BZbsjZokL8vkrjpHgC mUAqjeOVRux4 =5fZz -----END PGP SIGNATURE----- Fri Oct 10 12:51:31 UTC 2025 I: Checking whether the package is not for us Fri Oct 10 12:51:31 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Fri Oct 10 12:51:31 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Fri Oct 10 12:55:45 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Oct 10 00:51:33 -12 2025 I: pbuilder-time-stamp: 1760100693 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [gemmi_0.7.1+ds-2.dsc] I: copying [./gemmi_0.7.1+ds.orig.tar.xz] I: copying [./gemmi_0.7.1+ds-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./gemmi_0.7.1+ds-2.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-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-system-tao-pegtl.patch dpkg-source: info: applying use-system-doctest.patch dpkg-source: info: applying tao-pegtl-3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1666292/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='9b51514c6cc843198cd7595bed6aace5' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1666292' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.1fmMiLEQ/pbuilderrc_uHuP --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1fmMiLEQ/b1 --logfile b1/build.log gemmi_0.7.1+ds-2.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1666292/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 ... 20000 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-sphinxdoc{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} libngtcp2-16{a} libngtcp2-crypto-ossl0{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} libxml2-16{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-pygments{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 krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 113 newly installed, 0 to remove and 0 not upgraded. Need to get 54.5 MB of archives. After unpacking 231 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 libexpat1 arm64 2.7.3-1 [96.5 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 libpython3.13-minimal arm64 3.13.7-1 [857 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 python3.13-minimal arm64 3.13.7-1 [2001 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 python3-minimal arm64 3.13.7-1 [27.2 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 tzdata all 2025b-5 [260 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 readline-common all 8.3-3 [74.8 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 libreadline8t64 arm64 8.3-3 [169 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 libpython3.13-stdlib arm64 3.13.7-1 [1895 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 python3.13 arm64 3.13.7-1 [761 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 libpython3-stdlib arm64 3.13.7-1 [10.2 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 python3 arm64 3.13.7-1 [28.3 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1.2 [138 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 libblas3 arm64 3.12.1-7 [135 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 libgfortran5 arm64 15.2.0-4 [371 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 liblapack3 arm64 3.12.1-7 [1846 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 python3-numpy arm64 1:2.2.4+ds-1.2 [3620 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 libproc2-0 arm64 2:4.0.4-9 [62.8 kB] Get: 22 http://deb.debian.org/debian forky/main arm64 procps arm64 2:4.0.4-9 [871 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 30 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.2-1 [94.3 kB] Get: 31 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 32 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 33 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 34 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 35 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 36 http://deb.debian.org/debian forky/main arm64 automake all 1:1.17-4 [862 kB] Get: 37 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 38 http://deb.debian.org/debian forky/main arm64 cmake-data all 4.1.1+really3.31.6-2 [2268 kB] Get: 39 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.6+dfsg-0.1 [601 kB] Get: 40 http://deb.debian.org/debian forky/main arm64 libarchive13t64 arm64 3.7.4-4+b1 [323 kB] Get: 41 http://deb.debian.org/debian forky/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 42 http://deb.debian.org/debian forky/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 43 http://deb.debian.org/debian forky/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 44 http://deb.debian.org/debian forky/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 45 http://deb.debian.org/debian forky/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 46 http://deb.debian.org/debian forky/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 47 http://deb.debian.org/debian forky/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 48 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 49 http://deb.debian.org/debian forky/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get: 50 http://deb.debian.org/debian forky/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-10 [19.8 kB] Get: 51 http://deb.debian.org/debian forky/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-10 [55.0 kB] Get: 52 http://deb.debian.org/debian forky/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 53 http://deb.debian.org/debian forky/main arm64 libnghttp2-14 arm64 1.64.0-1.1+b1 [71.7 kB] Get: 54 http://deb.debian.org/debian forky/main arm64 libnghttp3-9 arm64 1.12.0-1 [63.6 kB] Get: 55 http://deb.debian.org/debian forky/main arm64 libngtcp2-16 arm64 1.16.0-1 [123 kB] Get: 56 http://deb.debian.org/debian forky/main arm64 libngtcp2-crypto-ossl0 arm64 1.16.0-1 [25.7 kB] Get: 57 http://deb.debian.org/debian forky/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 58 http://deb.debian.org/debian forky/main arm64 libp11-kit0 arm64 0.25.9-2 [420 kB] Get: 59 http://deb.debian.org/debian forky/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 60 http://deb.debian.org/debian forky/main arm64 libgnutls30t64 arm64 3.8.10-2 [1395 kB] Get: 61 http://deb.debian.org/debian forky/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3 [56.3 kB] Get: 62 http://deb.debian.org/debian forky/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 63 http://deb.debian.org/debian forky/main arm64 libcurl4t64 arm64 8.16.0-2 [368 kB] Get: 64 http://deb.debian.org/debian forky/main arm64 libjsoncpp26 arm64 1.9.6-4 [73.2 kB] Get: 65 http://deb.debian.org/debian forky/main arm64 librhash1 arm64 1.4.6-1 [131 kB] Get: 66 http://deb.debian.org/debian forky/main arm64 libuv1t64 arm64 1.51.0-2 [150 kB] Get: 67 http://deb.debian.org/debian forky/main arm64 cmake arm64 4.1.1+really3.31.6-2 [10.1 MB] Get: 68 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 69 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-5 [540 kB] Get: 70 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 71 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 72 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 73 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 74 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.193-3 [189 kB] Get: 75 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.16-2 [100 kB] Get: 76 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 77 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 78 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 79 http://deb.debian.org/debian forky/main arm64 debhelper all 13.28 [941 kB] Get: 80 http://deb.debian.org/debian forky/main arm64 dh-python all 6.20250414 [116 kB] Get: 81 http://deb.debian.org/debian forky/main arm64 doctest-dev all 2.4.12-1 [220 kB] Get: 82 http://deb.debian.org/debian forky/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 83 http://deb.debian.org/debian forky/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 84 http://deb.debian.org/debian forky/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 85 http://deb.debian.org/debian forky/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 86 http://deb.debian.org/debian forky/main arm64 pkg-config arm64 1.8.1-4 [14.0 kB] Get: 87 http://deb.debian.org/debian forky/main arm64 libeigen3-dev all 3.4.0-5 [1034 kB] Get: 88 http://deb.debian.org/debian forky/main arm64 libexpat1-dev arm64 2.7.3-1 [150 kB] Get: 89 http://deb.debian.org/debian forky/main arm64 libjs-sphinxdoc all 8.2.3-7 [27.6 kB] Get: 90 http://deb.debian.org/debian forky/main arm64 libpython3.13 arm64 3.13.7-1 [1978 kB] Get: 91 http://deb.debian.org/debian forky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 92 http://deb.debian.org/debian forky/main arm64 libpython3.13-dev arm64 3.13.7-1 [4924 kB] Get: 93 http://deb.debian.org/debian forky/main arm64 libpython3-dev arm64 3.13.7-1 [10.5 kB] Get: 94 http://deb.debian.org/debian forky/main arm64 libstb0t64 arm64 0.0~git20250907.fede005+ds-1 [210 kB] Get: 95 http://deb.debian.org/debian forky/main arm64 libstb-dev arm64 0.0~git20250907.fede005+ds-1 [651 kB] Get: 96 http://deb.debian.org/debian forky/main arm64 robin-map-dev all 1.3.0-1 [29.8 kB] Get: 97 http://deb.debian.org/debian forky/main arm64 nanobind-dev all 2.9.2-2 [173 kB] Get: 98 http://deb.debian.org/debian forky/main arm64 pybind11-dev all 2.13.6-2 [205 kB] Get: 99 http://deb.debian.org/debian forky/main arm64 python3-packaging all 25.0-1 [56.6 kB] Get: 100 http://deb.debian.org/debian forky/main arm64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get: 101 http://deb.debian.org/debian forky/main arm64 python3-wheel all 0.46.1-2 [21.7 kB] Get: 102 http://deb.debian.org/debian forky/main arm64 python3-build all 1.2.2-4 [36.2 kB] Get: 103 http://deb.debian.org/debian forky/main arm64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 104 http://deb.debian.org/debian forky/main arm64 pybuild-plugin-pyproject all 6.20250414 [11.8 kB] Get: 105 http://deb.debian.org/debian forky/main arm64 python3.13-dev arm64 3.13.7-1 [504 kB] Get: 106 http://deb.debian.org/debian forky/main arm64 python3-dev arm64 3.13.7-1 [26.1 kB] Get: 107 http://deb.debian.org/debian forky/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 108 http://deb.debian.org/debian forky/main arm64 python3-nanobind all 2.9.2-2 [46.3 kB] Get: 109 http://deb.debian.org/debian forky/main arm64 python3-pluggy all 1.6.0-1 [27.1 kB] Get: 110 http://deb.debian.org/debian forky/main arm64 python3-pybind11 all 2.13.6-2 [215 kB] Get: 111 http://deb.debian.org/debian forky/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 112 http://deb.debian.org/debian forky/main arm64 python3-pytest all 8.4.2-1 [266 kB] Get: 113 http://deb.debian.org/debian forky/main arm64 tao-pegtl-dev all 3.2.7-1 [69.4 kB] Fetched 54.5 MB in 0s (118 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (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 ... 20000 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_arm64.deb ... Unpacking python3.13 (3.13.7-1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/gemmi-0.7.1+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gemmi_0.7.1+ds-2_source.changes dpkg-buildpackage: info: source package gemmi dpkg-buildpackage: info: source version 0.7.1+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture 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 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- 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 "3.13.7") found components: Interpreter Development.Module -- Found nanobind 2.9.2: /usr/share/nanobind -- Configuring done (1.6s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/gemmi-0.7.1+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' 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'/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/build make[3]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' [ 1%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o [ 0%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o [ 1%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/ccp4.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 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-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_enum.cpp.o -MF CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_enum.cpp.o.d -o CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_enum.cpp.o -c /usr/share/nanobind/src/nb_enum.cpp [ 13%] Building CXX object CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_ndarray.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/nb_ndarray.cpp.o -MF CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_ndarray.cpp.o.d -o CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_ndarray.cpp.o -c /usr/share/nanobind/src/nb_ndarray.cpp [ 13%] Building CXX object CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_static_property.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/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 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/nb_ft.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/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 [ 15%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/ddl.cpp.o /usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.7.1+ds/third_party 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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) { | ^ [ 16%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/eig3.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 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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 [ 20%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/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/gz.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/gz.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/src/gz.cpp [ 20%] Building CXX object 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-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 [ 24%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/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/json.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/json.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/json.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/src/json.cpp [ 24%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/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/mmcif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mmcif.cpp.o -c /build/reproducible-path/gemmi-0.7.1+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 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-std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/src/monlib.cpp [ 28%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mtz.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/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 /usr/bin/ar qc libnanobind-static.a "CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_internals.cpp.o" "CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_func.cpp.o" "CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_type.cpp.o" "CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_enum.cpp.o" "CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_ndarray.cpp.o" "CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_static_property.cpp.o" "CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/nb_ft.cpp.o" "CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/common.cpp.o" "CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/error.cpp.o" "CMakeFiles/nanobind-static.dir/usr/share/nanobind/src/trampoline.cpp.o" 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'/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' [ 28%] Built target options [ 30%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/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/pdb.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/pdb.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/pdb.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/src/pdb.cpp [ 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 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/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/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. 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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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-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 /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 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CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o [ 54%] Building CXX object CMakeFiles/gemmi_py.dir/python/custom.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/cifdiff.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/prog/cifdiff.cpp /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/custom.cpp.o -MF CMakeFiles/gemmi_py.dir/python/custom.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/custom.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/python/custom.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 [ 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 [ 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 [ 56%] Building CXX object 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 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'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/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) { | ^ [ 58%] 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 [ 58%] 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 [ 60%] 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 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) { | ^ [ 62%] 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 -fvisibility-inlines-hidden -Wno-psabi -MD -MT CMakeFiles/gemmi_py.dir/python/hkl.cpp.o -MF CMakeFiles/gemmi_py.dir/python/hkl.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/hkl.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/python/hkl.cpp [ 62%] 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 [ 64%] 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 [ 66%] 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 [ 66%] 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 [ 67%] 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 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_py.dir/python/meta.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/meta.cpp.o -MF CMakeFiles/gemmi_py.dir/python/meta.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/meta.cpp.o -c /build/reproducible-path/gemmi-0.7.1+ds/python/meta.cpp [ 69%] 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 [ 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 [ 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 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) { | ^ /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++/15/bits/stl_algobase.h:64, from /usr/include/c++/15/algorithm:62, 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++/15/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++/15/bits/stl_algo.h:3453:28: required from 'constexpr std::pair<_FIter, _FIter> std::minmax(initializer_list<_Tp>) [with _Tp = double]' 3453 | 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++/15/bits/stl_pair.h:1164:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1164 | 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) { | ^~~~~~~~~~~~~~~~~~~~~ [ 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 [ 71%] 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 /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()) | ~~~~~^~~~ [ 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 /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ [ 75%] 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 [ 75%] 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_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 [ 79%] 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 [ 79%] 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 /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 [ 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 [ 81%] 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 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) { | ^ [ 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 /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) { | ^~~~~~~~~~~~~~~~~~~~~~~ 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; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ [ 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 [ 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 [ 86%] 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 [ 86%] 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 [ 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 /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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 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) { | ^ 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) { | ^ [ 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 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) { | ^ [ 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 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) { | ^ [ 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 [ 92%] 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 [ 94%] 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 [ 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 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 { | ^~~~~~~~~~~~~~~~~~~~~~~~~ [ 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 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; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ [ 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/lib/aarch64-linux-gnu/libz.so: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. 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The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/aarch64-linux-gnu/libc.so.6: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /lib/ld-linux-aarch64.so.1: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. /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 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--dependency-file=CMakeFiles/gemmi_py.dir/link.d -Wl,-z,relro -shared -o py/gemmi/gemmi_ext.cpython-313-aarch64-linux-gnu.so CMakeFiles/gemmi_py.dir/python/gemmi.cpp.o CMakeFiles/gemmi_py.dir/python/align.cpp.o CMakeFiles/gemmi_py.dir/python/ccp4.cpp.o CMakeFiles/gemmi_py.dir/python/chemcomp.cpp.o CMakeFiles/gemmi_py.dir/python/cif.cpp.o CMakeFiles/gemmi_py.dir/python/custom.cpp.o CMakeFiles/gemmi_py.dir/python/elem.cpp.o CMakeFiles/gemmi_py.dir/python/grid.cpp.o CMakeFiles/gemmi_py.dir/python/hkl.cpp.o CMakeFiles/gemmi_py.dir/python/meta.cpp.o CMakeFiles/gemmi_py.dir/python/mol.cpp.o CMakeFiles/gemmi_py.dir/python/monlib.cpp.o CMakeFiles/gemmi_py.dir/python/mtz.cpp.o CMakeFiles/gemmi_py.dir/python/read.cpp.o CMakeFiles/gemmi_py.dir/python/recgrid.cpp.o CMakeFiles/gemmi_py.dir/python/scaling.cpp.o CMakeFiles/gemmi_py.dir/python/search.cpp.o CMakeFiles/gemmi_py.dir/python/sf.cpp.o CMakeFiles/gemmi_py.dir/python/sym.cpp.o CMakeFiles/gemmi_py.dir/python/topo.cpp.o CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o CMakeFiles/gemmi_py.dir/python/write.cpp.o CMakeFiles/gemmi_cpp.dir/src/align.cpp.o CMakeFiles/gemmi_cpp.dir/src/assembly.cpp.o CMakeFiles/gemmi_cpp.dir/src/calculate.cpp.o CMakeFiles/gemmi_cpp.dir/src/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 libnanobind-static.a /usr/lib/aarch64-linux-gnu/libz.so make[3]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' [100%] Built target gemmi_py make -f CMakeFiles/gemmi_stub.dir/build.make CMakeFiles/gemmi_stub.dir/depend make[3]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make -f CMakeFiles/gemmi_cif_stub.dir/build.make CMakeFiles/gemmi_cif_stub.dir/depend 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_stub.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 /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_cif_stub.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make -f CMakeFiles/gemmi_cif_stub.dir/build.make CMakeFiles/gemmi_cif_stub.dir/build make[3]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make -f CMakeFiles/gemmi_stub.dir/build.make CMakeFiles/gemmi_stub.dir/build make[3]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' [100%] Generating py/gemmi/cif.pyi /usr/bin/python3 /usr/share/nanobind/stubgen.py -q -i py -m gemmi.cif -o py/gemmi/cif.pyi [100%] Generating py/gemmi/py.typed, py/gemmi/__init__.pyi /usr/bin/python3 /usr/share/nanobind/stubgen.py -q -i py -p 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CMakeFiles/gemmi_prog.dir/prog/cifdiff.cpp.o CMakeFiles/gemmi_prog.dir/prog/contact.cpp.o CMakeFiles/gemmi_prog.dir/prog/contents.cpp.o CMakeFiles/gemmi_prog.dir/prog/convert.cpp.o CMakeFiles/gemmi_prog.dir/prog/crd.cpp.o CMakeFiles/gemmi_prog.dir/prog/ecalc.cpp.o CMakeFiles/gemmi_prog.dir/prog/fprime.cpp.o CMakeFiles/gemmi_prog.dir/prog/grep.cpp.o CMakeFiles/gemmi_prog.dir/prog/h.cpp.o CMakeFiles/gemmi_prog.dir/prog/json2cif.cpp.o CMakeFiles/gemmi_prog.dir/prog/main.cpp.o CMakeFiles/gemmi_prog.dir/prog/map.cpp.o CMakeFiles/gemmi_prog.dir/prog/map2sf.cpp.o CMakeFiles/gemmi_prog.dir/prog/mapcoef.cpp.o CMakeFiles/gemmi_prog.dir/prog/mask.cpp.o CMakeFiles/gemmi_prog.dir/prog/merge.cpp.o CMakeFiles/gemmi_prog.dir/prog/mondiff.cpp.o CMakeFiles/gemmi_prog.dir/prog/monlib_opt.cpp.o CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o CMakeFiles/gemmi_prog.dir/prog/set.cpp.o CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o CMakeFiles/options.dir/prog/options.cpp.o -o gemmi libgemmi_cpp.a /usr/lib/aarch64-linux-gnu/libz.so make[3]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' [100%] Built target gemmi_prog make[2]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' debian/rules execute_before_dh_auto_test 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'/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make -f CMakeFiles/options.dir/build.make CMakeFiles/options.dir/depend make -f CMakeFiles/gemmi_cpp.dir/build.make CMakeFiles/gemmi_cpp.dir/depend make[5]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make -f CMakeFiles/hello.dir/build.make CMakeFiles/hello.dir/depend make[5]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make -f CMakeFiles/doc_example2.dir/build.make CMakeFiles/doc_example2.dir/depend 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[5]: Entering 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[ 2%] Building CXX object CMakeFiles/doc_example2.dir/docs/code/cif_cc.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 [ 4%] Built target options Consolidate compiler generated dependencies of target gemmi_cpp [ 6%] Building CXX object CMakeFiles/hello.dir/examples/hello.cpp.o make[5]: Leaving 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/build 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[ 41%] 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 [ 41%] Building CXX object CMakeFiles/doc_example.dir/docs/code/sym.cpp.o [ 43%] Building CXX object CMakeFiles/doc_example.dir/docs/code/elem.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 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hello make[5]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' [ 93%] Built target hello [ 95%] Linking CXX executable test_disulf /usr/bin/cmake -E cmake_link_script CMakeFiles/test_disulf.dir/link.txt --verbose=1 [ 95%] Linking CXX executable doc_example2 /usr/bin/cmake -E cmake_link_script CMakeFiles/doc_example2.dir/link.txt --verbose=1 /usr/bin/c++ -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 -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/test_disulf.dir/link.d CMakeFiles/test_disulf.dir/tests/disulf.cpp.o -o test_disulf libgemmi_cpp.a /usr/lib/aarch64-linux-gnu/libz.so make[5]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' [ 95%] Built target test_disulf /usr/bin/c++ -g -O2 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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/check.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/build make[5]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' /usr/bin/ctest -C "None" Test project /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu Connected to MAKE jobserver Start 1: cpptest 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[5]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' [100%] Built target check make[4]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' make[2]: Leaving directory '/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_test -O--buildsystem=cmake cd obj-aarch64-linux-gnu && make -j12 test ARGS\+=--verbose ARGS\+=-j12 make[1]: Entering directory '/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j12 UpdateCTestConfiguration from :/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/gemmi-0.7.1+ds/obj-aarch64-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end 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 "2.4.12" 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 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/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-dbgsym' in '../gemmi-dbgsym_0.7.1+ds-2_arm64.deb'. dpkg-deb: building package 'gemmi-dev' in '../gemmi-dev_0.7.1+ds-2_arm64.deb'. dpkg-deb: building package 'gemmi' in '../gemmi_0.7.1+ds-2_arm64.deb'. dpkg-deb: building package 'python3-gemmi' in '../python3-gemmi_0.7.1+ds-2_arm64.deb'. dpkg-deb: building package 'python3-gemmi-dbgsym' in '../python3-gemmi-dbgsym_0.7.1+ds-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../gemmi_0.7.1+ds-2_arm64.buildinfo dpkg-genchanges --build=binary -O../gemmi_0.7.1+ds-2_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: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1666292 and its subdirectories I: Current time: Fri Oct 10 00:55:37 -12 2025 I: pbuilder-time-stamp: 1760100937 Fri Oct 10 12:55:46 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Fri Oct 10 12:55:46 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Fri Oct 10 13:00:18 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Fri Oct 10 13:00:18 UTC 2025 I: gemmi_0.7.1+ds-2_arm64.changes: Format: 1.8 Date: Wed, 01 Oct 2025 04:45:14 -0400 Source: gemmi Binary: gemmi gemmi-dbgsym gemmi-dev python3-gemmi python3-gemmi-dbgsym Architecture: arm64 Version: 0.7.1+ds-2 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Andrius Merkys Description: gemmi - library for structural biology - executable gemmi-dev - library for structural biology python3-gemmi - library for structural biology - Python module Closes: 1116738 Changes: gemmi (0.7.1+ds-2) unstable; urgency=medium . * python3-nanobind is a hard dependency (Closes: #1116738). Checksums-Sha1: f9dce8f5a2dc02b9a524b1b8d899a62282988c73 31521500 gemmi-dbgsym_0.7.1+ds-2_arm64.deb 6260299a03a766febe455fe319b4f4c056aadfec 1103888 gemmi-dev_0.7.1+ds-2_arm64.deb 10c76e54d5dd819857f8083415fac89aaba03962 8343 gemmi_0.7.1+ds-2_arm64.buildinfo 755973ec497525c3e58c4677b0745f6de45a7110 1172852 gemmi_0.7.1+ds-2_arm64.deb d94645cfd85bab6cf786ac6887c418755405b5d2 40297152 python3-gemmi-dbgsym_0.7.1+ds-2_arm64.deb 0ce6b15d74f309d4f16847daf0b34f0d1d684462 1629300 python3-gemmi_0.7.1+ds-2_arm64.deb Checksums-Sha256: 2842c5fa0db75f436a455a77bf3f53a35f0a2ef539e62d6418b65a16e5d44a5b 31521500 gemmi-dbgsym_0.7.1+ds-2_arm64.deb cc43d0a384f3b358b14dbcf733a343c653eac1dfe6f2a61df7e5a87722e43bf5 1103888 gemmi-dev_0.7.1+ds-2_arm64.deb bec8af95d84f9759e955a57a29a6da7629bf17c2d5a57fb1b33878a7f7ca9fbe 8343 gemmi_0.7.1+ds-2_arm64.buildinfo 8f522dce709a5db74ae07546020f08343dc5f9da5b19f26c6738b8797cedc771 1172852 gemmi_0.7.1+ds-2_arm64.deb 94d4db2a88fbb764d765a8c9bfe0c3545626b0e05f545466a86f01087b2b2b8c 40297152 python3-gemmi-dbgsym_0.7.1+ds-2_arm64.deb 2d6ececc618e1d8640f2997aa97963cf6d7a9f61bde922e1be5748f1a3bd46f0 1629300 python3-gemmi_0.7.1+ds-2_arm64.deb Files: 4c1016a7241311f09fd6e62193abc20f 31521500 debug optional gemmi-dbgsym_0.7.1+ds-2_arm64.deb a0ca78b18eff86f18f15fab164e400f4 1103888 libdevel optional gemmi-dev_0.7.1+ds-2_arm64.deb 493b76f8eec235a9ac41422f880febb0 8343 science optional gemmi_0.7.1+ds-2_arm64.buildinfo 4856bc13f294f14f289942b1c3264e41 1172852 science optional gemmi_0.7.1+ds-2_arm64.deb 0ba46cf6ee222b250ac0c62f3a221421 40297152 debug optional python3-gemmi-dbgsym_0.7.1+ds-2_arm64.deb 51d2f0a203248dafe90e09c06caf6ede 1629300 python optional python3-gemmi_0.7.1+ds-2_arm64.deb Fri Oct 10 13:00:19 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_9-102660.service; invocation ID: 03e19ef6a19f4d69b4327be6ab7a186b # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.1fmMiLEQ/gemmi_0.7.1+ds-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.1fmMiLEQ/gemmi_0.7.1+ds-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.1fmMiLEQ/gemmi_0.7.1+ds-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.1fmMiLEQ/b1/gemmi_0.7.1+ds-2_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.1fmMiLEQ/b2/gemmi_0.7.1+ds-2_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 205ms CPU time consumed: 172ms Memory peak: 17.3M (swap: 0B) Fri Oct 10 13:00:21 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Fri Oct 10 13:00:21 UTC 2025 I: gemmi from forky built successfully and reproducibly on arm64. Fri Oct 10 13:00:22 UTC 2025 I: Removing signed gemmi_0.7.1+ds-2_arm64.buildinfo.asc files: removed './b1/gemmi_0.7.1+ds-2_arm64.buildinfo.asc' removed './b2/gemmi_0.7.1+ds-2_arm64.buildinfo.asc'