Mon Mar 3 08:28:35 UTC 2025 I: starting to build gemmi/unstable/amd64 on jenkins on '2025-03-03 08:28'
Mon Mar 3 08:28:35 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_2/33378/console.log
Mon Mar 3 08:28:35 UTC 2025 I: Downloading source for unstable/gemmi=0.6.5+ds-3
--2025-03-03 08:28:35-- http://deb.debian.org/debian/pool/main/g/gemmi/gemmi_0.6.5%2bds-3.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2280 (2.2K) [text/prs.lines.tag]
Saving to: ‘gemmi_0.6.5+ds-3.dsc’
0K .. 100% 359M=0s
2025-03-03 08:28:35 (359 MB/s) - ‘gemmi_0.6.5+ds-3.dsc’ saved [2280/2280]
Mon Mar 3 08:28:35 UTC 2025 I: gemmi_0.6.5+ds-3.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: gemmi
Binary: gemmi, gemmi-dev, python3-gemmi
Architecture: any
Version: 0.6.5+ds-3
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Uploaders: Andrius Merkys <merkys@debian.org>,
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-numpy, python3-pytest
Build-Depends: cmake, debhelper-compat (= 13), dh-python, doctest-dev, help2man, libstb-dev, python3-dev, python3-numpy <!nocheck>, python3-pybind11 (>= 2.6.0), python3-pytest <!nocheck>, 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:
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8aaf7a1b9ec07c9a3d2a1cf8b13aec90a5d4af9a 7464 gemmi_0.6.5+ds-3.debian.tar.xz
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1fae724e7ac8acfb90aff0c273d91cf041b7afd24d0c141ffcb8078580b9b985 7464 gemmi_0.6.5+ds-3.debian.tar.xz
Files:
79b8f330dd17157260a26b4afe821533 1290296 gemmi_0.6.5+ds.orig.tar.xz
89d17bf774701a810776d9cd4b5a869c 7464 gemmi_0.6.5+ds-3.debian.tar.xz
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Mon Mar 3 08:28:35 UTC 2025 I: Checking whether the package is not for us
Mon Mar 3 08:28:35 UTC 2025 I: Starting 1st build on remote node ionos5-amd64.debian.net.
Mon Mar 3 08:28:35 UTC 2025 I: Preparing to do remote build '1' on ionos5-amd64.debian.net.
Mon Mar 3 08:32:12 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sun Apr 5 02:51:36 -12 2026
I: pbuilder-time-stamp: 1775400696
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [gemmi_0.6.5+ds-3.dsc]
I: copying [./gemmi_0.6.5+ds.orig.tar.xz]
I: copying [./gemmi_0.6.5+ds-3.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./gemmi_0.6.5+ds-3.dsc: unsupported subcommand
dpkg-source: info: extracting gemmi in gemmi-0.6.5+ds
dpkg-source: info: unpacking gemmi_0.6.5+ds.orig.tar.xz
dpkg-source: info: unpacking gemmi_0.6.5+ds-3.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
dpkg-source: info: applying adjust-test-tolerance.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/2345260/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='6385e3586ff74952bb85b00fefe92035'
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='2345260'
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.ulC2Lwkg/pbuilderrc_vjPT --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ulC2Lwkg/b1 --logfile b1/build.log gemmi_0.6.5+ds-3.dsc'
SUDO_GID='110'
SUDO_UID='105'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://213.165.73.152:3128'
I: uname -a
Linux ionos5-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/2345260/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: cmake, debhelper-compat (= 13), dh-python, doctest-dev, help2man, libstb-dev, python3-dev, python3-numpy, python3-pybind11 (>= 2.6.0), python3-pytest, tao-pegtl-dev, zlib1g-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19778 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on cmake; however:
Package cmake is not installed.
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on dh-python; however:
Package dh-python is not installed.
pbuilder-satisfydepends-dummy depends on doctest-dev; however:
Package doctest-dev is not installed.
pbuilder-satisfydepends-dummy depends on help2man; however:
Package help2man is not installed.
pbuilder-satisfydepends-dummy depends on libstb-dev; however:
Package libstb-dev is not installed.
pbuilder-satisfydepends-dummy depends on python3-dev; however:
Package python3-dev is not installed.
pbuilder-satisfydepends-dummy depends on python3-numpy; however:
Package python3-numpy is not installed.
pbuilder-satisfydepends-dummy depends on python3-pybind11 (>= 2.6.0); however:
Package python3-pybind11 is not installed.
pbuilder-satisfydepends-dummy depends on python3-pytest; however:
Package python3-pytest is not installed.
pbuilder-satisfydepends-dummy depends on tao-pegtl-dev; however:
Package tao-pegtl-dev is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} doctest-dev{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgnutls30t64{a} libgssapi-krb5-2{a} libicu72{a} libidn2-0{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap2{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libp11-kit0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libstb-dev{a} libstb0t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} procps{a} pybind11-dev{a} python3{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pybind11{a} python3-pytest{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tao-pegtl-dev{a} tzdata{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libeigen3-dev libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-pygments wget
0 packages upgraded, 111 newly installed, 0 to remove and 0 not upgraded.
Need to get 68.5 MB of archives. After unpacking 268 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.2-1 [27.1 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 media-types all 12.0.0 [28.9 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-1 [745 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.2-1 [10.0 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.2-1 [28.1 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-4 [139 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-2 [160 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.3+ds-4 [5085 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-7 [878 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 36 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 37 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.6-1 [2268 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 40 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get: 41 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB]
Get: 42 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB]
Get: 43 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB]
Get: 44 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get: 45 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB]
Get: 46 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 47 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB]
Get: 48 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB]
Get: 49 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 50 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB]
Get: 51 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB]
Get: 52 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB]
Get: 53 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB]
Get: 54 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get: 55 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB]
Get: 56 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get: 57 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get: 58 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get: 59 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get: 60 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get: 61 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get: 62 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.12.1-3 [369 kB]
Get: 63 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB]
Get: 64 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB]
Get: 65 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB]
Get: 66 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.31.6-1 [12.0 MB]
Get: 67 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 68 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 69 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 70 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 71 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 72 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 73 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 74 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 75 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 76 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 77 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 78 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get: 79 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 80 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 81 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 82 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.2-1 [37.3 kB]
Get: 83 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 84 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 85 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 86 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.8.0-1 [222 kB]
Get: 87 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 88 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 89 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.8.0-1 [724 kB]
Get: 90 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250108 [113 kB]
Get: 91 http://deb.debian.org/debian unstable/main amd64 doctest-dev all 2.4.11-1 [216 kB]
Get: 92 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB]
Get: 93 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB]
Get: 94 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 95 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 96 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB]
Get: 97 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.2-1 [2151 kB]
Get: 98 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get: 99 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.2-1 [5005 kB]
Get: 100 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.2-1 [10.3 kB]
Get: 101 http://deb.debian.org/debian unstable/main amd64 libstb0t64 amd64 0.0~git20241109.5c20573+ds-1 [220 kB]
Get: 102 http://deb.debian.org/debian unstable/main amd64 libstb-dev amd64 0.0~git20241109.5c20573+ds-1 [655 kB]
Get: 103 http://deb.debian.org/debian unstable/main amd64 pybind11-dev all 2.13.6-2 [205 kB]
Get: 104 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.2-1 [507 kB]
Get: 105 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.2-1 [26.1 kB]
Get: 106 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B]
Get: 107 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB]
Get: 108 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB]
Get: 109 http://deb.debian.org/debian unstable/main amd64 python3-pybind11 all 2.13.6-2 [215 kB]
Get: 110 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.3.4-1 [250 kB]
Get: 111 http://deb.debian.org/debian unstable/main amd64 tao-pegtl-dev all 3.2.7-1 [69.4 kB]
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I: Building the package
I: Running cd /build/reproducible-path/gemmi-0.6.5+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_0.6.5+ds-3_source.changes
dpkg-buildpackage: info: source package gemmi
dpkg-buildpackage: info: source version 0.6.5+ds-3
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andrius Merkys <merkys@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean --buildsystem cmake --with python3
dh_auto_clean -O--buildsystem=cmake
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dh_auto_configure -- -DBUILD_SHARED_LIBS=OFF -DUSE_PYTHON=ON
cd obj-x86_64-linux-gnu && PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_SHARED_LIBS=OFF -DUSE_PYTHON=ON ..
-- The C compiler identification is GNU 14.2.0
-- The CXX compiler identification is GNU 14.2.0
-- Detecting C compiler ABI info
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-- Detecting CXX compile features
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-- Gemmi version 0.6.5
-- Build type: None
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-- Benchmarks not configured.
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-- Found Python: /usr/bin/python3 (found version "3.13.2") found components: Interpreter Development.Module
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- Found pybind11: /usr/lib/python3/dist-packages/pybind11/include (found version "2.13.6")
-- Found pybind11 2.13.6: /usr/lib/python3/dist-packages/pybind11/include;/usr/include/python3.13
-- Configuring done (1.8s)
-- Generating done (0.1s)
CMake Warning:
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[ 22%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o
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[ 22%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o
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[ 22%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/json.cpp.o
/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mtz2cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/mtz2cif.cpp
[ 22%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o
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/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/read_cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/read_cif.cpp
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/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/resinfo.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/resinfo.cpp
/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/riding_h.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/riding_h.cpp
/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/mmread_gz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/mmread_gz.cpp
[ 27%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o
[ 27%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o
[ 27%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o
[ 27%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o
/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/monlib.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/monlib.cpp
/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/sprintf.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/sprintf.cpp
[ 29%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o
/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/to_mmcif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/to_mmcif.cpp
[ 29%] Building CXX object CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o
/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/to_pdb.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/to_pdb.cpp
/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/topo.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/topo.cpp
/usr/bin/c++ -DGEMMI_BUILD -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o -MF CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o.d -o CMakeFiles/gemmi_cpp.dir/src/xds_ascii.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/src/xds_ascii.cpp
/build/reproducible-path/gemmi-0.6.5+ds/src/sprintf.cpp:30:86: note: '#pragma message: Using system stb_sprintf.h, not the bundled one. It may not work.'
30 | # pragma message("Using system stb_sprintf.h, not the bundled one. It may not work.")
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23,
from /build/reproducible-path/gemmi-0.6.5+ds/src/mtz.cpp:3:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23,
from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz2cif.hpp:14,
from /build/reproducible-path/gemmi-0.6.5+ds/src/mtz2cif.cpp:3:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/src/gz.cpp:15:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/prog/options.cpp:8:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23,
from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/intensit.hpp:14,
from /build/reproducible-path/gemmi-0.6.5+ds/src/intensit.cpp:3:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:11,
from /build/reproducible-path/gemmi-0.6.5+ds/src/xds_ascii.cpp:3:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10,
from /build/reproducible-path/gemmi-0.6.5+ds/src/json.cpp:3:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10,
from /build/reproducible-path/gemmi-0.6.5+ds/src/read_cif.cpp:5:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10,
from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mmread.hpp:12,
from /build/reproducible-path/gemmi-0.6.5+ds/src/mmread_gz.cpp:4:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
make[3]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu'
[ 29%] Built target options
In file included from /usr/include/c++/14/bits/stl_tree.h:63,
from /usr/include/c++/14/map:62,
from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/topo.hpp:8,
from /build/reproducible-path/gemmi-0.6.5+ds/src/topo.cpp:3:
In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = gemmi::Topo::Rule; _Up = gemmi::Topo::Rule; bool _IsMove = true]',
inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = true; _II = gemmi::Topo::Rule*; _OI = gemmi::Topo::Rule*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30,
inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = true; _II = gemmi::Topo::Rule*; _OI = gemmi::Topo::Rule*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42,
inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = true; _II = __gnu_cxx::__normal_iterator<gemmi::Topo::Rule*, vector<gemmi::Topo::Rule> >; _OI = gemmi::Topo::Rule*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31,
inlined from '_OI std::copy(_II, _II, _OI) [with _II = move_iterator<__gnu_cxx::__normal_iterator<gemmi::Topo::Rule*, vector<gemmi::Topo::Rule> > >; _OI = gemmi::Topo::Rule*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7,
inlined from 'static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<__gnu_cxx::__normal_iterator<gemmi::Topo::Rule*, std::vector<gemmi::Topo::Rule> > >; _ForwardIterator = gemmi::Topo::Rule*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27,
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = move_iterator<__gnu_cxx::__normal_iterator<gemmi::Topo::Rule*, vector<gemmi::Topo::Rule> > >; _ForwardIterator = gemmi::Topo::Rule*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = move_iterator<__gnu_cxx::__normal_iterator<gemmi::Topo::Rule*, vector<gemmi::Topo::Rule> > >; _ForwardIterator = gemmi::Topo::Rule*; _Tp = gemmi::Topo::Rule]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37,
inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = std::move_iterator<__gnu_cxx::__normal_iterator<gemmi::Topo::Rule*, std::vector<gemmi::Topo::Rule> > >; _Tp = gemmi::Topo::Rule; _Alloc = std::allocator<gemmi::Topo::Rule>]' at /usr/include/c++/14/bits/vector.tcc:1022:38,
inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::move_iterator<__gnu_cxx::__normal_iterator<gemmi::Topo::Rule*, std::vector<gemmi::Topo::Rule> > >; <template-parameter-2-2> = void; _Tp = gemmi::Topo::Rule; _Alloc = std::allocator<gemmi::Topo::Rule>]' at /usr/include/c++/14/bits/stl_vector.h:1488:19,
inlined from 'void gemmi::vector_move_extend(std::vector<Value>&, std::vector<Value>&&) [with T = Topo::Rule]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/util.hpp:260:15,
inlined from 'void gemmi::Topo::apply_all_restraints(const gemmi::MonLib&)' at /build/reproducible-path/gemmi-0.6.5+ds/src/topo.cpp:608:27:
/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 17 and 9223372036854775792 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=]
452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33,
from /usr/include/c++/14/bits/allocator.h:46,
from /usr/include/c++/14/bits/stl_tree.h:64:
In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = gemmi::Topo::Rule]',
inlined from 'static _Tp* std::allocator_traits<std::allocator<_Tp1> >::allocate(allocator_type&, size_type) [with _Tp = gemmi::Topo::Rule]' at /usr/include/c++/14/bits/alloc_traits.h:515:28,
inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = gemmi::Topo::Rule; _Alloc = std::allocator<gemmi::Topo::Rule>]' at /usr/include/c++/14/bits/stl_vector.h:380:33,
inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = std::move_iterator<__gnu_cxx::__normal_iterator<gemmi::Topo::Rule*, std::vector<gemmi::Topo::Rule> > >; _Tp = gemmi::Topo::Rule; _Alloc = std::allocator<gemmi::Topo::Rule>]' at /usr/include/c++/14/bits/vector.tcc:1013:40,
inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::move_iterator<__gnu_cxx::__normal_iterator<gemmi::Topo::Rule*, std::vector<gemmi::Topo::Rule> > >; <template-parameter-2-2> = void; _Tp = gemmi::Topo::Rule; _Alloc = std::allocator<gemmi::Topo::Rule>]' at /usr/include/c++/14/bits/stl_vector.h:1488:19,
inlined from 'void gemmi::vector_move_extend(std::vector<Value>&, std::vector<Value>&&) [with T = Topo::Rule]' at /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/util.hpp:260:15,
inlined from 'void gemmi::Topo::apply_all_restraints(const gemmi::MonLib&)' at /build/reproducible-path/gemmi-0.6.5+ds/src/topo.cpp:608:27:
/usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [16, 9223372036854775792] allocated by 'operator new'
151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
| ^
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/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -Wno-psabi -MD -MT CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz.cpp
[ 79%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o
/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/mtz2cif.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz2cif.cpp
[ 81%] Building CXX object CMakeFiles/gemmi_py.dir/python/sym.cpp.o
/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/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-0.6.5+ds/python/sym.cpp
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23,
from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz2cif.hpp:14,
from /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz2cif.cpp:8:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19,
from /build/reproducible-path/gemmi-0.6.5+ds/prog/map.cpp:6:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23,
from /build/reproducible-path/gemmi-0.6.5+ds/prog/mtz.cpp:8:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19,
from /build/reproducible-path/gemmi-0.6.5+ds/prog/mask.cpp:5:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19,
from /build/reproducible-path/gemmi-0.6.5+ds/python/ccp4.cpp:3:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23,
from /build/reproducible-path/gemmi-0.6.5+ds/python/mtz.cpp:3:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23,
from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cif2mtz.hpp:15,
from /build/reproducible-path/gemmi-0.6.5+ds/prog/cif2mtz.cpp:10:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23,
from /build/reproducible-path/gemmi-0.6.5+ds/prog/ecalc.cpp:5:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23,
from /build/reproducible-path/gemmi-0.6.5+ds/prog/map2sf.cpp:10:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23,
from /build/reproducible-path/gemmi-0.6.5+ds/prog/mapcoef.cpp:11:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
[ 81%] Building CXX object CMakeFiles/gemmi_py.dir/python/topo.cpp.o
/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/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-0.6.5+ds/python/topo.cpp
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23,
from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz2cif.hpp:14,
from /build/reproducible-path/gemmi-0.6.5+ds/prog/merge.cpp:12:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23,
from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/cif2mtz.hpp:15,
from /build/reproducible-path/gemmi-0.6.5+ds/python/hkl.cpp:9:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/pdb.hpp:23,
from /build/reproducible-path/gemmi-0.6.5+ds/python/read.cpp:7:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
[ 83%] Building CXX object CMakeFiles/gemmi_py.dir/python/unitcell.cpp.o
/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/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-0.6.5+ds/python/unitcell.cpp
[ 85%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o
/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/reindex.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/reindex.cpp
[ 87%] Building CXX object CMakeFiles/gemmi_py.dir/python/write.cpp.o
/usr/bin/c++ -Dgemmi_py_EXPORTS -I/build/reproducible-path/gemmi-0.6.5+ds/include -isystem /usr/include/python3.13 -isystem /usr/lib/python3/dist-packages/pybind11/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -flto -fno-fat-lto-objects -MD -MT CMakeFiles/gemmi_py.dir/python/write.cpp.o -MF CMakeFiles/gemmi_py.dir/python/write.cpp.o.d -o CMakeFiles/gemmi_py.dir/python/write.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/python/write.cpp
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23,
from /build/reproducible-path/gemmi-0.6.5+ds/prog/reindex.cpp:9:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
[ 87%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o
/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/residues.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/residues.cpp
[ 89%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o
/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/rmsz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/rmsz.cpp
[ 91%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o
/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sf2map.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/sf2map.cpp
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19,
from /build/reproducible-path/gemmi-0.6.5+ds/prog/sf2map.cpp:6:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
[ 91%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o
/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sfcalc.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp
[ 93%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o
/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/sg.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/sg.cpp
[ 93%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o
/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/tags.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/tags.cpp
[ 95%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o
/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/validate.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/validate.cpp
[ 95%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o
/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/validate_mon.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/validate_mon.cpp
[ 97%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o
/usr/bin/c++ -DGEMMI_ALL_IN_ONE=1 -I/build/reproducible-path/gemmi-0.6.5+ds/third_party -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o -MF CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o.d -o CMakeFiles/gemmi_prog.dir/prog/wcn.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/prog/wcn.cpp
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/ccp4.hpp:19,
from /build/reproducible-path/gemmi-0.6.5+ds/prog/sfcalc.cpp:9:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
[100%] Building CXX object CMakeFiles/gemmi_prog.dir/prog/xds2mtz.cpp.o
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In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/xds_ascii.hpp:11,
from /build/reproducible-path/gemmi-0.6.5+ds/prog/xds2mtz.cpp:8:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/prog/wcn.cpp:10:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
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/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -MF CMakeFiles/check_conn.dir/examples/check_conn.cpp.o.d -o CMakeFiles/check_conn.dir/examples/check_conn.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/examples/check_conn.cpp
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/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -MF CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o.d -o CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/newmtz.cpp
[ 45%] Building CXX object CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o
/usr/bin/c++ -I/build/reproducible-path/gemmi-0.6.5+ds/include -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++17 -fvisibility=hidden -fvisibility-inlines-hidden -MD -MT CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -MF CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o.d -o CMakeFiles/doc_maybegz.dir/docs/code/mutate.cpp.o -c /build/reproducible-path/gemmi-0.6.5+ds/docs/code/mutate.cpp
Consolidate compiler generated dependencies of target gemmi_prog
make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu'
make -f CMakeFiles/gemmi_prog.dir/build.make CMakeFiles/gemmi_prog.dir/build
make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu'
make[5]: Nothing to be done for 'CMakeFiles/gemmi_prog.dir/build'.
make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu'
[ 87%] Built target gemmi_prog
make -f CMakeFiles/print-version.dir/build.make CMakeFiles/print-version.dir/depend
make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu'
cd /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/CMakeFiles/print-version.dir/DependInfo.cmake "--color="
make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu'
make -f CMakeFiles/print-version.dir/build.make CMakeFiles/print-version.dir/build
make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu'
[ 87%] gemmi --version
cd /build/reproducible-path/gemmi-0.6.5+ds && /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu/gemmi --version
gemmi 0.6.5
make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu'
[ 87%] Built target print-version
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mtz.hpp:23,
from /build/reproducible-path/gemmi-0.6.5+ds/docs/code/newmtz.cpp:1:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10,
from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mmread.hpp:12,
from /build/reproducible-path/gemmi-0.6.5+ds/docs/code/maybegz.cpp:2:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
In file included from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/json.hpp:10,
from /build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/mmread.hpp:12,
from /build/reproducible-path/gemmi-0.6.5+ds/tests/disulf.cpp:11:
/build/reproducible-path/gemmi-0.6.5+ds/include/gemmi/fileutil.hpp:37:58: warning: ignoring attributes on template argument 'int (*)(FILE*)' [-Wignored-attributes]
37 | typedef std::unique_ptr<std::FILE, decltype(&std::fclose)> fileptr_t;
| ^
[ 89%] Linking CXX executable doc_example
/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_example.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/doc_example.dir/link.d CMakeFiles/doc_example.dir/docs/code/sym.cpp.o CMakeFiles/doc_example.dir/docs/code/elem.cpp.o CMakeFiles/doc_example.dir/docs/code/resinfo.cpp.o CMakeFiles/doc_example.dir/docs/code/cell.cpp.o CMakeFiles/doc_example.dir/src/resinfo.cpp.o -o doc_example
make[5]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu'
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[ 91%] Linking CXX executable doc_newmtz
/usr/bin/cmake -E cmake_link_script CMakeFiles/doc_newmtz.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/gemmi-0.6.5+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fexcess-precision=fast -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/doc_newmtz.dir/link.d CMakeFiles/doc_newmtz.dir/docs/code/newmtz.cpp.o -o doc_newmtz libgemmi_cpp.a /usr/lib/x86_64-linux-gnu/libz.so
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[ 97%] Linking CXX executable doc_maybegz
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make -f CMakeFiles/check.dir/build.make CMakeFiles/check.dir/depend
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make[5]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu'
/usr/bin/ctest -C None
Test project /build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu
Connected to MAKE jobserver
Start 1: cpptest
1/1 Test #1: cpptest .......................... Passed 0.00 sec
100% tests passed, 0 tests failed out of 1
Total Test time (real) = 0.01 sec
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PYTHONPATH=$(find . -name 'obj-*') pytest-3 -k 'not test_sfcalc_'
........................................................................ [ 38%]
.............................s.................s......sssssssssssssss... [ 76%]
............................................. [100%]
=========================== short test summary info ============================
SKIPPED [1] tests/test_mol.py:535: BioPython not installed.
SKIPPED [1] tests/test_monlib.py:110: $CLIBD_MON not defined.
SKIPPED [1] tests/test_prog.py:131: Program gemmi not found.
SKIPPED [1] tests/test_prog.py:140: Program gemmi not found.
SKIPPED [1] tests/test_prog.py:149: Program gemmi not found.
SKIPPED [1] tests/test_prog.py:47: Program gemmi not found.
SKIPPED [1] tests/test_prog.py:55: Program gemmi not found.
SKIPPED [1] tests/test_prog.py:62: Program gemmi not found.
SKIPPED [1] tests/test_prog.py:68: Program gemmi not found.
SKIPPED [1] tests/test_prog.py:74: Program gemmi not found.
SKIPPED [1] tests/test_prog.py:80: Program gemmi not found.
SKIPPED [1] tests/test_seq.py:127: BioPython not installed.
SKIPPED [1] tests/test_seq.py:132: BioPython not installed.
SKIPPED [1] tests/test_seq.py:139: BioPython not installed.
SKIPPED [1] tests/test_seq.py:146: BioPython not installed.
SKIPPED [1] tests/test_seq.py:105: BioPython not installed.
SKIPPED [1] tests/test_seq.py:114: BioPython not installed.
172 passed, 17 skipped, 2 deselected in 1.04s
make[1]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds'
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=cmake
dh_prep -O--buildsystem=cmake
dh_auto_install -O--buildsystem=cmake
cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/gemmi-0.6.5\+ds/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/build/reproducible-path/gemmi-0.6.5+ds -B/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
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Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/bin/gemmi
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/monlib.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/model.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmread_gz.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/gz.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/blob.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/contact.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pdb_id.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/bessel.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pirfasta.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/stats.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/resinfo.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/recgrid.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/addends.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/chemcomp_xyz.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/math.hpp
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-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/serialize.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/symmetry.hpp
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-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmread.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/smcif.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_cif.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_json.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmcif_impl.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmcif.hpp
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-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/bond_idx.hpp
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-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cif2mtz.hpp
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-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/topo.hpp
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-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/span.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/input.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/atof.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/dencalc.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/iterator.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/refln.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/riding_h.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/floodfill.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fileutil.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/small.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqid.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/neutron92.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/elem.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fprime.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/unitcell.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/scaling.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/crd.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_chemcomp.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/asumask.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/enumstr.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/formfact.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/xds_ascii.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/atox.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/chemcomp.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ddl.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/calculate.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqtools.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cifdoc.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/neighbor.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/seqalign.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/linkhunt.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fstream.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/binner.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/dirwalk.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/select.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/levmar.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/utf.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mtz2cif.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/sprintf.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/sfcalc.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/mmdb.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/metadata.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ccp4.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/polyheur.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/read_map.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/numb.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/cellred.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/fourier.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/twin.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/reciproc.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/modify.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/asudata.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/qcp.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/eig3.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/pdb.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/c4322.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/to_mmcif.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/align.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/version.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/it92.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/ecalc.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/tinydir.h
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/pocketfft_hdronly.h
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/third_party/fast_float.h
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/assembly.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/grid.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/include/gemmi/intensit.hpp
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/x86_64-linux-gnu/libgemmi_cpp.a
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/gemmi/gemmi-targets.cmake
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/gemmi/gemmi-targets-none.cmake
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/gemmi/gemmi-config.cmake
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/gemmi/gemmi-config-version.cmake
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi.cpython-313-x86_64-linux-gnu.so
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/mtz_i_sigi.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/patterson_slice.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/multiproc.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/rama_gather.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/map2mtz.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/rama_plot.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/mtrix_iso.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/col_order.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/aafreq.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/monomers.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/maskdiff.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/cif_i_sigi.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/matthews.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/from_json.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/weight.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/ccd_subgraph.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/refln-stats.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/maskcheck.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/ccd_gi.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/long_geom.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/sub_ccd.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/hello.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/simple_search.py
-- Installing: /build/reproducible-path/gemmi-0.6.5+ds/debian/tmp/usr/lib/python3/dist-packages/gemmi/examples/merge_mtz_mmcif.py
make[1]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds/obj-x86_64-linux-gnu'
dh_install -O--buildsystem=cmake
dh_installdocs -O--buildsystem=cmake
dh_installchangelogs -O--buildsystem=cmake
debian/rules override_dh_installman
make[1]: Entering directory '/build/reproducible-path/gemmi-0.6.5+ds'
help2man 'tail -n +9 docs/gemmi-help.txt' \
--version-string 0.6.5+ds --name 'CLI for GEMMI library' \
--no-info --help-option '' > debian/gemmi.1
sed -i 's/.TH GEMMI-HELP.TXT/.TH gemmi/' debian/gemmi.1
sed -i 's/gemmi-help.txt/gemmi/' debian/gemmi.1
dh_installman
make[1]: Leaving directory '/build/reproducible-path/gemmi-0.6.5+ds'
dh_python3 -O--buildsystem=cmake
dh_installsystemduser -O--buildsystem=cmake
dh_perl -O--buildsystem=cmake
dh_link -O--buildsystem=cmake
dh_strip_nondeterminism -O--buildsystem=cmake
dh_compress -O--buildsystem=cmake
dh_fixperms -O--buildsystem=cmake
dh_missing -O--buildsystem=cmake
dh_dwz -a -O--buildsystem=cmake
dwz: debian/python3-gemmi/usr/lib/python3/dist-packages/gemmi.cpython-313-x86_64-linux-gnu.so: .debug_info section not present
dh_strip -a -O--buildsystem=cmake
dh_makeshlibs -a -O--buildsystem=cmake
dh_shlibdeps -a -O--buildsystem=cmake
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib64/ld-linux-x86-64.so.2
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged
dh_installdeb -O--buildsystem=cmake
dh_gencontrol -O--buildsystem=cmake
dpkg-gencontrol: warning: Provides field of package python3-gemmi: substitution variable ${python3:Provides} used, but is not defined
dh_md5sums -O--buildsystem=cmake
dh_builddeb -O--buildsystem=cmake
dpkg-deb: building package 'gemmi' in '../gemmi_0.6.5+ds-3_amd64.deb'.
dpkg-deb: building package 'gemmi-dbgsym' in '../gemmi-dbgsym_0.6.5+ds-3_amd64.deb'.
dpkg-deb: building package 'gemmi-dev' in '../gemmi-dev_0.6.5+ds-3_amd64.deb'.
dpkg-deb: building package 'python3-gemmi' in '../python3-gemmi_0.6.5+ds-3_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../gemmi_0.6.5+ds-3_amd64.buildinfo
dpkg-genchanges --build=binary -O../gemmi_0.6.5+ds-3_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/2345260 and its subdirectories
I: Current time: Sun Apr 5 02:55:10 -12 2026
I: pbuilder-time-stamp: 1775400910
Mon Mar 3 08:32:13 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net.
Mon Mar 3 08:32:13 UTC 2025 I: Preparing to do remote build '2' on ionos1-amd64.debian.net.
Mon Mar 3 09:16:13 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net.
Mon Mar 3 09:16:14 UTC 2025 I: gemmi_0.6.5+ds-3_amd64.changes:
Format: 1.8
Date: Mon, 03 Feb 2025 09:49:19 -0500
Source: gemmi
Binary: gemmi gemmi-dbgsym gemmi-dev python3-gemmi
Architecture: amd64
Version: 0.6.5+ds-3
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Changed-By: Andrius Merkys <merkys@debian.org>
Description:
gemmi - library for structural biology - executable
gemmi-dev - library for structural biology
python3-gemmi - library for structural biology - Python module
Closes: 1094697
Changes:
gemmi (0.6.5+ds-3) unstable; urgency=medium
.
* Adjust test tolerance (Closes: #1094697)
Checksums-Sha1:
f57feb8ec2c3ad0b1c49bbfdaed9d819a878259c 32769424 gemmi-dbgsym_0.6.5+ds-3_amd64.deb
71a6f3eebb6c386810b1ea14e5684c14d935b0d4 1140160 gemmi-dev_0.6.5+ds-3_amd64.deb
0475f91995e06f1a9d042b3b68a2ce51843f7727 8077 gemmi_0.6.5+ds-3_amd64.buildinfo
2a87290a3112eeddd4d280a7aed8de0f91627bf3 1330024 gemmi_0.6.5+ds-3_amd64.deb
234991ddbb58f6f43e15253f79746c6a5e6d0516 2442292 python3-gemmi_0.6.5+ds-3_amd64.deb
Checksums-Sha256:
7172294449bb0132a6af3e29db8a81c1e7a14042090b4af808bc4f572e4572cf 32769424 gemmi-dbgsym_0.6.5+ds-3_amd64.deb
3cbd7c9eaaeae4e07ee5ea4ea3adeb9cdfa827b2aa086765c4aa7097c1b119a7 1140160 gemmi-dev_0.6.5+ds-3_amd64.deb
95e825b8406fe5d25cb19486079be8d50e7c5c77e56158e72123be80ac654978 8077 gemmi_0.6.5+ds-3_amd64.buildinfo
bd48f73bce747374b86bbe3959df730ebb8ade89603c03830dd8a4d0811dafa6 1330024 gemmi_0.6.5+ds-3_amd64.deb
ab946ca88fb59a9c0a938a4d1e85cc54bc804873309211985538b0ecf86fe903 2442292 python3-gemmi_0.6.5+ds-3_amd64.deb
Files:
2411e291db4b4282a19cb9489752dba9 32769424 debug optional gemmi-dbgsym_0.6.5+ds-3_amd64.deb
4219436c9eb1358bc97a363e5bec0db9 1140160 libdevel optional gemmi-dev_0.6.5+ds-3_amd64.deb
44422a4fac40ca3ba800fa7a60fa6a7d 8077 science optional gemmi_0.6.5+ds-3_amd64.buildinfo
b1ebdbe457e5e3d9c6f568869a287782 1330024 science optional gemmi_0.6.5+ds-3_amd64.deb
f14f8881dd3ec4f8bfecaedc68d3a24c 2442292 python optional python3-gemmi_0.6.5+ds-3_amd64.deb
Mon Mar 3 09:16:15 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-amd64_2-33378.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ulC2Lwkg/gemmi_0.6.5+ds-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ulC2Lwkg/gemmi_0.6.5+ds-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ulC2Lwkg/gemmi_0.6.5+ds-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ulC2Lwkg/b1/gemmi_0.6.5+ds-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ulC2Lwkg/b2/gemmi_0.6.5+ds-3_amd64.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call diffoscope.comparators.binary.FilesystemFile
## main (total time: 0.003s)
0.003s 2 calls outputs
0.000s 1 call cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 219ms
CPU time consumed: 220ms
Mon Mar 3 09:16:15 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Mon Mar 3 09:16:15 UTC 2025 I: gemmi from unstable built successfully and reproducibly on amd64.
Mon Mar 3 09:16:16 UTC 2025 I: Submitting .buildinfo files to external archives:
Mon Mar 3 09:16:16 UTC 2025 I: Submitting 12K b1/gemmi_0.6.5+ds-3_amd64.buildinfo.asc
Mon Mar 3 09:16:18 UTC 2025 I: Submitting 12K b2/gemmi_0.6.5+ds-3_amd64.buildinfo.asc
Mon Mar 3 09:16:20 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Mon Mar 3 09:16:20 UTC 2025 I: Done submitting .buildinfo files.
Mon Mar 3 09:16:20 UTC 2025 I: Removing signed gemmi_0.6.5+ds-3_amd64.buildinfo.asc files:
removed './b1/gemmi_0.6.5+ds-3_amd64.buildinfo.asc'
removed './b2/gemmi_0.6.5+ds-3_amd64.buildinfo.asc'