I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 3 15:03:35 +14 2024 I: pbuilder-time-stamp: 1725325415 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libpdb-redo_1.0.2-2.dsc] I: copying [./libpdb-redo_1.0.2.orig.tar.gz] I: copying [./libpdb-redo_1.0.2-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.6yWxCM15/trustedkeys.kbx': General error gpgv: Signature made Thu Jan 7 00:54:36 2021 +14 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./libpdb-redo_1.0.2-2.dsc dpkg-source: info: extracting libpdb-redo in libpdb-redo-1.0.2 dpkg-source: info: unpacking libpdb-redo_1.0.2.orig.tar.gz dpkg-source: info: unpacking libpdb-redo_1.0.2-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no-data-update.patch dpkg-source: info: applying unit-test.patch dpkg-source: info: applying configure.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2286990/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Sep 3 15:03 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2286990/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2286990/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16 ' DIRSTACK=() DISTRIBUTION=bullseye EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=3c96a28930b741a9b4c31a1acc000cda LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2286990 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.gQUzctiw/pbuilderrc_Vfi6 --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gQUzctiw/b2 --logfile b2/build.log libpdb-redo_1.0.2-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.38-2 (2023-07-27) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jan 21 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 21 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 8 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jan 21 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 21 2022 more -rwsr-xr-x 1 root root 55528 Jan 21 2022 mount -rwxr-xr-x 1 root root 18664 Jan 21 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 9 Sep 3 15:03 sh -> /bin/bash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jan 21 2022 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 21 2022 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 21 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/2286990/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libcifpp-dev (>= 1.0.1), autoconf-archive, libnewuoa-dev, pkg-config, libgsl-dev, libboost-dev, libboost-iostreams-dev, libzeep-dev (>= 5.0.2), libclipper-dev, libccp4-dev (>= 6.5.1-5) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19707 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libcifpp-dev (>= 1.0.1); however: Package libcifpp-dev is not installed. pbuilder-satisfydepends-dummy depends on autoconf-archive; however: Package autoconf-archive is not installed. pbuilder-satisfydepends-dummy depends on libnewuoa-dev; however: Package libnewuoa-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libzeep-dev (>= 5.0.2); however: Package libzeep-dev is not installed. pbuilder-satisfydepends-dummy depends on libclipper-dev; however: Package libclipper-dev is not installed. pbuilder-satisfydepends-dummy depends on libccp4-dev (>= 6.5.1-5); however: Package libccp4-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} autoconf-archive{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} fftw-dev{a} fftw2{a} file{a} gettext{a} gettext-base{a} groff-base{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-date-time-dev{a} libboost-date-time1.74-dev{a} libboost-date-time1.74.0{a} libboost-dev{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-serialization1.74-dev{a} libboost-serialization1.74.0{a} libboost-system-dev{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost1.74-dev{a} libbsd0{a} libccp4-data{a} libccp4-dev{a} libccp4c0{a} libccp4f0{a} libcifpp-dev{a} libcifpp1{a} libclipper-dev{a} libclipper2{a} libdebhelper-perl{a} libelf1{a} libevent-core-2.1-7{a} libevent-pthreads-2.1-7{a} libfabric1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgsl-dev{a} libgsl25{a} libgslcblas0{a} libhwloc-plugins{a} libhwloc15{a} libibverbs1{a} libicu-dev{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmmdb2-0{a} libmmdb2-dev{a} libnewuoa-dev{a} libnewuoa0{a} libnl-3-200{a} libnl-route-3-200{a} libnuma1{a} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpmix2{a} libpsm-infinipath1{a} libpsm2-2{a} librdmacm1{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libucx0{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libzeep-dev{a} libzeep5{a} m4{a} man-db{a} ocl-icd-libopencl1{a} pkg-config{a} po-debconf{a} sensible-utils{a} sfftw-dev{a} sfftw2{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 102 newly installed, 0 to remove and 0 not upgraded. Need to get 59.9 MB of archives. After unpacking 363 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 autoconf-archive all 20190106-2.1 [746 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-1 [139 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-1 [57.1 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libnl-3-200 amd64 3.4.0-1+b1 [63.6 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libnl-route-3-200 amd64 3.4.0-1+b1 [161 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libibverbs1 amd64 33.2-1 [59.4 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 ibverbs-providers amd64 33.2-1 [253 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.1 [169 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libnuma1 amd64 2.0.12-1+b1 [26.3 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libpsm2-2 amd64 11.2.185-1 [181 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 librdmacm1 amd64 33.2-1 [68.9 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libfabric1 amd64 1.11.0-2 [521 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libhwloc15 amd64 2.4.1+dfsg-1 [150 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1 [311 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1 [772 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libxnvctrl0 amd64 470.141.03-1~deb11u1 [27.5 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 ocl-icd-libopencl1 amd64 2.2.14-2 [42.5 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libhwloc-plugins amd64 2.4.1+dfsg-1 [21.4 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libpmix2 amd64 4.0.0-4.1 [552 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libucx0 amd64 1.10.1~rc1+really.1.10.0-1 [649 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libopenmpi3 amd64 4.1.0-10 [2370 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 fftw2 amd64 2.1.5-4.2+b1 [239 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 fftw-dev amd64 2.1.5-4.2+b1 [262 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 icu-devtools amd64 67.1-7 [201 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 libboost1.74-dev amd64 1.74.0-9 [9534 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 libboost-date-time1.74.0 amd64 1.74.0-9 [241 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libboost-serialization1.74.0 amd64 1.74.0-9 [340 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libboost-serialization1.74-dev amd64 1.74.0-9 [383 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libboost-date-time1.74-dev amd64 1.74.0-9 [250 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libboost-date-time-dev amd64 1.74.0.3 [4332 B] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libboost-regex1.74.0 amd64 1.74.0-9 [516 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libicu-dev amd64 67.1-7 [9597 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libboost-regex1.74-dev amd64 1.74.0-9 [588 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libboost-iostreams1.74-dev amd64 1.74.0-9 [273 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libboost-iostreams-dev amd64 1.74.0.3 [4316 B] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libboost-program-options1.74.0 amd64 1.74.0-9 [356 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libboost-program-options1.74-dev amd64 1.74.0-9 [386 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libboost-program-options-dev amd64 1.74.0.3 [4340 B] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libboost-system1.74.0 amd64 1.74.0-9 [241 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libboost-system1.74-dev amd64 1.74.0-9 [243 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libboost-system-dev amd64 1.74.0.3 [4468 B] Get: 81 http://deb.debian.org/debian bullseye/main amd64 libccp4-data all 6.5.1-5 [61.6 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libccp4c0 amd64 6.5.1-5 [88.3 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libmmdb2-0 amd64 2.0.5-1 [333 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 libccp4f0 amd64 6.5.1-5 [231 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libccp4-dev amd64 6.5.1-5 [42.8 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libcifpp1 amd64 1.0.1-3 [1447 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libcifpp-dev amd64 1.0.1-3 [65.1 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 sfftw2 amd64 2.1.5-4.2+b1 [235 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libclipper2 amd64 2.1.20201109-1 [1156 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libmmdb2-dev amd64 2.0.5-1 [91.9 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 sfftw-dev amd64 2.1.5-4.2+b1 [259 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 libclipper-dev amd64 2.1.20201109-1 [82.6 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1 [1370 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 libgslcblas0 amd64 2.6+dfsg-2 [102 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 libgsl25 amd64 2.6+dfsg-2 [934 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 libgsl-dev amd64 2.6+dfsg-2 [1123 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 libnewuoa0 amd64 0.1.1-2 [18.4 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 libnewuoa-dev amd64 0.1.1-2 [4924 B] Get: 100 http://deb.debian.org/debian bullseye/main amd64 libzeep5 amd64 5.0.2-3 [668 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 libzeep-dev amd64 5.0.2-3 [1058 kB] Fetched 59.9 MB in 1s (42.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting 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Selecting previously unselected package libboost-date-time-dev:amd64. Preparing to unpack .../067-libboost-date-time-dev_1.74.0.3_amd64.deb ... Unpacking libboost-date-time-dev:amd64 (1.74.0.3) ... Selecting previously unselected package libboost-dev:amd64. Preparing to unpack .../068-libboost-dev_1.74.0.3_amd64.deb ... Unpacking libboost-dev:amd64 (1.74.0.3) ... Selecting previously unselected package libboost-regex1.74.0:amd64. Preparing to unpack .../069-libboost-regex1.74.0_1.74.0-9_amd64.deb ... Unpacking libboost-regex1.74.0:amd64 (1.74.0-9) ... Selecting previously unselected package libicu-dev:amd64. Preparing to unpack .../070-libicu-dev_67.1-7_amd64.deb ... Unpacking libicu-dev:amd64 (67.1-7) ... Selecting previously unselected package libboost-regex1.74-dev:amd64. Preparing to unpack .../071-libboost-regex1.74-dev_1.74.0-9_amd64.deb ... Unpacking libboost-regex1.74-dev:amd64 (1.74.0-9) ... Selecting previously unselected package libboost-iostreams1.74-dev:amd64. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2286990/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bullseye I: user script /srv/workspace/pbuilder/2286990/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/libpdb-redo-1.0.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libpdb-redo_1.0.2-2_source.changes dpkg-buildpackage: info: source package libpdb-redo dpkg-buildpackage: info: source version 1.0.2-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Maarten L. Hekkelman dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac, libtoolize: and rerunning libtoolize and aclocal. libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am. debian/rules override_dh_auto_configure make[1]: Entering directory '/build/libpdb-redo-1.0.2' dh_auto_configure -- --enable-shared --disable-static ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-shared --disable-static checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether g++ supports C++17 features with -std=c++17... yes checking for a BSD-compatible install... /usr/bin/install -c checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking for gawk... no checking for mawk... mawk checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... g++ -std=c++17 -E checking for ld used by g++ -std=c++17... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ -std=c++17 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ -std=c++17 option to produce PIC... -fPIC -DPIC checking if g++ -std=c++17 PIC flag -fPIC -DPIC works... yes checking if g++ -std=c++17 static flag -static works... yes checking if g++ -std=c++17 supports -c -o file.o... yes checking if g++ -std=c++17 supports -c -o file.o... (cached) yes checking whether the g++ -std=c++17 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether C++ compiler accepts -fstandalone-debug... no checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for mrc... USE_RSRC=1 checking for sin in -lm... yes checking for gsl ... yes checking whether gcc is Clang... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking whether more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking for boostlib >= 1.71 (107100)... yes checking whether the Boost::IOStreams library is available... yes checking for exit in -lboost_iostreams... yes checking filesystem usability... yes checking filesystem presence... yes checking for filesystem... yes checking endian.h usability... yes checking endian.h presence... yes checking for endian.h... yes checking for libcifpp ... yes checking for libzeep ... yes checking for clipper ... yes checking clipper version... ok checking dlib/global_optimization.h usability... no checking dlib/global_optimization.h presence... no checking for dlib/global_optimization.h... no configure: WARNING: libdlib-dev not found checking for newuoa ... yes configure: creating ./config.status config.status: creating GNUmakefile config.status: creating libpdb-redo.pc config.status: creating src/config.hpp config.status: executing libtool commands make[1]: Leaving directory '/build/libpdb-redo-1.0.2' dh_auto_build make -j16 make[1]: Entering directory '/build/libpdb-redo-1.0.2' mkdir -p obj >> src/AtomShape.cpp >> src/BondMap.cpp >> src/ClipperWrapper.cpp >> src/DistanceMap.cpp >> src/MapMaker.cpp >> src/Minimizer.cpp >> src/Ramachandran.cpp >> src/ResolutionCalculator.cpp >> src/Restraints.cpp >> src/SkipList.cpp >> src/Statistics.cpp >> src/Symmetry-2.cpp /bin/sh /build/libpdb-redo-1.0.2/libtool --silent --tag=CXX --mode=link g++ -std=c++17 -g -O2 -fdebug-prefix-map=/build/libpdb-redo-1.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wall -Wno-multichar -I include -O2 -DDATADIR='"/usr/share/libpdb-redo"' -DNDEBUG -Wl,-z,relro -Wl,-z,now -pthread -version-info 1:0:0 -o libpdb-redo.la -rpath /usr/lib/x86_64-linux-gnu obj/AtomShape.lo obj/BondMap.lo obj/ClipperWrapper.lo obj/DistanceMap.lo obj/MapMaker.lo obj/Minimizer.lo obj/Ramachandran.lo obj/ResolutionCalculator.lo obj/Restraints.lo obj/SkipList.lo obj/Statistics.lo obj/Symmetry-2.lo -lcifpp -lzeep -lgsl -lgslcblas -lm -lnewuoa -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lboost_iostreams -lm make[1]: Leaving directory '/build/libpdb-redo-1.0.2' debian/rules override_dh_auto_test make[1]: Entering directory '/build/libpdb-redo-1.0.2' make test make[2]: Entering directory '/build/libpdb-redo-1.0.2' >> test/unit-test.cpp >>> building unit-test g++ -std=c++17 -g -O2 -fdebug-prefix-map=/build/libpdb-redo-1.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wall -Wno-multichar -I include -O2 -DDATADIR='"/usr/share/libpdb-redo"' -DNDEBUG -Wl,-z,relro -Wl,-z,now -pthread -o test/unit-test obj/unit-test.o -L.libs -lpdb-redo -lcifpp -lzeep -lgsl -lgslcblas -lm -lnewuoa -lclipper-fortran -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -lboost_iostreams -lm cd test; BOND_INFO_FILE=/build/libpdb-redo-1.0.2/rsrc/bond-info.bin.gz LD_LIBRARY_PATH=../.libs ./unit-test Running 7 test cases... Missing bond information for compound U_K Missing information for compound 'U_K' Missing bond information for compound U_K *** No errors detected make[2]: Leaving directory '/build/libpdb-redo-1.0.2' make[1]: Leaving directory '/build/libpdb-redo-1.0.2' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j1 install DESTDIR=/build/libpdb-redo-1.0.2/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/libpdb-redo-1.0.2' install -d /build/libpdb-redo-1.0.2/debian/tmp/usr/lib/x86_64-linux-gnu /bin/sh /build/libpdb-redo-1.0.2/libtool --mode=install install libpdb-redo.la /build/libpdb-redo-1.0.2/debian/tmp/usr/lib/x86_64-linux-gnu libtool: install: install .libs/libpdb-redo.so.1.0.0 /build/libpdb-redo-1.0.2/debian/tmp/usr/lib/x86_64-linux-gnu/libpdb-redo.so.1.0.0 libtool: install: (cd /build/libpdb-redo-1.0.2/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libpdb-redo.so.1.0.0 libpdb-redo.so.1 || { rm -f libpdb-redo.so.1 && ln -s libpdb-redo.so.1.0.0 libpdb-redo.so.1; }; }) libtool: install: (cd /build/libpdb-redo-1.0.2/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libpdb-redo.so.1.0.0 libpdb-redo.so || { rm -f libpdb-redo.so && ln -s libpdb-redo.so.1.0.0 libpdb-redo.so; }; }) libtool: install: install .libs/libpdb-redo.lai /build/libpdb-redo-1.0.2/debian/tmp/usr/lib/x86_64-linux-gnu/libpdb-redo.la libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' install -d /build/libpdb-redo-1.0.2/debian/tmp/usr/include/pdb-redo for f in AtomShape.hpp BondMap.hpp ClipperWrapper.hpp DistanceMap.hpp MapMaker.hpp Minimizer.hpp Ramachandran.hpp ResolutionCalculator.hpp Restraints.hpp SkipList.hpp Statistics.hpp Symmetry-2.hpp; do install include/pdb-redo/$f /build/libpdb-redo-1.0.2/debian/tmp/usr/include/pdb-redo/$f; done install -d /build/libpdb-redo-1.0.2/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig install -m 644 libpdb-redo.pc /build/libpdb-redo-1.0.2/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/libpdb-redo.pc install -d /build/libpdb-redo-1.0.2/debian/tmp/usr/share/libpdb-redo install -m 644 rsrc/bond-info.bin.gz /build/libpdb-redo-1.0.2/debian/tmp/usr/share/libpdb-redo/bond-info.bin make[1]: Leaving directory '/build/libpdb-redo-1.0.2' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libpdb-redo1-dbgsym' in '../libpdb-redo1-dbgsym_1.0.2-2_amd64.deb'. dpkg-deb: building package 'libpdb-redo-dev' in '../libpdb-redo-dev_1.0.2-2_amd64.deb'. dpkg-deb: building package 'libpdb-redo1' in '../libpdb-redo1_1.0.2-2_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libpdb-redo_1.0.2-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2286990/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2286990/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2286990 and its subdirectories I: Current time: Tue Sep 3 15:12:12 +14 2024 I: pbuilder-time-stamp: 1725325932