I: pbuilder: network access will be disabled during build
I: Current time: Wed Dec 10 21:27:31 +14 2025
I: pbuilder-time-stamp: 1765351651
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: using eatmydata during job
I: Copying source file
I: copying [libpdb-redo_3.1.5-5.dsc]
I: copying [./libpdb-redo_3.1.5.orig.tar.gz]
I: copying [./libpdb-redo_3.1.5-5.debian.tar.xz]
I: Extracting source
gpgv: Signature made Thu Oct 31 22:16:16 2024 
gpgv:                using RSA key A72B6824226BB407E24B9E80587503EC7AE7EDCE
gpgv:                issuer "maarten@hekkelman.com"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./libpdb-redo_3.1.5-5.dsc: no acceptable signature found
dpkg-source: info: extracting libpdb-redo in libpdb-redo-3.1.5
dpkg-source: info: unpacking libpdb-redo_3.1.5.orig.tar.gz
dpkg-source: info: unpacking libpdb-redo_3.1.5-5.debian.tar.xz
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/16263/tmp/hooks/D01_modify_environment starting
debug: Running on infom08-i386.
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 Dec 10 07:27 /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/16263/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/16263/tmp/hooks/D02_print_environment starting
I: set
  BASH=/bin/sh
  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
  BASH_ALIASES=()
  BASH_ARGC=()
  BASH_ARGV=()
  BASH_CMDS=()
  BASH_LINENO=([0]="12" [1]="0")
  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
  BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
  BASH_VERSION='5.2.32(1)-release'
  BUILDDIR=/build/reproducible-path
  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
  BUILDUSERNAME=pbuilder2
  BUILD_ARCH=i386
  DEBIAN_FRONTEND=noninteractive
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 '
  DIRSTACK=()
  DISTRIBUTION=unstable
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=i686
  HOST_ARCH=i386
  IFS=' 	
  '
  INVOCATION_ID=668f09e6c7964648bff6a104cc0d9ac2
  LANG=C
  LANGUAGE=de_CH:de
  LC_ALL=C
  LD_LIBRARY_PATH=/usr/lib/libeatmydata
  LD_PRELOAD=libeatmydata.so
  MACHTYPE=i686-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=16263
  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.qWBRMgRI/pbuilderrc_D2l4 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qWBRMgRI/b2 --logfile b2/build.log libpdb-redo_3.1.5-5.dsc'
  SUDO_GID=111
  SUDO_UID=104
  SUDO_USER=jenkins
  TERM=unknown
  TZ=/usr/share/zoneinfo/Etc/GMT-14
  UID=0
  USER=root
  _='I: set'
I: uname -a
  Linux i-capture-the-hostname 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Aug  4  2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/16263/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: i386
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: debhelper-compat (= 13), libcifpp-dev (>= 7), cmake, libnewuoa-dev (>= 0.1.2), pkgconf, libgsl-dev, libboost-dev, libboost-regex-dev, libeigen3-dev, libclipper-dev, zlib1g-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 ... 19954 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 (>= 7); however:
  Package libcifpp-dev is not installed.
 pbuilder-satisfydepends-dummy depends on cmake; however:
  Package cmake is not installed.
 pbuilder-satisfydepends-dummy depends on libnewuoa-dev (>= 0.1.2); however:
  Package libnewuoa-dev is not installed.
 pbuilder-satisfydepends-dummy depends on pkgconf; however:
  Package pkgconf 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-regex-dev; however:
  Package libboost-regex-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libeigen3-dev; however:
  Package libeigen3-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libclipper-dev; however:
  Package libclipper-dev is not installed.
 pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
  Package zlib1g-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} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{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} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-dev{a} libboost-regex-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost1.83-dev{a} libbrotli1{a} libccp4-data{a} libccp4-dev{a} libccp4c0t64{a} libccp4f0t64{a} libcifpp-data{a} libcifpp-dev{a} libcifpp7{a} libclipper-dev{a} libclipper2{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libeigen3-dev{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libgssapi-krb5-2{a} libhwloc15{a} libicu-dev{a} libicu72{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libmmdb2-0{a} libmmdb2-dev{a} libmpich12{a} libnewuoa-dev{a} libnewuoa0{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{a} sfftw-dev{a} sfftw2{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  ca-certificates curl krb5-locales libarchive-cpio-perl libhwloc-plugins libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget 
0 packages upgraded, 88 newly installed, 0 to remove and 0 not upgraded.
Need to get 72.3 MB of archives. After unpacking 412 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main i386 libproc2-0 i386 2:4.0.4-6 [65.7 kB]
Get: 2 http://deb.debian.org/debian unstable/main i386 procps i386 2:4.0.4-6 [876 kB]
Get: 3 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 4 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 5 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 6 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 7 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-2 [201 kB]
Get: 8 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 9 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-5 [1196 kB]
Get: 10 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-10 [102 kB]
Get: 11 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 12 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 13 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB]
Get: 14 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB]
Get: 15 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 16 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 17 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-2 [723 kB]
Get: 18 http://deb.debian.org/debian unstable/main i386 cmake-data all 3.30.5-1 [2223 kB]
Get: 19 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5+b1 [9583 kB]
Get: 20 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.1 [733 kB]
Get: 21 http://deb.debian.org/debian unstable/main i386 libarchive13t64 i386 3.7.4-1.1 [390 kB]
Get: 22 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b5 [298 kB]
Get: 23 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB]
Get: 24 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.1-1+b1 [23.4 kB]
Get: 25 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB]
Get: 26 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B]
Get: 27 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-3 [350 kB]
Get: 28 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB]
Get: 29 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB]
Get: 30 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB]
Get: 31 http://deb.debian.org/debian unstable/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3+b1 [200 kB]
Get: 32 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB]
Get: 33 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB]
Get: 34 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB]
Get: 35 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB]
Get: 36 http://deb.debian.org/debian unstable/main i386 libcurl4t64 i386 8.10.1-2 [391 kB]
Get: 37 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.3-2 [107 kB]
Get: 38 http://deb.debian.org/debian unstable/main i386 libjsoncpp26 i386 1.9.6-2 [90.0 kB]
Get: 39 http://deb.debian.org/debian unstable/main i386 librhash1 i386 1.4.5-1 [144 kB]
Get: 40 http://deb.debian.org/debian unstable/main i386 libuv1t64 i386 1.48.0-7 [157 kB]
Get: 41 http://deb.debian.org/debian unstable/main i386 cmake i386 3.30.5-1 [12.5 MB]
Get: 42 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.20 [89.7 kB]
Get: 43 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-8 [517 kB]
Get: 44 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 45 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 46 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 47 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 48 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 49 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 50 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-2 [1631 kB]
Get: 51 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 52 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 53 http://deb.debian.org/debian unstable/main i386 debhelper all 13.20 [915 kB]
Get: 54 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.2.0-8 [735 kB]
Get: 55 http://deb.debian.org/debian unstable/main i386 libhwloc15 i386 2.11.2-1 [177 kB]
Get: 56 http://deb.debian.org/debian unstable/main i386 libmpich12 i386 4.2.0-14 [1518 kB]
Get: 57 http://deb.debian.org/debian unstable/main i386 fftw2 i386 2.1.5-7 [196 kB]
Get: 58 http://deb.debian.org/debian unstable/main i386 fftw-dev i386 2.1.5-7 [234 kB]
Get: 59 http://deb.debian.org/debian unstable/main i386 icu-devtools i386 72.1-5+b1 [218 kB]
Get: 60 http://deb.debian.org/debian unstable/main i386 libboost1.83-dev i386 1.83.0-3.2 [10.6 MB]
Get: 61 http://deb.debian.org/debian unstable/main i386 libboost-dev i386 1.83.0.2+b2 [3840 B]
Get: 62 http://deb.debian.org/debian unstable/main i386 libboost-regex1.83.0 i386 1.83.0-3.2 [329 kB]
Get: 63 http://deb.debian.org/debian unstable/main i386 libicu-dev i386 72.1-5+b1 [10.6 MB]
Get: 64 http://deb.debian.org/debian unstable/main i386 libboost-regex1.83-dev i386 1.83.0-3.2 [347 kB]
Get: 65 http://deb.debian.org/debian unstable/main i386 libboost-regex-dev i386 1.83.0.2+b2 [3872 B]
Get: 66 http://deb.debian.org/debian unstable/main i386 libccp4-data all 8.0.0-4 [62.7 kB]
Get: 67 http://deb.debian.org/debian unstable/main i386 libccp4c0t64 i386 8.0.0-4 [96.4 kB]
Get: 68 http://deb.debian.org/debian unstable/main i386 libmmdb2-0 i386 2.0.22-1+b2 [370 kB]
Get: 69 http://deb.debian.org/debian unstable/main i386 libccp4f0t64 i386 8.0.0-4 [184 kB]
Get: 70 http://deb.debian.org/debian unstable/main i386 libccp4-dev i386 8.0.0-4 [42.9 kB]
Get: 71 http://deb.debian.org/debian unstable/main i386 libcifpp-data all 7.0.7-3 [484 kB]
Get: 72 http://deb.debian.org/debian unstable/main i386 libcifpp7 i386 7.0.7-3 [1074 kB]
Get: 73 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Get: 74 http://deb.debian.org/debian unstable/main i386 libcifpp-dev i386 7.0.7-3 [111 kB]
Get: 75 http://deb.debian.org/debian unstable/main i386 sfftw2 i386 2.1.5-7 [192 kB]
Get: 76 http://deb.debian.org/debian unstable/main i386 libclipper2 i386 2.1.20201109-2+b3 [1191 kB]
Get: 77 http://deb.debian.org/debian unstable/main i386 libmmdb2-dev i386 2.0.22-1+b2 [92.9 kB]
Get: 78 http://deb.debian.org/debian unstable/main i386 sfftw-dev i386 2.1.5-7 [230 kB]
Get: 79 http://deb.debian.org/debian unstable/main i386 libclipper-dev i386 2.1.20201109-2+b3 [82.4 kB]
Get: 80 http://deb.debian.org/debian unstable/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB]
Get: 81 http://deb.debian.org/debian unstable/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB]
Get: 82 http://deb.debian.org/debian unstable/main i386 pkgconf i386 1.8.1-4 [26.2 kB]
Get: 83 http://deb.debian.org/debian unstable/main i386 libeigen3-dev all 3.4.0-4 [1041 kB]
Get: 84 http://deb.debian.org/debian unstable/main i386 libgslcblas0 i386 2.8+dfsg-5 [106 kB]
Get: 85 http://deb.debian.org/debian unstable/main i386 libgsl28 i386 2.8+dfsg-5 [978 kB]
Get: 86 http://deb.debian.org/debian unstable/main i386 libgsl-dev i386 2.8+dfsg-5 [1240 kB]
Get: 87 http://deb.debian.org/debian unstable/main i386 libnewuoa0 i386 0.1.2-1 [18.7 kB]
Get: 88 http://deb.debian.org/debian unstable/main i386 libnewuoa-dev i386 0.1.2-1 [7504 B]
Fetched 72.3 MB in 1s (70.1 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libproc2-0:i386.
(Reading database ... 
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(Reading database ... 19954 files and directories currently installed.)
Preparing to unpack .../00-libproc2-0_2%3a4.0.4-6_i386.deb ...
Unpacking libproc2-0:i386 (2:4.0.4-6) ...
Selecting previously unselected package procps.
Preparing to unpack .../01-procps_2%3a4.0.4-6_i386.deb ...
Unpacking procps (2:4.0.4-6) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../02-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:i386.
Preparing to unpack .../04-libmagic1t64_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic1t64:i386 (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../05-file_1%3a5.45-3+b1_i386.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../06-gettext-base_0.22.5-2_i386.deb ...
Unpacking gettext-base (0.22.5-2) ...
Selecting previously unselected package libuchardet0:i386.
Preparing to unpack .../07-libuchardet0_0.0.8-1+b2_i386.deb ...
Unpacking libuchardet0:i386 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../08-groff-base_1.23.0-5_i386.deb ...
Unpacking groff-base (1.23.0-5) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../09-bsdextrautils_2.40.2-10_i386.deb ...
Unpacking bsdextrautils (2.40.2-10) ...
Selecting previously unselected package libpipeline1:i386.
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Reading package lists...
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 -> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/16263/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/16263/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/libpdb-redo-3.1.5/ && 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_3.1.5-5_source.changes
dpkg-buildpackage: info: source package libpdb-redo
dpkg-buildpackage: info: source version 3.1.5-5
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Maarten L. Hekkelman <maarten@hekkelman.com>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
 debian/rules clean
dh clean
   dh_clean
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5'
dh_auto_configure -- -DBUILD_SHARED_LIBS=ON -DPDB_REDO_BUILD_TESTS=ON -DBUILD_MINIMIZER=OFF
	cd obj-i686-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb 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/i386-linux-gnu -DBUILD_SHARED_LIBS=ON -DPDB_REDO_BUILD_TESTS=ON -DBUILD_MINIMIZER=OFF ..
-- The CXX compiler identification is GNU 14.2.0
-- The C compiler identification is GNU 14.2.0
-- Detecting CXX compiler ABI info
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-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
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-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Looking for ccp4/ccp4_general.h - /usr/include
-- Found CCP4: /usr/lib/i386-linux-gnu/libccp4c.so
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for clipper/clipper.h - /usr/include
-- Found CCP4: /usr/lib/i386-linux-gnu/libclipper-core.so
-- FFTW2 libraries - /usr/lib/libsfftw.so
--                 - /usr/lib/libsrfftw.so
-- FFTW2 header directory - /usr/include
-- Performing Test _LINKING_WITH_CLIPPER_CORE
-- Performing Test _LINKING_WITH_CLIPPER_CORE - Success
-- Looking for clipper/clipper-ccp4.h - /usr/include
-- Found CCP4: /usr/lib/i386-linux-gnu/libclipper-ccp4.so
-- Looking for clipper/clipper-contrib.h - /usr/include
-- Found CCP4: /usr/lib/i386-linux-gnu/libclipper-contrib.so
-- CCP4 include directory: /usr/include
-- Found ZLIB: /usr/lib/i386-linux-gnu/libz.so (found version "1.3.1")
-- Git hash not found
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- Looking for ccp4/ccp4_general.h - /usr/include
-- Found CCP4: /usr/lib/i386-linux-gnu/libccp4c.so
-- Looking for clipper/clipper.h - /usr/include
-- Found CCP4: /usr/lib/i386-linux-gnu/libclipper-core.so
-- FFTW2 libraries - /usr/lib/libsfftw.so
--                 - /usr/lib/libsrfftw.so
-- FFTW2 header directory - /usr/include
-- Looking for clipper/clipper-ccp4.h - /usr/include
-- Found CCP4: /usr/lib/i386-linux-gnu/libclipper-ccp4.so
-- Looking for clipper/clipper-contrib.h - /usr/include
-- Found CCP4: /usr/lib/i386-linux-gnu/libclipper-contrib.so
-- CCP4 include directory: /usr/include
-- Configuring done (2.5s)
-- Generating done (0.0s)
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_EXPORT_NO_PACKAGE_REGISTRY
    CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
    FETCHCONTENT_FULLY_DISCONNECTED
    PDB_REDO_BUILD_TESTS


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cd /build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libpdb-redo-3.1.5 /build/reproducible-path/libpdb-redo-3.1.5 /build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu /build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu /build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu/CMakeFiles/pdb-redo.dir/DependInfo.cmake "--color="
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[  5%] Building CXX object CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o
/usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o -MF CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/AtomShape.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/src/AtomShape.cpp
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/usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o -MF CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/BondMap.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/src/BondMap.cpp
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/usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/Compound.cpp.o -MF CMakeFiles/pdb-redo.dir/src/Compound.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/Compound.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/src/Compound.cpp
/usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o -MF CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/DistanceMap.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/src/DistanceMap.cpp
[ 35%] Building CXX object CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o
/usr/bin/c++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Dpdb_redo_EXPORTS -I/build/reproducible-path/libpdb-redo-3.1.5/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++20 -fPIC -MD -MT CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o -MF CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o.d -o CMakeFiles/pdb-redo.dir/src/MapMaker.cpp.o -c /build/reproducible-path/libpdb-redo-3.1.5/src/MapMaker.cpp
[ 41%] Building CXX object CMakeFiles/pdb-redo.dir/src/Ramachandran.cpp.o
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[ 52%] Building CXX object CMakeFiles/pdb-redo.dir/src/SkipList.cpp.o
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[ 94%] Linking CXX executable pdb-redo-example
cd /build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu/examples && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb-redo-example.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wl,-z,relro -Wl,-z,now "CMakeFiles/pdb-redo-example.dir/example.cpp.o" -o pdb-redo-example  -Wl,-rpath,/build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu ../libpdb-redo.so.3.1.5 /usr/lib/i386-linux-gnu/libcifpp.so.7.0.7 /usr/lib/i386-linux-gnu/libz.so /usr/lib/i386-linux-gnu/libnewuoa.so.0.1.2 /usr/lib/i386-linux-gnu/libclipper-ccp4.so /usr/lib/i386-linux-gnu/libclipper-contrib.so /usr/lib/i386-linux-gnu/libclipper-core.so /usr/lib/i386-linux-gnu/libccp4c.so
make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu'
[ 94%] Built target pdb-redo-example
[100%] Linking CXX executable pdb-redo-unit-test
/usr/bin/cmake -E cmake_link_script CMakeFiles/pdb-redo-unit-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libpdb-redo-3.1.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wl,-z,relro -Wl,-z,now "CMakeFiles/pdb-redo-unit-test.dir/test/pdb-redo-unit-test.cpp.o" -o pdb-redo-unit-test  -Wl,-rpath,/build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu libpdb-redo.so.3.1.5 /usr/lib/i386-linux-gnu/libcifpp.so.7.0.7 /usr/lib/i386-linux-gnu/libz.so /usr/lib/i386-linux-gnu/libnewuoa.so.0.1.2 /usr/lib/i386-linux-gnu/libclipper-ccp4.so /usr/lib/i386-linux-gnu/libclipper-contrib.so /usr/lib/i386-linux-gnu/libclipper-core.so /usr/lib/i386-linux-gnu/libccp4c.so
make[3]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu'
[100%] Built target pdb-redo-unit-test
make[2]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu'
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu/CMakeFiles 0
make[1]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu'
   dh_auto_test
	cd obj-i686-linux-gnu && make -j5 test ARGS\+=--verbose ARGS\+=-j5
make[1]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu'
Running tests...
/usr/bin/ctest --force-new-ctest-process --verbose -j5
UpdateCTestConfiguration  from :/build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu/DartConfiguration.tcl
Parse Config file:/build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu/DartConfiguration.tcl
UpdateCTestConfiguration  from :/build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu/DartConfiguration.tcl
Parse Config file:/build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu/DartConfiguration.tcl
Test project /build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
    Start 1: pdb-redo-unit-test

1: Test command: /build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu/pdb-redo-unit-test "--" "/build/reproducible-path/libpdb-redo-3.1.5/test"
1: Working Directory: /build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu
1: Test timeout computed to be: 1500
test 2
    Start 2: pdb-redo-example

2: Test command: /build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu/examples/pdb-redo-example
2: Working Directory: /build/reproducible-path/libpdb-redo-3.1.5/examples
2: Test timeout computed to be: 1500
2: 
2: Configuration error:
2: 
2: The attempt to retrieve compound information for "PRO" failed.
2: 
2: This information is searched for in a CCD file called components.cif or
2: components.cif.gz which should be located in one of the following directories:
2: 
2: "/var/cache/libcifpp"
2: "/usr/share/libcifpp"
2: 
2: (Note that you can add a directory to the search paths by setting the 
2: LIBCIFPP_DATA_DIR environmental variable)
2: 
2: On Linux an optional cron script might have been installed that automatically updates
2: components.cif and mmCIF dictionary files. This script only works when the file
2: libcifpp.conf contains an uncommented line with the text:
2: 
2: update=true
2: 
2: If you do not have a working cron script, you can manually update the files
2: in /var/cache/libcifpp using the following commands:
2: 
2: curl -o /var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif
2: curl -o /var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic
2: curl -o /var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic
2: 
2: No compound factory objects are created since none of the data sources is found.
2: Missing compound bond info for ALA
2: Missing compound bond info for ARG
2: Missing compound bond info for ASN
2: Missing compound bond info for ASP
2: Missing compound bond info for CYS
2: Missing compound bond info for GLN
2: Missing compound bond info for GLU
2: Missing compound bond info for GLY
2: Missing compound bond info for ILE
2: Missing compound bond info for LEU
2: Missing compound bond info for LYS
2: Missing compound bond info for MET
2: Missing compound bond info for PHE
2: Missing compound bond info for PRO
2: Missing compound bond info for REA
2: Missing compound bond info for SER
2: Missing compound bond info for THR
2: Missing compound bond info for TRP
2: Missing compound bond info for TYR
2: Missing compound bond info for VAL
2: Missing information for compound 'PRO'
2: Missing bond information for compound PRO
2: Missing information for compound 'ASN'
2: Missing bond information for compound ASN
2: Missing information for compound 'PHE'
2: Missing bond information for compound PHE
2: Missing information for compound 'SER'
2: Missing bond information for compound SER
2: Missing information for compound 'GLY'
2: Missing bond information for compound GLY
2: Missing information for compound 'TRP'
2: Missing bond information for compound TRP
2: Missing information for compound 'LYS'
2: Missing bond information for compound LYS
2: Missing information for compound 'ILE'
2: Missing bond information for compound ILE
2: Missing information for compound 'ARG'
2: Missing bond information for compound ARG
2: Missing information for compound 'GLU'
2: Missing bond information for compound GLU
2: Missing information for compound 'LEU'
2: Missing bond information for compound LEU
2: Missing information for compound 'VAL'
2: Missing bond information for compound VAL
2: Missing information for compound 'MET'
2: Missing bond information for compound MET
2: Missing information for compound 'ALA'
2: Missing bond information for compound ALA
2: Missing information for compound 'GLN'
2: Missing bond information for compound GLN
2: Missing information for compound 'ASP'
2: Missing bond information for compound ASP
2: Missing information for compound 'THR'
2: Missing bond information for compound THR
2: Missing information for compound 'TYR'
2: Missing bond information for compound TYR
2: Missing information for compound 'CYS'
2: Missing bond information for compound CYS
2: Missing information for compound 'REA'
2: Missing bond information for compound REA
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: nan
2: 0.962323
2: 0.961218
2: 1.2
2: 0.804563
2: 0.956281
2: 1.16442
2: 1.17157
2: 0.736907
2: 0.98891
2: 0.63726
2: 0.899501
2: 1.13951
2: 1.10304
2: 0.993256
2: 0.843706
2: 1.2
2: 0.394465
2: 0.622517
2: 1.13009
2: 0.811815
2: 1.12736
2: 1.04113
2: 1.15404
2: 0.966251
2: 0.264242
2: 0.896923
2: 0.947966
2: 0.759697
2: 0.714667
2: 0
2: 0
2: 0.58491
2: 0.883804
2: 0.6127
2: 0
2: 1.2
2: 0.816853
2: 1.2
2: 0.863403
2: 0.930392
2: 1.2
2: 0
2: 1.17888
2: 0.883952
2: 0.696931
2: 0.306483
2: 1.05932
2: 1.16462
2: 0.985143
2: 1.14584
2: 0.625949
2: 0.499085
2: 0.99743
2: 0.896065
2: 0.897962
2: 0
2: 1.2
2: 0.534169
2: 0.365134
2: 0.794768
2: 0.74366
2: 0.800938
2: 1.08071
2: 1.16712
2: 0.63442
2: 0.969202
2: 1.2
2: 0.984084
2: 0.359675
2: 0.780296
2: 0.601323
2: 0
2: 0.437713
2: 1.00255
2: 0.966267
2: 0.967664
2: 1.01481
2: 0.61683
2: 0.542967
2: 0.278281
2: 0.801292
2: 0
2: 0.611326
2: 0.396568
2: 0.641594
2: 0.460736
2: 0.794802
2: 0.0962642
2: 0.856458
2: 0.115798
2: 1.06967
2: 0.580771
2: 0.93537
2: 1.1918
2: 0.235196
2: 0.511667
2: 0.550865
2: 0.32908
2: 1.18026
2: 0.943706
1/2 Test #2: pdb-redo-example .................   Passed    0.55 sec
1: Running 7 test cases...
1: Reading map from "/build/reproducible-path/libpdb-redo-3.1.5/test/../examples/1cbs_map.mtz"
1:   with labels: FB: FWT,PHWT
1:   with labels: FD: DELFWT,PHDELWT
1:   with labels: FA: FAN,PHAN
1:   with labels: FO: FP,SIGFP
1:   with labels: FC: FC_ALL,PHIC_ALL
1: Read Xmaps with sampling rate: 1.5
1:   stored resolution: 1.79991
1:   calculated reshi = 1.80009 reslo = 7.99918
1:   spacegroup: P 21 21 21
1:   cell:  Cell ( 45.65, 47.56, 77.61,    90,    90,    90)
1:   grid: Nuvw = (  80,  80, 132)
1: R-factor      : 0.180853
1: Free R-factor : 0.184876
1: Loading component LYS... done
1: Loading component ILE... done
1: Loading component ARG... done
1: Loading component GLU... done
1: Loading component LEU... done
1: Loading component VAL... done
1: Loading component MET... done
1: Loading component ALA... done
1: Loading component GLN... done
1: Loading component ASP... done
1: Loading component THR... done
1: Loading component TYR... done
1: Loading component CYS... done
1: Loading component REA... done
1: Loading component HOH...
1: Configuration error:
1: 
1: The attempt to retrieve compound information for "HOH" failed.
1: 
1: This information is searched for in a CCD file called components.cif or
1: components.cif.gz which should be located in one of the following directories:
1: 
1: "/var/cache/libcifpp"
1: "/usr/share/libcifpp"
1: 
1: (Note that you can add a directory to the search paths by setting the 
1: LIBCIFPP_DATA_DIR environmental variable)
1: 
1: On Linux an optional cron script might have been installed that automatically updates
1: components.cif and mmCIF dictionary files. This script only works when the file
1: libcifpp.conf contains an uncommented line with the text:
1: 
1: update=true
1: 
1: If you do not have a working cron script, you can manually update the files
1: in /var/cache/libcifpp using the following commands:
1: 
1: curl -o /var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif
1: curl -o /var/cache/libcifpp/mmcif_pdbx.dic https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic
1: curl -o /var/cache/libcifpp/mmcif_ma.dic https://github.com/ihmwg/ModelCIF/raw/master/dist/mmcif_ma.dic
1: 
1: The current order of compound factory objects is:
1: 
1: CCD components file: "/build/reproducible-path/libpdb-redo-3.1.5/test/minimal-components.cif"
1:  done
1: 
1: Intercept & gradient before LS: -0.076201 (0.000425224) 0.1134 (0.00066587)
1: 
1: Rescale SD(delta-rho) using Q-Q plot for asym A:
1: ======================================================
1: Input & updated SD(delta-rho): 0.123854 ; 0.137899
1: 
1: 
1: Intercept & gradient before LS: 0.112013 (0.00322152) -0.0975523 (0.00506053)
1: 
1: Rescale SD(delta-rho) using Q-Q plot for asym B:
1: ======================================================
1: Input & updated SD(delta-rho): 0.123854 ; 0.111772
1: 
1: 
1: Intercept & gradient before LS: -0.038699 (0.00144741) -0.0997851 (0.00226694)
1: 
1: Rescale SD(delta-rho) using Q-Q plot for asym C:
1: ======================================================
1: Input & updated SD(delta-rho): 0.123854 ; 0.111495
1: 
1: Calculating radii with B Factor 24.9788
1: Radius for atom with type N is 1.03582
1: Radius for atom with type C is 1.04896
1: Radius for atom with type O is 1.02401
1: Radius for atom with type S is 1.01993
1: skipping water in bond map calculation
1: Loading component HOH... done
1: Unknown compound: HOH
1: Missing compound information for HOH
1: The asym ID's of ndb_poly_seq_scheme and pdbx_poly_seq_scheme are not equal, dropping ndb_poly_seq_scheme
1: Reading map from "/build/reproducible-path/libpdb-redo-3.1.5/test/../examples/1cbs_map.mtz"
1:   with labels: FB: FWT,PHWT
1:   with labels: FD: DELFWT,PHDELWT
1:   with labels: FA: FAN,PHAN
1:   with labels: FO: FP,SIGFP
1:   with labels: FC: FC_ALL,PHIC_ALL
1: Read Xmaps with sampling rate: 0.75
1:   stored resolution: 1.79991
1:   calculated reshi = 1.80009 reslo = 7.99918
1:   spacegroup: P 21 21 21
1:   cell:  Cell ( 45.65, 47.56, 77.61,    90,    90,    90)
1:   grid: Nuvw = (  40,  40,  72)
1: R-factor      : 0.180853
1: Free R-factor : 0.184876
1: Loading component U_K... done
1: 
1: Intercept & gradient before LS: -0.0615663 (0.000573911) 0.0873704 (0.000898727)
1: 
1: Rescale SD(delta-rho) using Q-Q plot for asym A:
1: ======================================================
1: Input & updated SD(delta-rho): 0.11509 ; 0.125146
1: 
1: 
1: Intercept & gradient before LS: 0.0679982 (0.0146148) -0.0420235 (0.0228119)
1: 
1: Rescale SD(delta-rho) using Q-Q plot for asym B:
1: ======================================================
1: Input & updated SD(delta-rho): 0.11509 ; 0.110254
1: 
1: 
1: Intercept & gradient before LS: -0.00860157 (0.000800546) -0.185508 (0.00125356)
1: 
1: Rescale SD(delta-rho) using Q-Q plot for asym C:
1: ======================================================
1: Input & updated SD(delta-rho): 0.11509 ; 0.09374
1: 
1: Calculating radii with B Factor 24.9788
1: Radius for atom with type N is 1.03582
1: Radius for atom with type C is 1.04896
1: Radius for atom with type O is 1.02401
1: Radius for atom with type S is 1.01993
1: skipping water in bond map calculation
1: Missing compound bond info for U_K
1: Missing information for compound 'U_K'
1: Missing bond information for compound U_K
1: Loading component HOH... done
1: Unknown compound: HOH
1: Missing compound information for HOH
1: The asym ID's of ndb_poly_seq_scheme and pdbx_poly_seq_scheme are not equal, dropping ndb_poly_seq_scheme
1: skipping water in bond map calculation
1: skipping water in bond map calculation
1: 
1: *** No errors detected
1: 
2/2 Test #1: pdb-redo-unit-test ...............   Passed    3.19 sec

100% tests passed, 0 tests failed out of 2

Total Test time (real) =   3.19 sec
make[1]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu'
   create-stamp debian/debhelper-build-stamp
   dh_prep
   dh_auto_install
	cd obj-i686-linux-gnu && make -j5 install DESTDIR=/build/reproducible-path/libpdb-redo-3.1.5/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu'
/usr/bin/cmake -S/build/reproducible-path/libpdb-redo-3.1.5 -B/build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
make  -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/i386-linux-gnu/libpdb-redo.so.3.1.5
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/i386-linux-gnu/libpdb-redo.so.3.1
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/i386-linux-gnu/libpdb-redo.so
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/i386-linux-gnu/cmake/pdb-redo/pdb-redoTargets.cmake
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/i386-linux-gnu/cmake/pdb-redo/pdb-redoTargets-none.cmake
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Ramachandran.hpp
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Statistics.hpp
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/ClipperWrapper.hpp
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/TLS.hpp
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/ResolutionCalculator.hpp
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/exports.hpp
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Version.hpp
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/AtomShape.hpp
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/BondMap.hpp
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/SkipList.hpp
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/DistanceMap.hpp
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Minimizer.hpp
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Compound.hpp
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/Restraints.hpp
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/include/pdb-redo/MapMaker.hpp
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/i386-linux-gnu/cmake/pdb-redo/pdb-redoConfig.cmake
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/i386-linux-gnu/cmake/pdb-redo/pdb-redoConfigVersion.cmake
-- Installing: /build/reproducible-path/libpdb-redo-3.1.5/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig/libpdb-redo.pc
make[1]: Leaving directory '/build/reproducible-path/libpdb-redo-3.1.5/obj-i686-linux-gnu'
   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-redo-dev' in '../libpdb-redo-dev_3.1.5-5_i386.deb'.
dpkg-deb: building package 'libpdb-redo3-dbgsym' in '../libpdb-redo3-dbgsym_3.1.5-5_i386.deb'.
dpkg-deb: building package 'libpdb-redo3' in '../libpdb-redo3_3.1.5-5_i386.deb'.
 dpkg-genbuildinfo --build=binary -O../libpdb-redo_3.1.5-5_i386.buildinfo
 dpkg-genchanges --build=binary -O../libpdb-redo_3.1.5-5_i386.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/16263/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/16263/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/16263 and its subdirectories
I: Current time: Wed Dec 10 21:29:11 +14 2025
I: pbuilder-time-stamp: 1765351751