I: pbuilder: network access will be disabled during build I: Current time: Mon Jan 2 01:37:29 +14 2023 I: pbuilder-time-stamp: 1672573049 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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 [bio-eagle_2.4.1-1.dsc] I: copying [./bio-eagle_2.4.1.orig.tar.gz] I: copying [./bio-eagle_2.4.1-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Nov 28 21:00:55 2018 +14 gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54 gpgv: issuer "daissi@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bio-eagle_2.4.1-1.dsc dpkg-source: info: extracting bio-eagle in bio-eagle-2.4.1 dpkg-source: info: unpacking bio-eagle_2.4.1.orig.tar.gz dpkg-source: info: unpacking bio-eagle_2.4.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Makefile_config.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1164015/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 Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/1164015/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1164015/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]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.0.3(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 parallel=16' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=2c21ea6d613b43beb7b6cebde791ad06 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=1164015 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/tmp.IXPN5JzLoq/pbuilderrc_2GGh --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.IXPN5JzLoq/b2 --logfile b2/build.log bio-eagle_2.4.1-1.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 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash -rwxr-xr-x 1 root root 109408 Mar 1 2019 date -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd -rwxr-xr-x 1 root root 93744 Mar 1 2019 df -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 35424 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln -rwxr-xr-x 1 root root 56760 Jul 27 2018 login -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 10 2019 more -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jan 2 01:37 sh -> bash lrwxrwxrwx 1 root root 4 Dec 11 18:21 sh.distrib -> dash -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty -rwsr-xr-x 1 root root 63568 Jan 10 2019 su -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch -rwxr-xr-x 1 root root 35424 Mar 1 2019 true -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/1164015/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 (>= 11), libopenblas-dev, libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libhts-dev (>= 1.4), 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 ... 19195 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 (>= 11); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libopenblas-dev; however: Package libopenblas-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 libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.4); however: Package libhts-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} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost-iostreams-dev{a} libboost-iostreams1.67-dev{a} libboost-program-options-dev{a} libboost-program-options1.67-dev{a} libboost-program-options1.67.0{a} libboost-regex1.67-dev{a} libboost-regex1.67.0{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libcurl3-gnutls{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu-dev{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libopenblas-base{a} libopenblas-dev{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 67 newly installed, 0 to remove and 0 not upgraded. Need to get 56.6 MB of archives. After unpacking 378 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 icu-devtools amd64 63.1-6+deb10u1 [189 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libboost1.67-dev amd64 1.67.0-13+deb10u1 [8388 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libboost-dev amd64 1.67.0.1 [3864 B] Get: 37 http://deb.debian.org/debian buster/main amd64 libboost-regex1.67.0 amd64 1.67.0-13+deb10u1 [485 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libicu-dev amd64 63.1-6+deb10u1 [9186 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libboost-regex1.67-dev amd64 1.67.0-13+deb10u1 [539 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libboost-iostreams1.67-dev amd64 1.67.0-13+deb10u1 [255 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libboost-iostreams-dev amd64 1.67.0.1 [3632 B] Get: 42 http://deb.debian.org/debian buster/main amd64 libboost-program-options1.67.0 amd64 1.67.0-13+deb10u1 [357 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libboost-program-options1.67-dev amd64 1.67.0-13+deb10u1 [385 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libboost-program-options-dev amd64 1.67.0.1 [3656 B] Get: 45 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u3 [65.8 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u3 [122 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u7 [1539 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u3 [370 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u3 [158 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 liblzma-dev amd64 5.2.4-1 [210 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libhts-dev amd64 1.9-12~deb10u1 [4347 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libopenblas-base amd64 0.3.5+ds-3 [4290 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libopenblas-dev amd64 0.3.5+ds-3 [4390 kB] Fetched 56.6 MB in 1s (61.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. 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Setting up libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... No schema files found: doing nothing. Setting up libssl1.1:amd64 (1.1.1d-0+deb10u7) ... Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u6) ... Setting up libicu63:amd64 (63.1-6+deb10u1) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libboost-program-options-dev:amd64 (1.67.0.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up icu-devtools (63.1-6+deb10u1) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up libgfortran5:amd64 (8.3.0-6) ... Setting up liblzma-dev:amd64 (5.2.4-1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u3) ... Setting up libboost-dev:amd64 (1.67.0.1) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libicu-dev:amd64 (63.1-6+deb10u1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libopenblas-base:amd64 (0.3.5+ds-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libboost-regex1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libtool (2.4.6-9) ... Setting up libboost-regex1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up m4 (1.4.18-2) ... Setting up libopenblas-dev:amd64 (0.3.5+ds-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libboost-iostreams1.67-dev:amd64 (1.67.0-13+deb10u1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up libboost-iostreams-dev:amd64 (1.67.0.1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up po-debconf (1.0.21) ... Setting up libhts-dev:amd64 (1.9-12~deb10u1) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package hostname: Name or service not known I: Running cd /build/bio-eagle-2.4.1/ && 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 > ../bio-eagle_2.4.1-1_source.changes dpkg-buildpackage: info: source package bio-eagle dpkg-buildpackage: info: source version 2.4.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Dylan Aïssi dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j16 clean make[1]: Entering directory '/build/bio-eagle-2.4.1/src' rm -f *.o rm -f eagle make[1]: Leaving directory '/build/bio-eagle-2.4.1/src' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules build dh build --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src dh_auto_build -O--sourcedirectory=src cd src && make -j16 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bio-eagle-2.4.1/src' g++ -g -O2 -ffile-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o EagleMain.o -c EagleMain.cpp g++ -g -O2 -ffile-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o DipTreePBWT.o -c DipTreePBWT.cpp g++ -g -O2 -ffile-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o Eagle.o -c Eagle.cpp g++ -g -O2 -ffile-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o EagleImpMiss.o -c EagleImpMiss.cpp g++ -g -O2 -ffile-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o EagleParams.o -c EagleParams.cpp g++ -g -O2 -ffile-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o EaglePBWT.o -c EaglePBWT.cpp g++ -g -O2 -ffile-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o FileUtils.o -c FileUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o GenoData.o -c GenoData.cpp g++ -g -O2 -ffile-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o HapHedge.o -c HapHedge.cpp g++ -g -O2 -ffile-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o MapInterpolater.o -c MapInterpolater.cpp g++ -g -O2 -ffile-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o MemoryUtils.o -c MemoryUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o NumericUtils.o -c NumericUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o StaticMultimap.o -c StaticMultimap.cpp g++ -g -O2 -ffile-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o StringUtils.o -c StringUtils.cpp g++ -g -O2 -ffile-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o SyncedVcfData.o -c SyncedVcfData.cpp g++ -g -O2 -ffile-prefix-map=/build/bio-eagle-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -o Timer.o -c Timer.cpp EagleMain.cpp: In function 'void phaseWithRef(EAGLE::EagleParams&, Timer&, double, int, char**)': EagleMain.cpp:109:17: warning: unused variable 'hapBitsTptr' [-Wunused-variable] HapBitsT *hapBitsTptr = NULL; ^~~~~~~~~~~ EagleMain.cpp:110:17: warning: unused variable 'hapHedgePtr' [-Wunused-variable] HapHedge *hapHedgePtr = NULL; ^~~~~~~~~~~ EagleMain.cpp:104:25: warning: unused variable 'timeImpMissing' [-Wunused-variable] double timeMN2 = 0, timeImpMissing = 0; ^~~~~~~~~~~~~~ EagleMain.cpp: In function 'int main(int, char**)': EagleMain.cpp:448:61: warning: unused variable 'timeImpMissing' [-Wunused-variable] double t23 = timer.get_time(); timer.update_time(); double timeImpMissing = 0; ^~~~~~~~~~~~~~ Eagle.cpp: In member function 'void EAGLE::Eagle::readPhaseConfs(const string&)': Eagle.cpp:3108:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(phaseConfs, 1, 2*N*Mseg64*64, fout); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Eagle.cpp: In member function 'std::__cxx11::string EAGLE::Eagle::computePhaseString(uint64, uint64, uint64, const std::vector&, const std::vector&, uint64, double, bool) const': Eagle.cpp:1124:31: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 0 and 11 [-Wformat-overflow=] char buf[20]; sprintf(buf, "[%.1fcM:%d/%d]", cM-lastPhased, hetCount, snpCount); ^~~~~~~~~~~~~~~~ Eagle.cpp:1124:31: note: directive argument in the range [1, 2147483647] In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from /usr/include/c++/8/ext/string_conversions.h:43, from /usr/include/c++/8/bits/basic_string.h:6400, from /usr/include/c++/8/string:52, from Eagle.cpp:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 12 and 339 bytes into a destination of size 20 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Eagle.cpp:1156:29: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 0 and 11 [-Wformat-overflow=] char buf[20]; sprintf(buf, "[%.1fcM:%d/%d]", cM-lastPhased, hetCount, snpCount); ^~~~~~~~~~~~~~~~ Eagle.cpp:1156:29: note: directive argument in the range [0, 2147483647] In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from /usr/include/c++/8/ext/string_conversions.h:43, from /usr/include/c++/8/bits/basic_string.h:6400, from /usr/include/c++/8/string:52, from Eagle.cpp:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 12 and 339 bytes into a destination of size 20 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Eagle.cpp: In member function 'void EAGLE::Eagle::printMatch(uint64, uint64, uint64, const EAGLE::Match&, double (*)[4]) const': Eagle.cpp:1197:31: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 0 and 11 [-Wformat-overflow=] char buf[20]; sprintf(buf, "[%.1fcM:%d/%d]", cM-lastPhased, hetCount, snpCount); ^~~~~~~~~~~~~~~~ Eagle.cpp:1197:31: note: directive argument in the range [0, 2147483647] In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from /usr/include/c++/8/ext/string_conversions.h:43, from /usr/include/c++/8/bits/basic_string.h:6400, from /usr/include/c++/8/string:52, from Eagle.cpp:20: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 12 and 339 bytes into a destination of size 20 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -fopenmp -Wl,-z,relro -Wl,-z,now -o eagle EagleMain.o DipTreePBWT.o Eagle.o EagleImpMiss.o EagleParams.o EaglePBWT.o FileUtils.o GenoData.o HapHedge.o MapInterpolater.o MemoryUtils.o NumericUtils.o StaticMultimap.o StringUtils.o SyncedVcfData.o Timer.o -lhts -lboost_program_options -lboost_iostreams -lz -lopenblas -lpthread -lm make[1]: Leaving directory '/build/bio-eagle-2.4.1/src' dh_auto_test -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --sourcedirectory=src dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install -O--sourcedirectory=src dh_install -O--sourcedirectory=src dh_installdocs -O--sourcedirectory=src debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/bio-eagle-2.4.1' dh_installchangelogs debian/upstream.changelog make[1]: Leaving directory '/build/bio-eagle-2.4.1' dh_installman -O--sourcedirectory=src dh_installinit -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_strip -O--sourcedirectory=src dh_makeshlibs -O--sourcedirectory=src dh_shlibdeps -O--sourcedirectory=src dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/bio-eagle/usr/lib/debian-med/bin/eagle was not linked against libz.so.1 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/bio-eagle/usr/lib/debian-med/bin/eagle was not linked against libpthread.so.0 (it uses none of the library's symbols) dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'bio-eagle-dbgsym' in '../bio-eagle-dbgsym_2.4.1-1_amd64.deb'. dpkg-deb: building package 'bio-eagle-examples' in '../bio-eagle-examples_2.4.1-1_all.deb'. dpkg-deb: building package 'bio-eagle' in '../bio-eagle_2.4.1-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bio-eagle_2.4.1-1_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: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1164015/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1164015/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/1164015 and its subdirectories I: Current time: Mon Jan 2 01:39:27 +14 2023 I: pbuilder-time-stamp: 1672573167