I: pbuilder: network access will be disabled during build I: Current time: Fri Aug 20 01:48:52 +14 2021 I: pbuilder-time-stamp: 1629373732 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 [snpomatic_1.0-4.dsc] I: copying [./snpomatic_1.0.orig.tar.gz] I: copying [./snpomatic_1.0-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sat Jul 7 07:00:05 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./snpomatic_1.0-4.dsc dpkg-source: info: extracting snpomatic in snpomatic-1.0 dpkg-source: info: unpacking snpomatic_1.0.orig.tar.gz dpkg-source: info: unpacking snpomatic_1.0-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_ungap dpkg-source: info: applying hardening dpkg-source: info: applying build_all_binaries I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3621/tmp/hooks/D01_modify_environment starting debug: Running on codethink-sled11-arm64. 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/3621/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3621/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]="aarch64-unknown-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=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=3621 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.1XCegZuPmT/pbuilderrc_Jkw9 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.1XCegZuPmT/b2 --logfile b2/build.log snpomatic_1.0-4.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.4.0-185-generic #215-Ubuntu SMP Mon Jun 8 21:55:24 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 18 2019 bash -rwxr-xr-x 3 root root 34808 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 34808 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 34808 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14264 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 35576 Mar 1 2019 cat -rwxr-xr-x 1 root root 60256 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 56096 Mar 1 2019 chmod -rwxr-xr-x 1 root root 64368 Mar 1 2019 chown -rwxr-xr-x 1 root root 134632 Mar 1 2019 cp -rwxr-xr-x 1 root root 129536 Jan 18 2019 dash -rwxr-xr-x 1 root root 97136 Mar 1 2019 date -rwxr-xr-x 1 root root 76736 Mar 1 2019 dd -rwxr-xr-x 1 root root 93752 Mar 1 2019 df -rwxr-xr-x 1 root root 138848 Mar 1 2019 dir -rwxr-xr-x 1 root root 75984 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 31368 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 27256 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 174304 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 89656 Jan 6 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 27 2018 hostname -rwxr-xr-x 1 root root 64472 Mar 1 2019 ln -rwxr-xr-x 1 root root 52544 Jul 27 2018 login -rwxr-xr-x 1 root root 138848 Mar 1 2019 ls -rwxr-xr-x 1 root root 108552 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 76840 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 64480 Mar 1 2019 mknod -rwxr-xr-x 1 root root 39736 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 10 2019 more -rwsr-xr-x 1 root root 47112 Jan 10 2019 mount -rwxr-xr-x 1 root root 14344 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138736 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 35560 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68440 Mar 1 2019 rm -rwxr-xr-x 1 root root 39624 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Aug 20 01:49 sh -> bash lrwxrwxrwx 1 root root 4 Aug 19 04:48 sh.distrib -> dash -rwxr-xr-x 1 root root 31384 Mar 1 2019 sleep -rwxr-xr-x 1 root root 72480 Mar 1 2019 stty -rwsr-xr-x 1 root root 59424 Jan 10 2019 su -rwxr-xr-x 1 root root 31416 Mar 1 2019 sync -rwxr-xr-x 1 root root 449416 Apr 24 2019 tar -rwxr-xr-x 1 root root 10560 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 88968 Mar 1 2019 touch -rwxr-xr-x 1 root root 27256 Mar 1 2019 true -rwxr-xr-x 1 root root 14264 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 10 2019 umount -rwxr-xr-x 1 root root 31384 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138848 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34824 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/3621/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), asciidoctor, antiword dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19168 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 asciidoctor; however: Package asciidoctor is not installed. pbuilder-satisfydepends-dummy depends on antiword; however: Package antiword 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: antiword{a} asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libreadline7{a} libruby2.5{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} openssl{a} po-debconf{a} rake{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-did-you-mean{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-test-unit{a} ruby-xmlrpc{a} ruby2.5{a} rubygems-integration{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-lato libarchive-cpio-perl libglib2.0-data libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs zip 0 packages upgraded, 53 newly installed, 0 to remove and 0 not upgraded. Need to get 25.6 MB of archives. After unpacking 93.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 readline-common all 7.0-5 [70.6 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 antiword arm64 0.37-14 [127 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 openssl arm64 1.1.1d-0+deb10u3 [823 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 ca-certificates all 20190110 [157 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 rubygems-integration all 1.11+deb10u1 [5212 B] Get: 18 http://deb.debian.org/debian buster/main arm64 rake all 12.3.1-3+deb10u1 [67.1 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 ruby-did-you-mean all 1.2.1-1 [14.4 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 ruby-minitest all 5.11.3-1 [54.8 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 ruby-power-assert all 1.1.1-1 [10.9 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 ruby-test-unit all 3.2.8-1 [72.4 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 libreadline7 arm64 7.0-5 [134 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libyaml-0-2 arm64 0.2.1-1 [41.4 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libruby2.5 arm64 2.5.5-3+deb10u1 [3304 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 ruby2.5 arm64 2.5.5-3+deb10u1 [400 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 ruby arm64 1:2.5.1 [11.3 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 ruby-asciidoctor all 1.5.8-1 [188 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 asciidoctor all 1.5.8-1 [75.8 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 52 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 53 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Fetched 25.6 MB in 2s (16.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../06-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../07-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../08-libmagic-mgc_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../09-libmagic1_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../10-file_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../11-gettext-base_0.19.8.1-9_arm64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package antiword. Preparing to unpack .../12-antiword_0.37-14_arm64.deb ... Unpacking antiword (0.37-14) ... Selecting previously unselected package libssl1.1:arm64. Preparing to unpack .../13-libssl1.1_1.1.1d-0+deb10u3_arm64.deb ... Unpacking libssl1.1:arm64 (1.1.1d-0+deb10u3) ... Selecting previously unselected package openssl. Preparing to unpack .../14-openssl_1.1.1d-0+deb10u3_arm64.deb ... Unpacking openssl (1.1.1d-0+deb10u3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../15-ca-certificates_20190110_all.deb ... Unpacking ca-certificates (20190110) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../16-rubygems-integration_1.11+deb10u1_all.deb ... Unpacking rubygems-integration (1.11+deb10u1) ... Selecting previously unselected package rake. Preparing to unpack .../17-rake_12.3.1-3+deb10u1_all.deb ... Unpacking rake (12.3.1-3+deb10u1) ... Selecting previously unselected package ruby-did-you-mean. Preparing to unpack .../18-ruby-did-you-mean_1.2.1-1_all.deb ... Unpacking ruby-did-you-mean (1.2.1-1) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../19-ruby-minitest_5.11.3-1_all.deb ... Unpacking ruby-minitest (5.11.3-1) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../20-ruby-net-telnet_0.1.1-2_all.deb ... Unpacking ruby-net-telnet (0.1.1-2) ... Selecting previously unselected package ruby-power-assert. Preparing to unpack .../21-ruby-power-assert_1.1.1-1_all.deb ... Unpacking ruby-power-assert (1.1.1-1) ... Selecting previously unselected package ruby-test-unit. Preparing to unpack .../22-ruby-test-unit_3.2.8-1_all.deb ... Unpacking ruby-test-unit (3.2.8-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../23-ruby-xmlrpc_0.3.0-2_all.deb ... Unpacking ruby-xmlrpc (0.3.0-2) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../24-libncurses6_6.1+20181013-2+deb10u2_arm64.deb ... Unpacking libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package libreadline7:arm64. Preparing to unpack .../25-libreadline7_7.0-5_arm64.deb ... Unpacking libreadline7:arm64 (7.0-5) ... Selecting previously unselected package libyaml-0-2:arm64. Preparing to unpack .../26-libyaml-0-2_0.2.1-1_arm64.deb ... Unpacking libyaml-0-2:arm64 (0.2.1-1) ... Selecting previously unselected package libruby2.5:arm64. Preparing to unpack .../27-libruby2.5_2.5.5-3+deb10u1_arm64.deb ... Unpacking libruby2.5:arm64 (2.5.5-3+deb10u1) ... Selecting previously unselected package ruby2.5. Preparing to unpack .../28-ruby2.5_2.5.5-3+deb10u1_arm64.deb ... Unpacking ruby2.5 (2.5.5-3+deb10u1) ... Selecting previously unselected package ruby. Preparing to unpack .../29-ruby_1%3a2.5.1_arm64.deb ... Unpacking ruby (1:2.5.1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../30-ruby-asciidoctor_1.5.8-1_all.deb ... Unpacking ruby-asciidoctor (1.5.8-1) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../31-asciidoctor_1.5.8-1_all.deb ... Unpacking asciidoctor (1.5.8-1) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../32-libsigsegv2_2.12-2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../33-m4_1.4.18-2_arm64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../34-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../35-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../36-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../37-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../38-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../39-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../40-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../41-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../42-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../43-libelf1_0.176-1.1_arm64.deb ... Unpacking libelf1:arm64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../44-dwz_0.12-3_arm64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../45-libglib2.0-0_2.58.3-2+deb10u2_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:arm64. Preparing to unpack .../46-libicu63_63.1-6+deb10u1_arm64.deb ... Unpacking libicu63:arm64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../47-libxml2_2.9.4+dfsg1-7+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:arm64. Preparing to unpack .../48-libcroco3_0.6.12-3_arm64.deb ... Unpacking libcroco3:arm64 (0.6.12-3) ... Selecting previously unselected package gettext. Preparing to unpack .../49-gettext_0.19.8.1-9_arm64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../50-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../51-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../52-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Setting up libpipeline1:arm64 (1.5.1-2) ... Setting up ruby-power-assert (1.1.1-1) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libyaml-0-2:arm64 (0.2.1-1) ... Setting up libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libssl1.1:arm64 (1.1.1d-0+deb10u3) ... Setting up libmagic1:arm64 (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:arm64 (63.1-6+deb10u1) ... Setting up ruby-minitest (5.11.3-1) ... Setting up autotools-dev (20180224.1) ... Setting up ruby-test-unit (3.2.8-1) ... Setting up libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up antiword (0.37-14) ... Setting up ruby-did-you-mean (1.2.1-1) ... Setting up openssl (1.1.1d-0+deb10u3) ... Setting up libbsd0:arm64 (0.9.1-2) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Setting up libreadline7:arm64 (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up m4 (1.4.18-2) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. 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 libcroco3:arm64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... 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 rubygems-integration (1.11+deb10u1) ... 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 po-debconf (1.0.21) ... Setting up rake (12.3.1-3+deb10u1) ... Setting up libruby2.5:arm64 (2.5.5-3+deb10u1) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up ruby2.5 (2.5.5-3+deb10u1) ... Setting up ruby (1:2.5.1) ... Setting up ruby-asciidoctor (1.5.8-1) ... Setting up asciidoctor (1.5.8-1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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 I: Running cd /build/snpomatic-1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package snpomatic dpkg-buildpackage: info: source version 1.0-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/snpomatic-1.0' /usr/bin/make clean make[2]: Entering directory '/build/snpomatic-1.0' rm -f *.o rm -f src/*.o rm -f findknownsnps rm -f variety make[2]: Leaving directory '/build/snpomatic-1.0' rm -rf debian/findknownsnps.1 rm -rf debian/findknownsnps.1.html rm -f mapcontigs reassemble ungap dh_auto_clean -- make -j8 clean make[2]: Entering directory '/build/snpomatic-1.0' rm -f *.o rm -f src/*.o rm -f findknownsnps rm -f variety make[2]: Leaving directory '/build/snpomatic-1.0' make[1]: Leaving directory '/build/snpomatic-1.0' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/snpomatic.substvars debian/files rm -fr -- debian/snpomatic/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j8 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/snpomatic-1.0' g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/findknownsnps.cpp -o src/findknownsnps.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/global_functions.cpp -o src/global_functions.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosome.cpp -o src/TChromosome.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomalIndices.cpp -o src/TChromosomalIndices.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TAlignmentOutput.cpp -o src/TAlignmentOutput.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/TChromosomeAlign.cpp -o src/TChromosomeAlign.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/reassemble.cpp -o src/reassemble.o g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/variety.cpp -o src/variety.o src/global_functions.cpp: In function 'void load_all_chromosomes(std::__cxx11::string, std::vector&, bool)': src/global_functions.cpp:146:40: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector::size_type' {aka 'long unsigned int'} [-Wformat=] if ( DEBUGGING ) { fprintf ( stdout , "read %d chromosomes.\n" , chrs.size() ) ; fflush(stdout); } ^~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ src/global_functions.cpp:116:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/global_functions.cpp: In function 'void incorporate_all_gff(std::__cxx11::string, std::vector&)': src/global_functions.cpp:165:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/global_functions.cpp: In function 'void incorporate_simple_snps(std::__cxx11::string, std::vector&)': src/global_functions.cpp:220:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosome.cpp: In member function 'void TChromosome::read_chromosome(std::__cxx11::string, std::__cxx11::string)': src/TChromosome.cpp:41:40: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] if ( DEBUGGING ) { fprintf ( stdout , "read %d nucleotides.\n" , sequence.length() ) ; fflush(stdout); } ^~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~ src/TChromosome.cpp:13:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps_gff(std::__cxx11::string)': src/TChromosome.cpp:54:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosome.cpp: In member function 'void TChromosome::incorporate_known_snps(std::__cxx11::string)': src/TChromosome.cpp:95:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run(chrvec*)': src/TChromosomalIndices.cpp:262:62: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector::size_type' {aka 'long unsigned int'} [-Wformat=] if ( index_from == 0 && index_to == 0 ) fprintf ( stdout , "Indexing %d chromosomes ... " , chrs->size() ) ; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ src/TChromosomalIndices.cpp:263:27: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector::size_type' {aka 'long unsigned int'} [-Wformat=] else fprintf ( stdout , "Indexing %d chromosomes (%d-%d) ... " , chrs->size() , index_from , index_to ) ; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::init()': src/TChromosomeAlign.cpp:83:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] fprintf ( sam , "@SQ\tSN:%s\tLN:%d\n" , (*chrs)[i].name.c_str() , (*chrs)[i].sequence.length() ) ; ^~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run_reads(std::__cxx11::string)': src/TChromosomalIndices.cpp:33:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:37:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::reassemble_reads(FILE*, uint, index2type, index2type)': src/TChromosomalIndices.cpp:126:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:127:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::run_regions(chrvec*, std::__cxx11::string)': src/TChromosomalIndices.cpp:167:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp: In member function 'void TChromosomalIndices::load_index(std::__cxx11::string)': src/TChromosomalIndices.cpp:409:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( &temp , sizeof ( temp ) , 1 , file ) ; // Version ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:410:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( &temp , sizeof ( temp ) , 1 , file ) ; // position size ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:415:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( &temp , sizeof ( temp ) , 1 , file ) ; // Sub-index size ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:419:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( &i.index2 , sizeof ( i.index2 ) , 1 , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:420:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( &i.position , sizeof ( i.position ) , 1 , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:421:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( &i.chromosome , sizeof ( i.chromosome ) , 1 , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomalIndices.cpp:422:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread ( &i.reverse_complement , sizeof ( i.reverse_complement ) , 1 , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::finish_sqlite(int, int, int)': src/TChromosomeAlign.cpp:956:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] fprintf ( sqlite , "INSERT INTO chromosomes ( name , size ) VALUES ( \"%s\" , \"%d\") ;\n" , (*chrs)[a].name.c_str() , (*chrs)[a].sequence.length() ) ; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::add_cigar_sqlite(const string&, const string&, uint, uint, char)': src/TChromosomeAlign.cpp:1583:21: warning: format '%d' expects argument of type 'int', but argument 5 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] fprintf ( cigar , "%s %d %d %c %s %d %d + %d %s\n" , ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1586:9: sequence.length() , // Read end ~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1583:21: warning: format '%d' expects argument of type 'int', but argument 9 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/mapcontigs.cpp -o src/mapcontigs.o src/reassemble.cpp: In function 'void read_fastq(std::__cxx11::string, std::vector&, int)': src/reassemble.cpp:319:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::add_nono_list(std::__cxx11::string)': src/TChromosomeAlign.cpp:93:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -c src/ungap.cpp -o src/ungap.o src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::finish_sqlite(int, int, int)': src/TChromosomeAlign.cpp:972:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , sqlite_cache ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_paired(std::__cxx11::string, std::__cxx11::string, uint, uint, uint)': src/TChromosomeAlign.cpp:1070:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1075:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( c1 , READ_CHAR_BUFFER , file2 ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_fastq(std::__cxx11::string)': src/TChromosomeAlign.cpp:1296:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1306:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1316:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1325:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_fasta(std::__cxx11::string)': src/TChromosomeAlign.cpp:1374:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp: In member function 'void TChromosomeAlign::align_solexa_fastq_variety(std::__cxx11::string)': src/TChromosomeAlign.cpp:1628:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1637:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1647:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/TChromosomeAlign.cpp:1655:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( dummy , READ_CHAR_BUFFER , file ) ; ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/findknownsnps.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o findknownsnps g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/reassemble.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o reassemble g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/variety.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o variety g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/mapcontigs.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o mapcontigs g++ -g -O2 -ffile-prefix-map=/build/snpomatic-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wl,-z,relro -Wl,-z,now -lm src/ungap.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o -o ungap make[1]: Leaving directory '/build/snpomatic-1.0' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep rm -f -- debian/snpomatic.substvars rm -fr -- debian/.debhelper/generated/snpomatic/ debian/snpomatic/ debian/tmp/ debian/rules override_dh_auto_install make[1]: Entering directory '/build/snpomatic-1.0' mkdir -p /build/snpomatic-1.0/debian/snpomatic/usr/bin install -p findknownsnps /build/snpomatic-1.0/debian/snpomatic/usr/bin # -- we don't install the others as they seem unmaintained/undocumented #cp reassemble /build/snpomatic-1.0/debian/snpomatic/usr/bin #cp variety /build/snpomatic-1.0/debian/snpomatic/usr/bin #cp mapcontigs /build/snpomatic-1.0/debian/snpomatic/usr/bin #cp ungap /build/snpomatic-1.0/debian/snpomatic/usr/bin make[1]: Leaving directory '/build/snpomatic-1.0' debian/rules override_dh_installdocs make[1]: Entering directory '/build/snpomatic-1.0' antiword doc/Manual.doc > doc/Manual.txt mkdir -p debian/snpomatic/usr/share/doc/snpomatic cp doc/Manual.txt debian/snpomatic/usr/share/doc/snpomatic mkdir -p debian/snpomatic/usr/share/doc-base cp debian/doc-base debian/snpomatic/usr/share/doc-base/snpomatic-doc dh_installdocs -- install -d debian/.debhelper/generated/snpomatic install -p -m0644 debian/copyright debian/snpomatic/usr/share/doc/snpomatic/copyright install -p -m0644 debian/doc-base debian/snpomatic/usr/share/doc-base/snpomatic make[1]: Leaving directory '/build/snpomatic-1.0' dh_installchangelogs install -p -m0644 debian/changelog debian/snpomatic/usr/share/doc/snpomatic/changelog.Debian rm -f debian/snpomatic.debhelper.log debian/rules override_dh_installman make[1]: Entering directory '/build/snpomatic-1.0' asciidoctor -a docdate='' -b manpage debian/findknownsnps.1.adoc dh_installman -- install -d debian/snpomatic/usr/share/man/man1/ install -p -m0644 ./debian/findknownsnps.1 debian/snpomatic/usr/share/man/man1/findknownsnps.1 man -l --recode UTF-8 ./debian/snpomatic/usr/share/man/man1/findknownsnps.1 > debian/snpomatic/usr/share/man/man1/findknownsnps.1.dh-new mv debian/snpomatic/usr/share/man/man1/findknownsnps.1.dh-new debian/snpomatic/usr/share/man/man1/findknownsnps.1 chmod 0644 -- debian/snpomatic/usr/share/man/man1/findknownsnps.1 make[1]: Leaving directory '/build/snpomatic-1.0' dh_perl dh_link dh_strip_nondeterminism dh_compress cd debian/snpomatic chmod a-x usr/share/doc/snpomatic/Manual.txt usr/share/doc/snpomatic/changelog.Debian usr/share/man/man1/findknownsnps.1 gzip -9nf usr/share/doc/snpomatic/Manual.txt usr/share/doc/snpomatic/changelog.Debian usr/share/man/man1/findknownsnps.1 cd '/build/snpomatic-1.0' dh_fixperms find debian/snpomatic -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/snpomatic ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/snpomatic/usr/share/doc -type f -a -true -a ! -regex 'debian/snpomatic/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/snpomatic/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/snpomatic/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/snpomatic -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/snpomatic/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_strip install -d debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/e9 objcopy --only-keep-debug --compress-debug-sections debian/snpomatic/usr/bin/findknownsnps debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/e9/0fa9a9ee7dfe82aebe0033c11633e031997b16.debug chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/e9/0fa9a9ee7dfe82aebe0033c11633e031997b16.debug chown 0:0 -- debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/e9/0fa9a9ee7dfe82aebe0033c11633e031997b16.debug strip --remove-section=.comment --remove-section=.note debian/snpomatic/usr/bin/findknownsnps objcopy --add-gnu-debuglink debian/.debhelper/snpomatic/dbgsym-root/usr/lib/debug/.build-id/e9/0fa9a9ee7dfe82aebe0033c11633e031997b16.debug debian/snpomatic/usr/bin/findknownsnps install -d debian/.debhelper/snpomatic/dbgsym-root/usr/share/doc ln -s snpomatic debian/.debhelper/snpomatic/dbgsym-root/usr/share/doc/snpomatic-dbgsym dh_makeshlibs rm -f debian/snpomatic/DEBIAN/shlibs dh_shlibdeps install -d debian/snpomatic/DEBIAN dpkg-shlibdeps -Tdebian/snpomatic.substvars debian/snpomatic/usr/bin/findknownsnps dh_installdeb dh_gencontrol echo misc:Depends= >> debian/snpomatic.substvars echo misc:Pre-Depends= >> debian/snpomatic.substvars install -d debian/.debhelper/snpomatic/dbgsym-root/DEBIAN dpkg-gencontrol -psnpomatic -ldebian/changelog -Tdebian/snpomatic.substvars -Pdebian/.debhelper/snpomatic/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=snpomatic-dbgsym "-DDepends=snpomatic (= \${binary:Version})" "-DDescription=debug symbols for snpomatic" -DBuild-Ids=e90fa9a9ee7dfe82aebe0033c11633e031997b16 -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/snpomatic/dbgsym-root/DEBIAN/control dpkg-gencontrol -psnpomatic -ldebian/changelog -Tdebian/snpomatic.substvars -Pdebian/snpomatic -UMulti-Arch chmod 0644 -- debian/snpomatic/DEBIAN/control chown 0:0 -- debian/snpomatic/DEBIAN/control dh_md5sums cd debian/snpomatic >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/snpomatic/DEBIAN/md5sums chown 0:0 -- debian/snpomatic/DEBIAN/md5sums cd debian/.debhelper/snpomatic/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/snpomatic/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/snpomatic/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --build debian/snpomatic .. dpkg-deb --build debian/.debhelper/snpomatic/dbgsym-root .. dpkg-deb: building package 'snpomatic-dbgsym' in '../snpomatic-dbgsym_1.0-4_arm64.deb'. dpkg-deb: building package 'snpomatic' in '../snpomatic_1.0-4_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../snpomatic_1.0-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: user script /srv/workspace/pbuilder/3621/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3621/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/3621 and its subdirectories I: Current time: Fri Aug 20 01:50:00 +14 2021 I: pbuilder-time-stamp: 1629373800