I: pbuilder: network access will be disabled during build I: Current time: Sat Apr 20 07:21:32 +14 2024 I: pbuilder-time-stamp: 1713547292 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [sibelia_3.0.7+dfsg-3.dsc] I: copying [./sibelia_3.0.7+dfsg.orig.tar.xz] I: copying [./sibelia_3.0.7+dfsg-3.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Apr 14 08:37:29 2020 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./sibelia_3.0.7+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting sibelia in sibelia-3.0.7+dfsg dpkg-source: info: unpacking sibelia_3.0.7+dfsg.orig.tar.xz dpkg-source: info: unpacking sibelia_3.0.7+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libdivsufsort.patch dpkg-source: info: applying use_debian_packaged_lagan.patch dpkg-source: info: applying snpeff_is_removed.patch dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/23055/tmp/hooks/D01_modify_environment starting debug: Running on virt32b. 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 Apr 19 17:21 /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/23055/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/23055/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]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=c3e0439f86a84e07be09c0cd34c33f1f LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf 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=23055 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.MexeB6LC/pbuilderrc_gc6o --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MexeB6LC/b2 --logfile b2/build.log sibelia_3.0.7+dfsg-3.dsc' SUDO_GID=112 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-20-armmp-lpae #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 17 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/23055/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: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12), cmake, libdivsufsort-dev, libboost-dev, libseqan2-dev, libtclap-dev, libhts-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 ... 19635 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 (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libdivsufsort-dev; however: Package libdivsufsort-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libseqan2-dev; however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on libtclap-dev; however: Package libtclap-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-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} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libboost-dev{a} libboost1.83-dev{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdivsufsort-dev{a} libdivsufsort3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libjsoncpp25{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libseqan2-dev{a} libssh2-1{a} libsub-override-perl{a} libtclap-dev{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 63 newly installed, 0 to remove and 0 not upgraded. Need to get 47.9 MB of archives. After unpacking 307 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libproc2-0 armhf 2:4.0.4-4 [55.7 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf procps armhf 2:4.0.4-4 [864 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-2+b1 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf libmagic1 armhf 1:5.45-2+b1 [97.9 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-2+b1 [42.2 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.39.3-6 [81.2 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.0-3 [1367 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libarchive13 armhf 3.7.2-1 [301 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-4+b1 [18.2 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-4+b1 [50.1 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5+b3 [158 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.59.0-1 [62.0 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf libssh2-1 armhf 1.11.0-4 [197 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf libcurl4 armhf 8.5.0-2 [383 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.2-1 [83.5 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libjsoncpp25 armhf 1.9.5-6+b2 [69.9 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf librhash0 armhf 1.4.3-3+b1 [143 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libuv1 armhf 1.48.0-1 [133 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf cmake-data all 3.28.3-1 [2128 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf cmake armhf 3.28.3-1 [5109 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian trixie/main armhf libelf1 armhf 0.190-1+b1 [171 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1 [101 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf libboost1.83-dev armhf 1.83.0-2+b2 [10.6 MB] Get: 50 http://deb.debian.org/debian trixie/main armhf libboost-dev armhf 1.83.0.2+b2 [3832 B] Get: 51 http://deb.debian.org/debian trixie/main armhf libcurl3-gnutls armhf 8.5.0-2 [378 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libcurl4-gnutls-dev armhf 8.5.0-2 [490 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf libdeflate-dev armhf 1.20-1 [44.0 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libdivsufsort3 armhf 2.0.1-6 [44.8 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libdivsufsort-dev armhf 2.0.1-6 [18.8 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf libhtscodecs2 armhf 1.6.0-1+b1 [61.3 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf libhts3 armhf 1.19+ds-1 [394 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf liblzma-dev armhf 5.6.1+really5.4.5-1 [281 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg-3+b1 [904 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf libhts-dev armhf 1.19+ds-1 [1598 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf libseqan2-dev all 2.4.0+dfsg-16 [1216 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf libtclap-dev armhf 1.2.5-1+b1 [3359 kB] Fetched 47.9 MB in 2s (21.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:armhf. (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 ... 19635 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.4-4_armhf.deb ... Unpacking libproc2-0:armhf (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../01-procps_2%3a4.0.4-4_armhf.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-2+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../04-libmagic1_1%3a5.45-2+b1_armhf.deb ... Unpacking libmagic1:armhf (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-2+b1_armhf.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../07-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-3_armhf.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.39.3-6_armhf.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../10-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.12.0-3_armhf.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../17-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../18-libxml2_2.9.14+dfsg-1.3+b2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package libarchive13:armhf. Preparing to unpack .../19-libarchive13_3.7.2-1_armhf.deb ... Unpacking libarchive13:armhf (3.7.2-1) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../20-libbrotli1_1.1.0-2+b3_armhf.deb ... Unpacking libbrotli1:armhf (1.1.0-2+b3) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../21-libsasl2-modules-db_2.1.28+dfsg1-4+b1_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../22-libsasl2-2_2.1.28+dfsg1-4+b1_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../23-libldap-2.5-0_2.5.13+dfsg-5+b3_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.13+dfsg-5+b3) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../24-libnghttp2-14_1.59.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.59.0-1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../25-libpsl5_0.21.2-1+b1_armhf.deb ... Unpacking libpsl5:armhf (0.21.2-1+b1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../26-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/23055/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/23055/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/sibelia-3.0.7+dfsg/ && 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 > ../sibelia_3.0.7+dfsg-3_source.changes dpkg-buildpackage: info: source package sibelia dpkg-buildpackage: info: source version 3.0.7+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src cd obj-arm-linux-gnueabihf && DEB_PYTHON_INSTALL_LAYOUT=deb 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 "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf ../src CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The CXX compiler identification is GNU 13.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done (2.2s) -- 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 CMAKE_FIND_USE_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf dh_auto_build -O--sourcedirectory=src cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/sibelia-3.0.7+dfsg/src -B/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/depend make[3]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' cd /build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sibelia-3.0.7+dfsg/src /build/reproducible-path/sibelia-3.0.7+dfsg/src /build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf /build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf /build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/Sibelia.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/build make[3]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' [ 15%] Building CXX object CMakeFiles/Sibelia.dir/sibelia.cpp.o [ 15%] Building CXX object CMakeFiles/Sibelia.dir/postprocessor.cpp.o [ 15%] Building CXX object CMakeFiles/Sibelia.dir/util.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/postprocessor.cpp.o -MF CMakeFiles/Sibelia.dir/postprocessor.cpp.o.d -o CMakeFiles/Sibelia.dir/postprocessor.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.cpp /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/sibelia.cpp.o -MF CMakeFiles/Sibelia.dir/sibelia.cpp.o.d -o CMakeFiles/Sibelia.dir/sibelia.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp [ 20%] Building CXX object CMakeFiles/Sibelia.dir/indexedsequence.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/util.cpp.o -MF CMakeFiles/Sibelia.dir/util.cpp.o.d -o CMakeFiles/Sibelia.dir/util.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.cpp /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/indexedsequence.cpp.o -MF CMakeFiles/Sibelia.dir/indexedsequence.cpp.o.d -o CMakeFiles/Sibelia.dir/indexedsequence.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/hashing.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ [ 25%] Building CXX object CMakeFiles/Sibelia.dir/outputgenerator.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -MF CMakeFiles/Sibelia.dir/outputgenerator.cpp.o.d -o CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:13, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:8: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:13, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.cpp:9: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 30%] Building CXX object CMakeFiles/Sibelia.dir/blockfinder.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/blockfinder.cpp.o -MF CMakeFiles/Sibelia.dir/blockfinder.cpp.o.d -o CMakeFiles/Sibelia.dir/blockfinder.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.cpp /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /usr/include/tclap/SwitchArg.h:29, from /usr/include/tclap/CmdLine.h:27, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:7: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:14: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:65, from /usr/include/c++/13/algorithm:60, from /usr/include/seqan/align.h:53, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:10: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:14: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:9: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from /usr/include/seqan/basic/test_system.h:53, from /usr/include/seqan/basic.h:65, from /usr/include/seqan/align.h:55, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:10: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp: In function ‘int main(int, char**)’: /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:239:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 239 | std::auto_ptr finder(inRAM.isSet() ? new SyntenyFinder::BlockFinder(chrList) : new SyntenyFinder::BlockFinder(chrList, tempDir)); | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:13: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 35%] Building CXX object CMakeFiles/Sibelia.dir/blockinstance.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/blockinstance.cpp.o -MF CMakeFiles/Sibelia.dir/blockinstance.cpp.o.d -o CMakeFiles/Sibelia.dir/blockinstance.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘std::vector SyntenyFinder::{anonymous}::CalculateCoverage(const SyntenyFinder::ChrList&, std::vector > >::const_iterator, std::vector > >::const_iterator)’ at /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:137:18, inlined from ‘void SyntenyFinder::OutputGenerator::GenerateReport(const BlockList&, const std::string&) const’ at /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:199:122: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_insert_rval(const_iterator, value_type&&) [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1391:30, inlined from ‘std::vector SyntenyFinder::{anonymous}::CalculateCoverage(const SyntenyFinder::ChrList&, std::vector > >::const_iterator, std::vector > >::const_iterator)’ at /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:141:14, inlined from ‘void SyntenyFinder::OutputGenerator::GenerateReport(const BlockList&, const std::string&) const’ at /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:199:122: /usr/include/c++/13/bits/vector.tcc:372:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 372 | _M_realloc_insert(begin() + __n, std::move(__v)); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 40%] Building CXX object CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -MF CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o.d -o CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp [ 45%] Building CXX object CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -MF CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o.d -o CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp [ 50%] Building CXX object CMakeFiles/Sibelia.dir/dnasequence.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/dnasequence.cpp.o -MF CMakeFiles/Sibelia.dir/dnasequence.cpp.o.d -o CMakeFiles/Sibelia.dir/dnasequence.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.cpp [ 55%] Building CXX object CMakeFiles/Sibelia.dir/edge.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/edge.cpp.o -MF CMakeFiles/Sibelia.dir/edge.cpp.o.d -o CMakeFiles/Sibelia.dir/edge.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/edge.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.h:11, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/edge.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ [ 60%] Building CXX object CMakeFiles/Sibelia.dir/fasta.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/fasta.cpp.o -MF CMakeFiles/Sibelia.dir/fasta.cpp.o.d -o CMakeFiles/Sibelia.dir/fasta.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.cpp [ 65%] Building CXX object CMakeFiles/Sibelia.dir/serialization.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/serialization.cpp.o -MF CMakeFiles/Sibelia.dir/serialization.cpp.o.d -o CMakeFiles/Sibelia.dir/serialization.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/serialization.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 70%] Building CXX object CMakeFiles/Sibelia.dir/synteny.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/synteny.cpp.o -MF CMakeFiles/Sibelia.dir/synteny.cpp.o.d -o CMakeFiles/Sibelia.dir/synteny.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/synteny.cpp [ 75%] Building CXX object CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o -MF CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o.d -o CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/serialization.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ [ 80%] Building CXX object CMakeFiles/Sibelia.dir/platform.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/platform.cpp.o -MF CMakeFiles/Sibelia.dir/platform.cpp.o.d -o CMakeFiles/Sibelia.dir/platform.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/synteny.cpp:9: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:12: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ [ 85%] Building CXX object CMakeFiles/Sibelia.dir/stranditerator.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/stranditerator.cpp.o -MF CMakeFiles/Sibelia.dir/stranditerator.cpp.o.d -o CMakeFiles/Sibelia.dir/stranditerator.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/stranditerator.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/stranditerator.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 90%] Building CXX object CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -MF CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o.d -o CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 95%] Building CXX object CMakeFiles/Sibelia.dir/resource.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/resource.cpp.o -MF CMakeFiles/Sibelia.dir/resource.cpp.o.d -o CMakeFiles/Sibelia.dir/resource.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/hashing.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.h:6, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.cpp:6: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/13/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here 65 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [100%] Linking CXX executable Sibelia /usr/bin/cmake -E cmake_link_script CMakeFiles/Sibelia.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/Sibelia.dir/sibelia.cpp.o CMakeFiles/Sibelia.dir/postprocessor.cpp.o CMakeFiles/Sibelia.dir/indexedsequence.cpp.o CMakeFiles/Sibelia.dir/util.cpp.o CMakeFiles/Sibelia.dir/outputgenerator.cpp.o CMakeFiles/Sibelia.dir/blockfinder.cpp.o CMakeFiles/Sibelia.dir/blockinstance.cpp.o CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o CMakeFiles/Sibelia.dir/dnasequence.cpp.o CMakeFiles/Sibelia.dir/edge.cpp.o CMakeFiles/Sibelia.dir/fasta.cpp.o CMakeFiles/Sibelia.dir/serialization.cpp.o CMakeFiles/Sibelia.dir/synteny.cpp.o CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o CMakeFiles/Sibelia.dir/platform.cpp.o CMakeFiles/Sibelia.dir/stranditerator.cpp.o CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o CMakeFiles/Sibelia.dir/resource.cpp.o -o Sibelia -ldivsufsort make[3]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' [100%] Built target Sibelia make[2]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_auto_test --no-parallel make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install -O--sourcedirectory=src cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/reproducible-path/sibelia-3.0.7\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/sibelia-3.0.7+dfsg/src -B/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/depend make[3]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' cd /build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sibelia-3.0.7+dfsg/src /build/reproducible-path/sibelia-3.0.7+dfsg/src /build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf /build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf /build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/Sibelia.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/build make[3]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' make[3]: Nothing to be done for 'CMakeFiles/Sibelia.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' [100%] Built target Sibelia make[2]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' Install the project... /usr/bin/cmake -P 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'/build/reproducible-path/sibelia-3.0.7+dfsg/obj-arm-linux-gnueabihf' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_install find debian -name LICENSE.txt -delete find debian -name INSTALL.md -delete make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src debian/rules override_dh_installman-arch make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_installman -a mv debian/sibelia/usr/share/man/py/man1/C-Sibelia.1 debian/sibelia/usr/share/man/man1/C-Sibelia.py.1 rm -rf debian/sibelia/usr/share/man/py make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_installman -O--sourcedirectory=src -Nsibelia dh_installinit -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_lintian -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_dwz -O--sourcedirectory=src dh_strip -O--sourcedirectory=src dh_makeshlibs -O--sourcedirectory=src dh_shlibdeps -O--sourcedirectory=src dpkg-shlibdeps: warning: debian/sibelia/usr/bin/Sibelia contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'sibelia' in '../sibelia_3.0.7+dfsg-3_armhf.deb'. dpkg-deb: building package 'sibelia-dbgsym' in '../sibelia-dbgsym_3.0.7+dfsg-3_armhf.deb'. dpkg-deb: building package 'sibelia-examples' in '../sibelia-examples_3.0.7+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary -O../sibelia_3.0.7+dfsg-3_armhf.buildinfo dpkg-genchanges --build=binary -O../sibelia_3.0.7+dfsg-3_armhf.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/23055/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/23055/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/23055 and its subdirectories I: Current time: Sat Apr 20 07:28:27 +14 2024 I: pbuilder-time-stamp: 1713547707