I: pbuilder: network access will be disabled during build I: Current time: Sat Feb 21 12:07:09 +14 2026 I: pbuilder-time-stamp: 1771625229 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [mindthegap_2.3.0-4.dsc] I: copying [./mindthegap_2.3.0.orig.tar.gz] I: copying [./mindthegap_2.3.0-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./mindthegap_2.3.0-4.dsc: unsupported subcommand dpkg-source: info: extracting mindthegap in mindthegap-2.3.0 dpkg-source: info: unpacking mindthegap_2.3.0.orig.tar.gz dpkg-source: info: unpacking mindthegap_2.3.0-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_gatb-core.patch dpkg-source: info: applying remove_unnecessary_installs.patch dpkg-source: info: applying modify_tests_for_autopkgtest.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying fix-use-as-function.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1888731/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-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 '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Feb 20 22:07 /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/1888731/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1888731/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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path 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=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=0fd8c3012b6943de9a89eae714f33825 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=1888731 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.JID3kYHC/pbuilderrc_yUuG --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.JID3kYHC/b2 --logfile b2/build.log mindthegap_2.3.0-4.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1888731/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-compat (= 13), cmake, libgatbcore-dev (>= 1.4.2+dfsg-7), libboost-dev, zlib1g-dev, libhdf5-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 ... 19965 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libgatbcore-dev (>= 1.4.2+dfsg-7); however: Package libgatbcore-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libhdf5-dev; however: Package libhdf5-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} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-dev{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libcom-err2{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgatbcore-dev{a} libgatbcore3{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-310{a} libhdf5-cpp-310{a} libhdf5-dev{a} libhdf5-fortran-310{a} libhdf5-hl-310{a} libhdf5-hl-cpp-310{a} libhdf5-hl-fortran-310{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsz2{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{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 krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 109 newly installed, 0 to remove and 0 not upgraded. Need to get 72.2 MB of archives. After unpacking 468 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.4-2 [2267 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 27 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.8-2 [1363 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.11.1-1+b1 [324 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.4-2 [9898 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.2-1 [55.9 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.23 [90.6 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-2 [539 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 55 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.23 [919 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 hdf5-helpers arm64 1.14.5+repack-3 [26.6 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-4 [56.9 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-4 [41.0 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-4 [41.0 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-4 [53.1 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-4 [126 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B] Get: 69 http://deb.debian.org/debian unstable/main arm64 libaec-dev arm64 1.1.3-1+b1 [20.2 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-4 [10.6 MB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 72 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-4 [15.9 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.6.9+dfsg-1 [305 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.22.0-1+b1 [553 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.8-2 [446 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.8-2 [446 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.5-3 [208 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.8-2 [1404 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.4.0-2 [3234 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.6+dfsg-2 [329 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libcurl4-openssl-dev arm64 8.11.1-1+b1 [449 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libgatbcore3 arm64 1.4.2+dfsg-13+b3 [1613 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libgatbcore-dev arm64 1.4.2+dfsg-13+b3 [4067 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-14 [361 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libhdf5-310 arm64 1.14.5+repack-3 [1155 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libhdf5-cpp-310 arm64 1.14.5+repack-3 [121 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libhdf5-fortran-310 arm64 1.14.5+repack-3 [110 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [66.1 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-fortran-310 arm64 1.14.5+repack-3 [42.1 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-cpp-310 arm64 1.14.5+repack-3 [24.4 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-3+b1 [293 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libjpeg-dev arm64 1:2.1.5-3+b1 [72.2 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libhdf5-dev arm64 1.14.5+repack-3 [3225 kB] Fetched 72.2 MB in 0s (238 MB/s) Preconfiguring packages ... Selecting previously unselected package libproc2-0: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 ... 19965 files and directories currently installed.) Preparing to unpack .../000-libproc2-0_2%3a4.0.4-6_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../001-procps_2%3a4.0.4-6_arm64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. 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Setting up libhdf5-dev (1.14.5+repack-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Processing triggers for libc-bin (2.40-5) ... 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 I: Building the package I: user script /srv/workspace/pbuilder/1888731/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/1888731/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/mindthegap-2.3.0/ && 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 > ../mindthegap_2.3.0-4_source.changes dpkg-buildpackage: info: source package mindthegap dpkg-buildpackage: info: source version 2.3.0-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu .. CMake Warning (dev) at CMakeLists.txt:142: Syntax Warning in cmake code at column 42 Argument not separated from preceding token by whitespace. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:147: Syntax Warning in cmake code at column 38 Argument not separated from preceding token by whitespace. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at CMakeLists.txt:21 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- 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 CMake Deprecation Warning at CMakeLists.txt:23 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- cxx: -g -O2 -ffile-prefix-map=/build/reproducible-path/mindthegap-2.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -- Configuring done (0.8s) -- 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 FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu dh_auto_build cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/mindthegap-2.3.0 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/build/reproducible-path/mindthegap-2.3.0/src/Finder.cpp /usr/bin/c++ -I/build/reproducible-path/mindthegap-2.3.0/src -I"/build/reproducible-path/mindthegap-2.3.0/src/*" -g -O2 -ffile-prefix-map=/build/reproducible-path/mindthegap-2.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/nwalign.dir/src/nwAlign/nwalign.cpp.o -MF CMakeFiles/nwalign.dir/src/nwAlign/nwalign.cpp.o.d -o CMakeFiles/nwalign.dir/src/nwAlign/nwalign.cpp.o -c /build/reproducible-path/mindthegap-2.3.0/src/nwAlign/nwalign.cpp /usr/bin/c++ -I/build/reproducible-path/mindthegap-2.3.0/src -I"/build/reproducible-path/mindthegap-2.3.0/src/*" -g -O2 -ffile-prefix-map=/build/reproducible-path/mindthegap-2.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/MindTheGap.dir/src/GraphAnalysis.cpp.o -MF CMakeFiles/MindTheGap.dir/src/GraphAnalysis.cpp.o.d -o CMakeFiles/MindTheGap.dir/src/GraphAnalysis.cpp.o -c /build/reproducible-path/mindthegap-2.3.0/src/GraphAnalysis.cpp [ 50%] Building CXX object CMakeFiles/MindTheGap.dir/src/main.cpp.o [ 10%] Building CXX object CMakeFiles/MindTheGap.dir/src/Filler.cpp.o /usr/bin/c++ -I/build/reproducible-path/mindthegap-2.3.0/src -I"/build/reproducible-path/mindthegap-2.3.0/src/*" -g -O2 -ffile-prefix-map=/build/reproducible-path/mindthegap-2.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/MindTheGap.dir/src/main.cpp.o -MF CMakeFiles/MindTheGap.dir/src/main.cpp.o.d -o CMakeFiles/MindTheGap.dir/src/main.cpp.o -c /build/reproducible-path/mindthegap-2.3.0/src/main.cpp /usr/bin/c++ -I/build/reproducible-path/mindthegap-2.3.0/src -I"/build/reproducible-path/mindthegap-2.3.0/src/*" -g -O2 -ffile-prefix-map=/build/reproducible-path/mindthegap-2.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/MindTheGap.dir/src/Filler.cpp.o -MF CMakeFiles/MindTheGap.dir/src/Filler.cpp.o.d -o CMakeFiles/MindTheGap.dir/src/Filler.cpp.o -c /build/reproducible-path/mindthegap-2.3.0/src/Filler.cpp [ 60%] Building CXX object CMakeFiles/MindTheGap.dir/src/GraphOutputDot.cpp.o [ 70%] Building CXX object CMakeFiles/MindTheGap.dir/src/IGraphOutput.cpp.o /usr/bin/c++ -I/build/reproducible-path/mindthegap-2.3.0/src -I"/build/reproducible-path/mindthegap-2.3.0/src/*" -g -O2 -ffile-prefix-map=/build/reproducible-path/mindthegap-2.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/MindTheGap.dir/src/GraphOutputDot.cpp.o -MF CMakeFiles/MindTheGap.dir/src/GraphOutputDot.cpp.o.d -o CMakeFiles/MindTheGap.dir/src/GraphOutputDot.cpp.o -c /build/reproducible-path/mindthegap-2.3.0/src/GraphOutputDot.cpp /usr/bin/c++ -I/build/reproducible-path/mindthegap-2.3.0/src -I"/build/reproducible-path/mindthegap-2.3.0/src/*" -g -O2 -ffile-prefix-map=/build/reproducible-path/mindthegap-2.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/MindTheGap.dir/src/IGraphOutput.cpp.o -MF CMakeFiles/MindTheGap.dir/src/IGraphOutput.cpp.o.d -o CMakeFiles/MindTheGap.dir/src/IGraphOutput.cpp.o -c /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.cpp [ 80%] Building CXX object CMakeFiles/MindTheGap.dir/src/Utils.cpp.o /usr/bin/c++ -I/build/reproducible-path/mindthegap-2.3.0/src -I"/build/reproducible-path/mindthegap-2.3.0/src/*" -g -O2 -ffile-prefix-map=/build/reproducible-path/mindthegap-2.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/MindTheGap.dir/src/Utils.cpp.o -MF CMakeFiles/MindTheGap.dir/src/Utils.cpp.o.d -o CMakeFiles/MindTheGap.dir/src/Utils.cpp.o -c /build/reproducible-path/mindthegap-2.3.0/src/Utils.cpp In file included from /build/reproducible-path/mindthegap-2.3.0/src/GraphOutputDot.hpp:24, from /build/reproducible-path/mindthegap-2.3.0/src/Filler.hpp:26, from /build/reproducible-path/mindthegap-2.3.0/src/GraphAnalysis.hpp:32, from /build/reproducible-path/mindthegap-2.3.0/src/GraphAnalysis.cpp:20: /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:54:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /build/reproducible-path/mindthegap-2.3.0/src/GraphAnalysis.hpp:20: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:58:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 58 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:62:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 62 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:66:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 66 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/mindthegap-2.3.0/src/GraphOutputDot.hpp:24, from /build/reproducible-path/mindthegap-2.3.0/src/Filler.hpp:26, from /build/reproducible-path/mindthegap-2.3.0/src/main.cpp:23: /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:54:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /usr/include/gatb/system/api/types.hpp:44, from /usr/include/gatb/system/api/IMemory.hpp:34, from /usr/include/gatb/system/impl/MemoryCommon.hpp:31, from /usr/include/gatb/system/impl/System.hpp:32, from /usr/include/gatb/gatb_core.hpp:31, from /build/reproducible-path/mindthegap-2.3.0/src/Finder.hpp:25, from /build/reproducible-path/mindthegap-2.3.0/src/main.cpp:22: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:58:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 58 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:62:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 62 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:66:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 66 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/mindthegap-2.3.0/src/GraphOutputDot.hpp:24, from /build/reproducible-path/mindthegap-2.3.0/src/Filler.hpp:26, from /build/reproducible-path/mindthegap-2.3.0/src/Filler.cpp:21: /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:54:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /usr/include/gatb/system/api/types.hpp:44, from /usr/include/gatb/system/api/IMemory.hpp:34, from /usr/include/gatb/system/impl/MemoryCommon.hpp:31, from /usr/include/gatb/system/impl/System.hpp:32, from /usr/include/gatb/gatb_core.hpp:31, from /build/reproducible-path/mindthegap-2.3.0/src/Filler.hpp:25: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:58:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 58 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:62:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 62 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:66:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 66 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.cpp:20: /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:54:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /usr/include/gatb/system/api/types.hpp:44, from /usr/include/gatb/system/api/IMemory.hpp:34, from /usr/include/gatb/system/impl/MemoryCommon.hpp:31, from /usr/include/gatb/system/impl/System.hpp:32, from /usr/include/gatb/gatb_core.hpp:31, from /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:24: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:58:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 58 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:62:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 62 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:66:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 66 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/mindthegap-2.3.0/src/GraphOutputDot.hpp:24, from /build/reproducible-path/mindthegap-2.3.0/src/GraphOutputDot.cpp:20: /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:54:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /usr/include/gatb/system/api/types.hpp:44, from /usr/include/gatb/system/api/IMemory.hpp:34, from /usr/include/gatb/system/impl/MemoryCommon.hpp:31, from /usr/include/gatb/system/impl/System.hpp:32, from /usr/include/gatb/gatb_core.hpp:31, from /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:24: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:58:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 58 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:62:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 62 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/IGraphOutput.hpp:66:61: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 66 | template <> struct hash::Type> : public unary_function::Type, size_t> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/Filler.cpp: In member function 'void Filler::writeFilledBreakpoint(std::vector&, std::string, std::string)': /build/reproducible-path/mindthegap-2.3.0/src/Filler.cpp:1052:65: warning: format '%f' expects argument of type 'double', but argument 6 has type 'const char*' [-Wformat=] 1052 | fprintf(_insert_file,">%s_len_%d_qual_%i_avg_cov_%.2f_median_cov_%.2f %s\n", | ~~~^ | | | double | %.2s 1053 | seedName.c_str(),llen,it->qual,solu_i.c_str() | ~~~~~~~~~~~~~~ | | | const char* /build/reproducible-path/mindthegap-2.3.0/src/Filler.cpp:1052:86: warning: format '%s' expects argument of type 'char*', but argument 8 has type 'double' [-Wformat=] 1052 | fprintf(_insert_file,">%s_len_%d_qual_%i_avg_cov_%.2f_median_cov_%.2f %s\n", | ~^ | | | char* | %f 1053 | seedName.c_str(),llen,it->qual,solu_i.c_str() 1054 | ,it->avg_coverage,it->median_coverage); | ~~~~~~~~~~~~~~~~~~~ | | | double /build/reproducible-path/mindthegap-2.3.0/src/Filler.cpp: In instantiation of 'void breakpointFunctor::operator()(gatb::core::bank::Sequence&) [with long unsigned int span = 128]': /usr/include/gatb/tools/designpattern/api/ICommand.hpp:324:69: required from 'void gatb::core::tools::dp::IDispatcher::IteratorCommand::execute() [with Item = gatb::core::bank::Sequence; Functor = breakpointFunctor<128>]' 324 | for (size_t i=0; i std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::substr(size_type, size_type) const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 654 | sourceSequence.substr(sourceSequence.size()- _object->_kmerSize,_object->_kmerSize); //suffix of size _kmerSize | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:54, from /usr/include/gatb/system/api/IMemory.hpp:35: /usr/include/c++/14/bits/basic_string.h:3208:7: note: declared here 3208 | substr(size_type __pos = 0, size_type __n = npos) const | ^~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/Filler.cpp:658:38: warning: ignoring return value of 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc> std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::substr(size_type, size_type) const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 658 | targetSequence.substr(0,_object->_kmerSize); //prefix of size _kmerSize | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/basic_string.h:3208:7: note: declared here 3208 | substr(size_type __pos = 0, size_type __n = npos) const | ^~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/Filler.cpp: In instantiation of 'void breakpointFunctor::operator()(gatb::core::bank::Sequence&) [with long unsigned int span = 96]': /usr/include/gatb/tools/designpattern/api/ICommand.hpp:324:69: required from 'void gatb::core::tools::dp::IDispatcher::IteratorCommand::execute() [with Item = gatb::core::bank::Sequence; Functor = breakpointFunctor<96>]' 324 | for (size_t i=0; i std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::substr(size_type, size_type) const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 654 | sourceSequence.substr(sourceSequence.size()- _object->_kmerSize,_object->_kmerSize); //suffix of size _kmerSize | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/basic_string.h:3208:7: note: declared here 3208 | substr(size_type __pos = 0, size_type __n = npos) const | ^~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/Filler.cpp:658:38: warning: ignoring return value of 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc> std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::substr(size_type, size_type) const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 658 | targetSequence.substr(0,_object->_kmerSize); //prefix of size _kmerSize | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/basic_string.h:3208:7: note: declared here 3208 | substr(size_type __pos = 0, size_type __n = npos) const | ^~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/Filler.cpp: In instantiation of 'void breakpointFunctor::operator()(gatb::core::bank::Sequence&) [with long unsigned int span = 64]': /usr/include/gatb/tools/designpattern/api/ICommand.hpp:324:69: required from 'void gatb::core::tools::dp::IDispatcher::IteratorCommand::execute() [with Item = gatb::core::bank::Sequence; Functor = breakpointFunctor<64>]' 324 | for (size_t i=0; i std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::substr(size_type, size_type) const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 654 | sourceSequence.substr(sourceSequence.size()- _object->_kmerSize,_object->_kmerSize); //suffix of size _kmerSize | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/basic_string.h:3208:7: note: declared here 3208 | substr(size_type __pos = 0, size_type __n = npos) const | ^~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/Filler.cpp:658:38: warning: ignoring return value of 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc> std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::substr(size_type, size_type) const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 658 | targetSequence.substr(0,_object->_kmerSize); //prefix of size _kmerSize | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/basic_string.h:3208:7: note: declared here 3208 | substr(size_type __pos = 0, size_type __n = npos) const | ^~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/Filler.cpp: In instantiation of 'void breakpointFunctor::operator()(gatb::core::bank::Sequence&) [with long unsigned int span = 32]': /usr/include/gatb/tools/designpattern/api/ICommand.hpp:324:69: required from 'void gatb::core::tools::dp::IDispatcher::IteratorCommand::execute() [with Item = gatb::core::bank::Sequence; Functor = breakpointFunctor<32>]' 324 | for (size_t i=0; i std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::substr(size_type, size_type) const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 654 | sourceSequence.substr(sourceSequence.size()- _object->_kmerSize,_object->_kmerSize); //suffix of size _kmerSize | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/basic_string.h:3208:7: note: declared here 3208 | substr(size_type __pos = 0, size_type __n = npos) const | ^~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/Filler.cpp:658:38: warning: ignoring return value of 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc> std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::substr(size_type, size_type) const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; size_type = long unsigned int]', declared with attribute 'nodiscard' [-Wunused-result] 658 | targetSequence.substr(0,_object->_kmerSize); //prefix of size _kmerSize | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/basic_string.h:3208:7: note: declared here 3208 | substr(size_type __pos = 0, size_type __n = npos) const | ^~~~~~ In file included from /build/reproducible-path/mindthegap-2.3.0/src/Finder.cpp:22: /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp: In instantiation of 'void FindBreakpoints::writeIndel(int, std::string&, uint64_t, std::string, std::string, int, std::string) [with long unsigned int span = 128; std::string = std::__cxx11::basic_string; uint64_t = long unsigned int]': /build/reproducible-path/mindthegap-2.3.0/src/FindHeteroInsertion.hpp:119:30: required from 'bool FindHeteroInsertion::update() [with long unsigned int span = 128]' 119 | this->_find->writeIndel(this->_find->breakpoint_id(), this->_find->chrom_name(), this->_find->position() - 1, ref, inser_base_one, i, STR_HET_TYPE); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindHeteroInsertion.hpp:48:6: required from here 48 | bool FindHeteroInsertion::update() | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp:693:46: warning: format '%lli' expects argument of type 'long long int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 693 | fprintf(this->finder->_vcf_file, "%s\t%lli\tbkpt%i\t%s\t%s\t.\tPASS\tTYPE=INS;LEN=%i;FUZZY=%i\tGT\t%s\n", | ~~~^ | | | long long int | %li 694 | chrom_name.c_str(), 695 | position + 1, //switch to 1-based | ~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp: In instantiation of 'void FindBreakpoints::writeBreakpoint(int, std::string&, uint64_t, std::string&, std::string&, int, std::string, bool, bool) [with long unsigned int span = 128; std::string = std::__cxx11::basic_string; uint64_t = long unsigned int]': /build/reproducible-path/mindthegap-2.3.0/src/FindHeteroInsertion.hpp:145:57: required from 'bool FindHeteroInsertion::update() [with long unsigned int span = 128]' 145 | this->_find->writeBreakpoint(this->_find->breakpoint_id(), this->_find->chrom_name(), this->_find->position() - 1 + i, kmer_begin_str, kmer_end_str, i, STR_HET_TYPE, this->_find->het_kmer_history(this->_find->het_kmer_begin_index() + i).is_repeated, this->_find->kmer_end_is_repeated()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindHeteroInsertion.hpp:48:6: required from here 48 | bool FindHeteroInsertion::update() | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp:642:63: warning: format '%lli' expects argument of type 'long long int', but argument 5 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 642 | fprintf(this->finder->_breakpoint_file,">bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s left_kmer\n%s\n>bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s right_kmer\n%s\n", | ~~~^ | | | long long int | %li ...... 645 | position+1, //switch to 1-based | ~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp:642:113: warning: format '%lli' expects argument of type 'long long int', but argument 12 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 642 | fprintf(this->finder->_breakpoint_file,">bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s left_kmer\n%s\n>bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s right_kmer\n%s\n", | ~~~^ | | | long long int | %li ...... 652 | position+1, //switch to 1-based | ~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp: In instantiation of 'void FindBreakpoints::writeVcfVariant(int, std::string&, uint64_t, char*, char*, int, std::string) [with long unsigned int span = 128; std::string = std::__cxx11::basic_string; uint64_t = long unsigned int]': /build/reproducible-path/mindthegap-2.3.0/src/FindDeletion.hpp:158:30: required from 'bool FindDeletion::update() [with long unsigned int span = 128]' 158 | this->_find->writeVcfVariant(this->_find->breakpoint_id(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 | this->_find->chrom_name(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 | del_start_pos, del_sequence, alt_char, repeat_size, STR_DEL_TYPE); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindDeletion.hpp:62:6: required from here 62 | bool FindDeletion::update() | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp:668:49: warning: format '%lli' expects argument of type 'long long int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 668 | fprintf(this->finder->_vcf_file,"%s\t%lli\tbkpt%i\t%s\t%s\t.\tPASS\tTYPE=%s;LEN=%i;FUZZY=%i\tGT\t1/1\n", | ~~~^ | | | long long int | %li 669 | chrom_name.c_str(), 670 | position+1, //switch to 1-based | ~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp: In instantiation of 'void FindBreakpoints::writeIndel(int, std::string&, uint64_t, std::string, std::string, int, std::string) [with long unsigned int span = 96; std::string = std::__cxx11::basic_string; uint64_t = long unsigned int]': /build/reproducible-path/mindthegap-2.3.0/src/FindHeteroInsertion.hpp:119:30: required from 'bool FindHeteroInsertion::update() [with long unsigned int span = 96]' 119 | this->_find->writeIndel(this->_find->breakpoint_id(), this->_find->chrom_name(), this->_find->position() - 1, ref, inser_base_one, i, STR_HET_TYPE); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindHeteroInsertion.hpp:48:6: required from here 48 | bool FindHeteroInsertion::update() | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp:693:46: warning: format '%lli' expects argument of type 'long long int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 693 | fprintf(this->finder->_vcf_file, "%s\t%lli\tbkpt%i\t%s\t%s\t.\tPASS\tTYPE=INS;LEN=%i;FUZZY=%i\tGT\t%s\n", | ~~~^ | | | long long int | %li 694 | chrom_name.c_str(), 695 | position + 1, //switch to 1-based | ~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp: In instantiation of 'void FindBreakpoints::writeBreakpoint(int, std::string&, uint64_t, std::string&, std::string&, int, std::string, bool, bool) [with long unsigned int span = 96; std::string = std::__cxx11::basic_string; uint64_t = long unsigned int]': /build/reproducible-path/mindthegap-2.3.0/src/FindHeteroInsertion.hpp:145:57: required from 'bool FindHeteroInsertion::update() [with long unsigned int span = 96]' 145 | this->_find->writeBreakpoint(this->_find->breakpoint_id(), this->_find->chrom_name(), this->_find->position() - 1 + i, kmer_begin_str, kmer_end_str, i, STR_HET_TYPE, this->_find->het_kmer_history(this->_find->het_kmer_begin_index() + i).is_repeated, this->_find->kmer_end_is_repeated()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindHeteroInsertion.hpp:48:6: required from here 48 | bool FindHeteroInsertion::update() | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp:642:63: warning: format '%lli' expects argument of type 'long long int', but argument 5 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 642 | fprintf(this->finder->_breakpoint_file,">bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s left_kmer\n%s\n>bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s right_kmer\n%s\n", | ~~~^ | | | long long int | %li ...... 645 | position+1, //switch to 1-based | ~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp:642:113: warning: format '%lli' expects argument of type 'long long int', but argument 12 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 642 | fprintf(this->finder->_breakpoint_file,">bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s left_kmer\n%s\n>bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s right_kmer\n%s\n", | ~~~^ | | | long long int | %li ...... 652 | position+1, //switch to 1-based | ~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp: In instantiation of 'void FindBreakpoints::writeVcfVariant(int, std::string&, uint64_t, char*, char*, int, std::string) [with long unsigned int span = 96; std::string = std::__cxx11::basic_string; uint64_t = long unsigned int]': /build/reproducible-path/mindthegap-2.3.0/src/FindDeletion.hpp:158:30: required from 'bool FindDeletion::update() [with long unsigned int span = 96]' 158 | this->_find->writeVcfVariant(this->_find->breakpoint_id(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 | this->_find->chrom_name(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 | del_start_pos, del_sequence, alt_char, repeat_size, STR_DEL_TYPE); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindDeletion.hpp:62:6: required from here 62 | bool FindDeletion::update() | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp:668:49: warning: format '%lli' expects argument of type 'long long int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 668 | fprintf(this->finder->_vcf_file,"%s\t%lli\tbkpt%i\t%s\t%s\t.\tPASS\tTYPE=%s;LEN=%i;FUZZY=%i\tGT\t1/1\n", | ~~~^ | | | long long int | %li 669 | chrom_name.c_str(), 670 | position+1, //switch to 1-based | ~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp: In instantiation of 'void FindBreakpoints::writeIndel(int, std::string&, uint64_t, std::string, std::string, int, std::string) [with long unsigned int span = 64; std::string = std::__cxx11::basic_string; uint64_t = long unsigned int]': /build/reproducible-path/mindthegap-2.3.0/src/FindHeteroInsertion.hpp:119:30: required from 'bool FindHeteroInsertion::update() [with long unsigned int span = 64]' 119 | this->_find->writeIndel(this->_find->breakpoint_id(), this->_find->chrom_name(), this->_find->position() - 1, ref, inser_base_one, i, STR_HET_TYPE); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindHeteroInsertion.hpp:48:6: required from here 48 | bool FindHeteroInsertion::update() | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp:693:46: warning: format '%lli' expects argument of type 'long long int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 693 | fprintf(this->finder->_vcf_file, "%s\t%lli\tbkpt%i\t%s\t%s\t.\tPASS\tTYPE=INS;LEN=%i;FUZZY=%i\tGT\t%s\n", | ~~~^ | | | long long int | %li 694 | chrom_name.c_str(), 695 | position + 1, //switch to 1-based | ~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp: In instantiation of 'void FindBreakpoints::writeBreakpoint(int, std::string&, uint64_t, std::string&, std::string&, int, std::string, bool, bool) [with long unsigned int span = 64; std::string = std::__cxx11::basic_string; uint64_t = long unsigned int]': /build/reproducible-path/mindthegap-2.3.0/src/FindHeteroInsertion.hpp:145:57: required from 'bool FindHeteroInsertion::update() [with long unsigned int span = 64]' 145 | this->_find->writeBreakpoint(this->_find->breakpoint_id(), this->_find->chrom_name(), this->_find->position() - 1 + i, kmer_begin_str, kmer_end_str, i, STR_HET_TYPE, this->_find->het_kmer_history(this->_find->het_kmer_begin_index() + i).is_repeated, this->_find->kmer_end_is_repeated()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindHeteroInsertion.hpp:48:6: required from here 48 | bool FindHeteroInsertion::update() | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp:642:63: warning: format '%lli' expects argument of type 'long long int', but argument 5 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 642 | fprintf(this->finder->_breakpoint_file,">bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s left_kmer\n%s\n>bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s right_kmer\n%s\n", | ~~~^ | | | long long int | %li ...... 645 | position+1, //switch to 1-based | ~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp:642:113: warning: format '%lli' expects argument of type 'long long int', but argument 12 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 642 | fprintf(this->finder->_breakpoint_file,">bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s left_kmer\n%s\n>bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s right_kmer\n%s\n", | ~~~^ | | | long long int | %li ...... 652 | position+1, //switch to 1-based | ~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp: In instantiation of 'void FindBreakpoints::writeVcfVariant(int, std::string&, uint64_t, char*, char*, int, std::string) [with long unsigned int span = 64; std::string = std::__cxx11::basic_string; uint64_t = long unsigned int]': /build/reproducible-path/mindthegap-2.3.0/src/FindDeletion.hpp:158:30: required from 'bool FindDeletion::update() [with long unsigned int span = 64]' 158 | this->_find->writeVcfVariant(this->_find->breakpoint_id(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 | this->_find->chrom_name(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 | del_start_pos, del_sequence, alt_char, repeat_size, STR_DEL_TYPE); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindDeletion.hpp:62:6: required from here 62 | bool FindDeletion::update() | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp:668:49: warning: format '%lli' expects argument of type 'long long int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 668 | fprintf(this->finder->_vcf_file,"%s\t%lli\tbkpt%i\t%s\t%s\t.\tPASS\tTYPE=%s;LEN=%i;FUZZY=%i\tGT\t1/1\n", | ~~~^ | | | long long int | %li 669 | chrom_name.c_str(), 670 | position+1, //switch to 1-based | ~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp: In instantiation of 'void FindBreakpoints::writeIndel(int, std::string&, uint64_t, std::string, std::string, int, std::string) [with long unsigned int span = 32; std::string = std::__cxx11::basic_string; uint64_t = long unsigned int]': /build/reproducible-path/mindthegap-2.3.0/src/FindHeteroInsertion.hpp:119:30: required from 'bool FindHeteroInsertion::update() [with long unsigned int span = 32]' 119 | this->_find->writeIndel(this->_find->breakpoint_id(), this->_find->chrom_name(), this->_find->position() - 1, ref, inser_base_one, i, STR_HET_TYPE); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindHeteroInsertion.hpp:48:6: required from here 48 | bool FindHeteroInsertion::update() | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp:693:46: warning: format '%lli' expects argument of type 'long long int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 693 | fprintf(this->finder->_vcf_file, "%s\t%lli\tbkpt%i\t%s\t%s\t.\tPASS\tTYPE=INS;LEN=%i;FUZZY=%i\tGT\t%s\n", | ~~~^ | | | long long int | %li 694 | chrom_name.c_str(), 695 | position + 1, //switch to 1-based | ~~~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp: In instantiation of 'void FindBreakpoints::writeBreakpoint(int, std::string&, uint64_t, std::string&, std::string&, int, std::string, bool, bool) [with long unsigned int span = 32; std::string = std::__cxx11::basic_string; uint64_t = long unsigned int]': /build/reproducible-path/mindthegap-2.3.0/src/FindHeteroInsertion.hpp:145:57: required from 'bool FindHeteroInsertion::update() [with long unsigned int span = 32]' 145 | this->_find->writeBreakpoint(this->_find->breakpoint_id(), this->_find->chrom_name(), this->_find->position() - 1 + i, kmer_begin_str, kmer_end_str, i, STR_HET_TYPE, this->_find->het_kmer_history(this->_find->het_kmer_begin_index() + i).is_repeated, this->_find->kmer_end_is_repeated()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindHeteroInsertion.hpp:48:6: required from here 48 | bool FindHeteroInsertion::update() | ^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp:642:63: warning: format '%lli' expects argument of type 'long long int', but argument 5 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 642 | fprintf(this->finder->_breakpoint_file,">bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s left_kmer\n%s\n>bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s right_kmer\n%s\n", | ~~~^ | | | long long int | %li ...... 645 | position+1, //switch to 1-based | ~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp:642:113: warning: format '%lli' expects argument of type 'long long int', but argument 12 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 642 | fprintf(this->finder->_breakpoint_file,">bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s left_kmer\n%s\n>bkpt%i_%s_pos_%lli_fuzzy_%i_%s %s right_kmer\n%s\n", | ~~~^ | | | long long int | %li ...... 652 | position+1, //switch to 1-based | ~~~~~~~~~~ | | | uint64_t {aka long unsigned int} /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp: In instantiation of 'void FindBreakpoints::writeVcfVariant(int, std::string&, uint64_t, char*, char*, int, std::string) [with long unsigned int span = 32; std::string = std::__cxx11::basic_string; uint64_t = long unsigned int]': /build/reproducible-path/mindthegap-2.3.0/src/FindDeletion.hpp:158:30: required from 'bool FindDeletion::update() [with long unsigned int span = 32]' 158 | this->_find->writeVcfVariant(this->_find->breakpoint_id(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 | this->_find->chrom_name(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 | del_start_pos, del_sequence, alt_char, repeat_size, STR_DEL_TYPE); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindDeletion.hpp:62:6: required from here 62 | bool FindDeletion::update() | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/mindthegap-2.3.0/src/FindBreakpoints.hpp:668:49: warning: format '%lli' expects argument of type 'long long int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 668 | fprintf(this->finder->_vcf_file,"%s\t%lli\tbkpt%i\t%s\t%s\t.\tPASS\tTYPE=%s;LEN=%i;FUZZY=%i\tGT\t1/1\n", | ~~~^ | | | long long int | %li 669 | chrom_name.c_str(), 670 | position+1, //switch to 1-based | ~~~~~~~~~~ | | | uint64_t {aka long unsigned int} [ 90%] Linking CXX executable bin/nwalign /usr/bin/cmake -E cmake_link_script CMakeFiles/nwalign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mindthegap-2.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/nwalign.dir/link.d CMakeFiles/nwalign.dir/src/nwAlign/nwalign.cpp.o -o bin/nwalign -L/usr/lib/aarch64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/aarch64-linux-gnu/hdf5/serial -lgatbcore -lhdf5 make[3]: Leaving directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' [ 90%] Built target nwalign [100%] Linking CXX executable bin/MindTheGap /usr/bin/cmake -E cmake_link_script CMakeFiles/MindTheGap.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mindthegap-2.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/MindTheGap.dir/link.d CMakeFiles/MindTheGap.dir/src/main.cpp.o CMakeFiles/MindTheGap.dir/src/Filler.cpp.o CMakeFiles/MindTheGap.dir/src/Finder.cpp.o CMakeFiles/MindTheGap.dir/src/GraphAnalysis.cpp.o CMakeFiles/MindTheGap.dir/src/GraphOutputDot.cpp.o CMakeFiles/MindTheGap.dir/src/IGraphOutput.cpp.o CMakeFiles/MindTheGap.dir/src/Utils.cpp.o -o bin/MindTheGap -L/usr/lib/aarch64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/aarch64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 make[3]: Leaving directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' [100%] Built target MindTheGap make[2]: Leaving directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-aarch64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/mindthegap-2.3.0/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/mindthegap-2.3.0 -B/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/mindthegap-2.3.0/debian/tmp/usr/bin/MindTheGap -- Set non-toolchain portion of runtime path of "/build/reproducible-path/mindthegap-2.3.0/debian/tmp/usr/bin/MindTheGap" to "" make[1]: Leaving directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mindthegap/usr/bin/MindTheGap was not linked against libhdf5_serial.so.310 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'mindthegap-examples' in '../mindthegap-examples_2.3.0-4_all.deb'. dpkg-deb: building package 'mindthegap-dbgsym' in '../mindthegap-dbgsym_2.3.0-4_arm64.deb'. dpkg-deb: building package 'mindthegap' in '../mindthegap_2.3.0-4_arm64.deb'. dpkg-genbuildinfo --build=binary -O../mindthegap_2.3.0-4_arm64.buildinfo dpkg-genchanges --build=binary -O../mindthegap_2.3.0-4_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) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1888731/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1888731/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/1888731 and its subdirectories I: Current time: Sat Feb 21 12:08:26 +14 2026 I: pbuilder-time-stamp: 1771625306