I: pbuilder: network access will be disabled during build I: Current time: Fri Feb 13 13:13:16 -12 2026 I: pbuilder-time-stamp: 1771031596 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/3428785/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='55749c0e37c3448c8f42639adc650050' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3428785' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.fsq9spGR/pbuilderrc_vy7C --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.fsq9spGR/b1 --logfile b1/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+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.11.10+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1~bpo12+1 (2024-12-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3428785/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-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 ... 19849 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-2.5-0{a} libldap-dev{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 75.0 MB of archives. After unpacking 465 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-4 [200 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.3-1 [92.1 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-4 [723 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.3-1 [2268 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 27 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.19.0-3+b3 [49.5 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.19+dfsg-1 [187 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.1-1 [351 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.31.3-1 [11.9 MB] Get: 48 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.23 [90.6 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 55 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-4 [1600 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.23 [919 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 hdf5-helpers amd64 1.14.5+repack-3 [26.6 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-3 [59.5 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-3 [41.7 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-3 [42.0 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-3 [53.5 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-3 [126 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 69 http://deb.debian.org/debian unstable/main amd64 libaec-dev amd64 1.1.3-1+b1 [21.5 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-4 [10.6 MB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 72 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-3 [15.7 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.5.19+dfsg-1 [303 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.8-2 [449 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2 [449 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.8-2 [1391 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.4.0-2 [2790 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libcurl4-openssl-dev amd64 8.11.1-1 [464 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libgatbcore3 amd64 1.4.2+dfsg-13+b3 [1841 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libgatbcore-dev amd64 1.4.2+dfsg-13+b3 [3819 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-12 [836 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libhdf5-cpp-310 amd64 1.14.5+repack-3 [133 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libhdf5-fortran-310 amd64 1.14.5+repack-3 [111 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [69.3 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-fortran-310 amd64 1.14.5+repack-3 [43.9 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-cpp-310 amd64 1.14.5+repack-3 [24.4 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3+b1 [292 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-3+b1 [72.2 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libhdf5-dev amd64 1.14.5+repack-3 [3165 kB] Fetched 75.0 MB in 3s (25.9 MB/s) Preconfiguring packages ... Selecting previously unselected package libproc2-0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19849 files and directories currently installed.) Preparing to unpack .../000-libproc2-0_2%3a4.0.4-6_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../001-procps_2%3a4.0.4-6_amd64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. 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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: Running cd /build/reproducible-path/mindthegap-2.3.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-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 amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-x86_64-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/x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -- Configuring done (0.6s) -- 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-x86_64-linux-gnu dh_auto_build cd obj-x86_64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/mindthegap-2.3.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/mindthegap-2.3.0 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-ffile-prefix-map=/build/reproducible-path/mindthegap-2.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 /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 -fcf-protection -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 -fcf-protection -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 /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 -fcf-protection -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/MindTheGap.dir/src/Finder.cpp.o -MF CMakeFiles/MindTheGap.dir/src/Finder.cpp.o.d -o CMakeFiles/MindTheGap.dir/src/Finder.cpp.o -c /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 -fcf-protection -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/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 | ^~~~~~~~~~~~~~ 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 | ^~~~~~~~~~~~~~ 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: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: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: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/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 -fcf-protection -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/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial -lgatbcore -lhdf5 make[3]: Leaving directory '/build/reproducible-path/mindthegap-2.3.0/obj-x86_64-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 -fcf-protection -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/x86_64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 make[3]: Leaving directory '/build/reproducible-path/mindthegap-2.3.0/obj-x86_64-linux-gnu' [100%] Built target MindTheGap make[2]: Leaving directory '/build/reproducible-path/mindthegap-2.3.0/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/mindthegap-2.3.0/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/mindthegap-2.3.0/obj-x86_64-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-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-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/mindthegap-2.3.0 -B/build/reproducible-path/mindthegap-2.3.0/obj-x86_64-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-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/mindthegap-2.3.0/obj-x86_64-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-x86_64-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: 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-dbgsym' in '../mindthegap-dbgsym_2.3.0-4_amd64.deb'. dpkg-deb: building package 'mindthegap' in '../mindthegap_2.3.0-4_amd64.deb'. dpkg-deb: building package 'mindthegap-examples' in '../mindthegap-examples_2.3.0-4_all.deb'. dpkg-genbuildinfo --build=binary -O../mindthegap_2.3.0-4_amd64.buildinfo dpkg-genchanges --build=binary -O../mindthegap_2.3.0-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration 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/3428785 and its subdirectories I: Current time: Fri Feb 13 13:15:14 -12 2026 I: pbuilder-time-stamp: 1771031714