Running as unit: rb-build-arm64_12-70470.service ==================================================================================== Tue Nov 26 09:08:15 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_12) on jenkins, called using "codethink04-arm64 codethink03-arm64" as arguments. Tue Nov 26 09:08:15 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-hb2G47Wb" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Nov 26 09:08:15 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Tue Nov 26 09:08:15 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-pIZsHt' Tue Nov 26 09:08:15 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Tue Nov 26 09:08:15 UTC 2024 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-vWrtOz' ok, let's check if mindthegap is building anywhere yet… ok, mindthegap is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of mindthegap in unstable on arm64 on jenkins now. 1st build will be done on codethink04-arm64.debian.net. 2nd build will be done on codethink03-arm64.debian.net. ============================================================================= Tue Nov 26 09:08:32 UTC 2024 I: starting to build mindthegap/unstable/arm64 on jenkins on '2024-11-26 09:08' Tue Nov 26 09:08:32 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_12/70470/console.log 1732612112 arm64 unstable mindthegap Tue Nov 26 09:08:32 UTC 2024 I: Downloading source for unstable/mindthegap=2.3.0-4 --2024-11-26 09:08:32-- http://deb.debian.org/debian/pool/main/m/mindthegap/mindthegap_2.3.0-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2441 (2.4K) [text/prs.lines.tag] Saving to: ‘mindthegap_2.3.0-4.dsc’ 0K .. 100% 363M=0s 2024-11-26 09:08:32 (363 MB/s) - ‘mindthegap_2.3.0-4.dsc’ saved [2441/2441] --2024-11-26 09:08:32-- http://deb.debian.org/debian/pool/main/m/mindthegap/mindthegap_2.3.0-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2441 (2.4K) [text/prs.lines.tag] Saving to: ‘mindthegap_2.3.0-4.dsc’ 0K .. 100% 363M=0s 2024-11-26 09:08:32 (363 MB/s) - ‘mindthegap_2.3.0-4.dsc’ saved [2441/2441] Tue Nov 26 09:08:32 UTC 2024 I: mindthegap_2.3.0-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: mindthegap Binary: mindthegap, mindthegap-examples Architecture: any-amd64 arm64 loong64 mips64el ppc64el ia64 ppc64 riscv64 sparc64 alpha all Version: 2.3.0-4 Maintainer: Debian Med Packaging Team Uploaders: Shayan Doust , Étienne Mollier Homepage: https://github.com/GATB/MindTheGap Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/mindthegap Vcs-Git: https://salsa.debian.org/med-team/mindthegap.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), cmake, libgatbcore-dev (>= 1.4.2+dfsg-7), libboost-dev, zlib1g-dev, libhdf5-dev Package-List: mindthegap deb science optional arch=any-amd64,arm64,loong64,mips64el,ppc64el,ia64,ppc64,riscv64,sparc64,alpha mindthegap-examples deb science optional arch=all Checksums-Sha1: 2822f481a334d040916ee2b4e875ef83de67e430 777831 mindthegap_2.3.0.orig.tar.gz 248efba0de4057bc4a90fe168dd33fc2f8a3e392 8148 mindthegap_2.3.0-4.debian.tar.xz Checksums-Sha256: 1d886d34bb892079121755c856329155f332e4bc19eaf31b41ce3d0333544ac5 777831 mindthegap_2.3.0.orig.tar.gz d53e6efe402f9e33e153af48a1ef4c41ffde7f5a95d3b6fe081b2dfb5d2dc10d 8148 mindthegap_2.3.0-4.debian.tar.xz Files: 7a5d75e60c812e921dd4a60fd71c9b74 777831 mindthegap_2.3.0.orig.tar.gz e0edfc0969b45deb1cd1d723dac5f7e9 8148 mindthegap_2.3.0-4.debian.tar.xz Dgit: 6736096075ffa4861be0620511992de69917750e debian archive/debian/2.3.0-4 https://git.dgit.debian.org/mindthegap -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmbbWQcUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdp7gxAAgEKVr8SwCVEV8e6ZypyZ9GYpLpgh IkKwpNvs6WuNdOa2aS4LRyLi2wmZt55dGcoIElBpQa8tp7OSL1GxPWzQGw6LRurh LU+bPIZMxBNqvqDENDPoPQ4Sh+W7RstYQ9gDcGiJtNZZBRP6By4cu6kJklerNnP+ jZ7iFvkkl66h/JesjGJq6b6Q2Q4f0y59FNpW2ExCqSgNwPDRunmBkotI0x1c5ZxY zsrc2yzOWyLqI7W3edRbKtIGD94SSsax5erDAeazJGCjanWOfQC+ozcUxrLneb2q Z5JubKukm111RvGzqv/muhXWdWDiKa8nyjijH8GEQArClHIUrcNMTTxCi85DxPpV SLwM/OYS5kAVOTNe2UTY2PP0hN4E9QMhQxtV4qZy9lYWqD8aI9V9dXxPbxZZUz7P LldImOki9LYT5wbArdaKuVGhdT3HLDhYw8z/h07TAhMVQblhTazfCv/f6u5iT5K3 kjhRUwQthpOwR6FN9+23L1tCIkg63Sc3I/6O6GwniKHIXmZXvbCSdTpbJEwUZLBU uMldXOXpAomzGxJPgw7npDSWeE42W5bb83fEgN2y1f50c1kvUg8IHkJ0gUw4gN5D R5PTtxD1Z33IETvw9WKkRScSrtd3sw0CDHJIxEJhgsfS+w1AZDbbxeV/lYEHYJix VyAqm7rK6bfrOec= =RxFO -----END PGP SIGNATURE----- Tue Nov 26 09:08:32 UTC 2024 I: Checking whether the package is not for us Tue Nov 26 09:08:32 UTC 2024 I: Starting 1st build on remote node codethink04-arm64.debian.net. Tue Nov 26 09:08:32 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Tue Nov 26 09:08:32 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Tue Nov 26 09:08:32 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-xJwyql' ==================================================================================== Tue Nov 26 09:08:34 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 mindthegap unstable /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem 2.3.0-4" as arguments. Tue Nov 26 09:08:34 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-81Jmelqw" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Nov 26 09:08:34 UTC 2024 I: Downloading source for unstable/mindthegap=2.3.0-4 Reading package lists... NOTICE: 'mindthegap' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/mindthegap.git Please use: git clone https://salsa.debian.org/med-team/mindthegap.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 788 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main mindthegap 2.3.0-4 (dsc) [2441 B] Get:2 http://deb.debian.org/debian unstable/main mindthegap 2.3.0-4 (tar) [778 kB] Get:3 http://deb.debian.org/debian unstable/main mindthegap 2.3.0-4 (diff) [8148 B] Fetched 788 kB in 0s (2615 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'mindthegap' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/mindthegap.git Please use: git clone https://salsa.debian.org/med-team/mindthegap.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 788 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main mindthegap 2.3.0-4 (dsc) [2441 B] Get:2 http://deb.debian.org/debian unstable/main mindthegap 2.3.0-4 (tar) [778 kB] Get:3 http://deb.debian.org/debian unstable/main mindthegap 2.3.0-4 (diff) [8148 B] Fetched 788 kB in 0s (2615 kB/s) Download complete and in download only mode ============================================================================= Building mindthegap in unstable on arm64 on codethink04-arm64 now. Date: Tue Nov 26 09:08:34 GMT 2024 Date UTC: Tue Nov 26 09:08:34 UTC 2024 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Mon Nov 25 21:08:34 -12 2024 I: pbuilder-time-stamp: 1732612114 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 gpgv: Signature made Fri Sep 6 19:33:27 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mindthegap_2.3.0-4.dsc: no acceptable signature found 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/1006890/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='d6e76ddf703a4fcca27efabb22419cb2' 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='1006890' 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.r3lD5Jem/pbuilderrc_Ux50 --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.r3lD5Jem/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' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1006890/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 ... 20083 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} 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} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-103-1t64{a} libhdf5-cpp-103-1t64{a} libhdf5-dev{a} libhdf5-fortran-102t64{a} libhdf5-hl-100t64{a} libhdf5-hl-cpp-100t64{a} libhdf5-hl-fortran-100t64{a} libicu72{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} 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-dev{a} libtool{a} libuchardet0{a} libunbound8{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, 103 newly installed, 0 to remove and 0 not upgraded. Need to get 68.7 MB of archives. After unpacking 457 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 0.22.5-2 [198 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 1.23.0-5 [1129 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 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 1.4.19-4 [277 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 0.22.5-2 [723 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.1-1 [2267 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [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 1.21.3-3 [32.1 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 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 1.21.3-3 [310 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.11.0-1 [322 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.1-1 [9873 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.1-1+b1 [55.1 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 hdf5-helpers arm64 1.10.10+repack-4 [23.5 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-3 [56.7 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-3 [40.3 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-3 [40.8 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-3 [52.2 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-3 [126 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B] Get: 63 http://deb.debian.org/debian unstable/main arm64 libaec-dev arm64 1.1.3-1+b1 [20.2 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-3.2+b1 [10.6 MB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 66 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-3 [15.8 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.5.18+dfsg-3+b1 [300 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-2+b2 [329 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-2+b2 [621 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.22.0-1 [553 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.8-2 [446 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.8-2 [446 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.5-2+b1 [208 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.8-2 [1404 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.6+dfsg-1+b1 [329 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libcurl4-openssl-dev arm64 8.11.0-1 [447 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libgatbcore3 arm64 1.4.2+dfsg-13+b2 [1617 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libgatbcore-dev arm64 1.4.2+dfsg-13+b2 [3989 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4 [1050 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libhdf5-cpp-103-1t64 arm64 1.10.10+repack-4 [118 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libhdf5-fortran-102t64 arm64 1.10.10+repack-4 [88.1 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4 [60.9 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-fortran-100t64 arm64 1.10.10+repack-4 [39.0 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-cpp-100t64 arm64 1.10.10+repack-4 [21.4 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-3+b1 [293 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libjpeg-dev arm64 1:2.1.5-3+b1 [72.2 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libhdf5-dev arm64 1.10.10+repack-4 [2697 kB] Fetched 68.7 MB in 0s (147 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 20083 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. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../004-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../007-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../010-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../012-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../013-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../014-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../015-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../016-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package cmake-data. Preparing to unpack .../017-cmake-data_3.31.1-1_all.deb ... Unpacking cmake-data (3.31.1-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../018-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../019-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package libarchive13t64:arm64. Preparing to unpack .../020-libarchive13t64_3.7.4-1.1_arm64.deb ... Unpacking libarchive13t64:arm64 (3.7.4-1.1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../021-libbrotli1_1.1.0-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b6) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../022-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../023-libcom-err2_1.47.1-1+b1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../024-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../025-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../026-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../027-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../028-libsasl2-modules-db_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../029-libsasl2-2_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../030-libldap-2.5-0_2.5.18+dfsg-3+b1_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../031-libnghttp2-14_1.64.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../032-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../033-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../034-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:arm64. Preparing to unpack .../035-libcurl4t64_8.11.0-1_arm64.deb ... Unpacking libcurl4t64:arm64 (8.11.0-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../036-libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package libjsoncpp26:arm64. Preparing to unpack .../037-libjsoncpp26_1.9.6-3_arm64.deb ... Unpacking libjsoncpp26:arm64 (1.9.6-3) ... Selecting previously unselected package librhash1:arm64. Preparing to unpack .../038-librhash1_1.4.5-1_arm64.deb ... Unpacking librhash1:arm64 (1.4.5-1) ... Selecting previously unselected package libuv1t64:arm64. Preparing to unpack .../039-libuv1t64_1.48.0-7_arm64.deb ... Unpacking libuv1t64:arm64 (1.48.0-7) ... Selecting previously unselected package cmake. Preparing to unpack .../040-cmake_3.31.1-1_arm64.deb ... Unpacking cmake (3.31.1-1) ... Selecting previously unselected package comerr-dev:arm64. Preparing to unpack .../041-comerr-dev_2.1-1.47.1-1+b1_arm64.deb ... Unpacking comerr-dev:arm64 (2.1-1.47.1-1+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../042-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../043-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../044-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../045-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../046-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../047-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../048-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../049-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../050-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../051-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../052-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../053-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../054-hdf5-helpers_1.10.10+repack-4_arm64.deb ... Unpacking hdf5-helpers (1.10.10+repack-4) ... Selecting previously unselected package libgssrpc4t64:arm64. Preparing to unpack .../055-libgssrpc4t64_1.21.3-3_arm64.deb ... Unpacking libgssrpc4t64:arm64 (1.21.3-3) ... Selecting previously unselected package libkadm5clnt-mit12:arm64. Preparing to unpack .../056-libkadm5clnt-mit12_1.21.3-3_arm64.deb ... Unpacking libkadm5clnt-mit12:arm64 (1.21.3-3) ... Selecting previously unselected package libkdb5-10t64:arm64. Preparing to unpack .../057-libkdb5-10t64_1.21.3-3_arm64.deb ... Unpacking libkdb5-10t64:arm64 (1.21.3-3) ... Selecting previously unselected package libkadm5srv-mit12:arm64. Preparing to unpack .../058-libkadm5srv-mit12_1.21.3-3_arm64.deb ... Unpacking libkadm5srv-mit12:arm64 (1.21.3-3) ... Selecting previously unselected package krb5-multidev:arm64. Preparing to unpack .../059-krb5-multidev_1.21.3-3_arm64.deb ... Unpacking krb5-multidev:arm64 (1.21.3-3) ... Selecting previously unselected package libaec0:arm64. Preparing to unpack .../060-libaec0_1.1.3-1+b1_arm64.deb ... Unpacking libaec0:arm64 (1.1.3-1+b1) ... Selecting previously unselected package libsz2:arm64. Preparing to unpack .../061-libsz2_1.1.3-1+b1_arm64.deb ... Unpacking libsz2:arm64 (1.1.3-1+b1) ... Selecting previously unselected package libaec-dev:arm64. Preparing to unpack .../062-libaec-dev_1.1.3-1+b1_arm64.deb ... Unpacking libaec-dev:arm64 (1.1.3-1+b1) ... Selecting previously unselected package libboost1.83-dev:arm64. Preparing to unpack .../063-libboost1.83-dev_1.83.0-3.2+b1_arm64.deb ... Unpacking libboost1.83-dev:arm64 (1.83.0-3.2+b1) ... Selecting previously unselected package libboost-dev:arm64. Preparing to unpack .../064-libboost-dev_1.83.0.2+b2_arm64.deb ... Unpacking libboost-dev:arm64 (1.83.0.2+b2) ... Selecting previously unselected package libbrotli-dev:arm64. Preparing to unpack .../065-libbrotli-dev_1.1.0-2+b6_arm64.deb ... Unpacking libbrotli-dev:arm64 (1.1.0-2+b6) ... Selecting previously unselected package libidn2-dev:arm64. Preparing to unpack .../066-libidn2-dev_2.3.7-2+b1_arm64.deb ... Unpacking libidn2-dev:arm64 (2.3.7-2+b1) ... Selecting previously unselected package libkrb5-dev:arm64. Preparing to unpack .../067-libkrb5-dev_1.21.3-3_arm64.deb ... Unpacking libkrb5-dev:arm64 (1.21.3-3) ... Selecting previously unselected package libldap-dev:arm64. Preparing to unpack .../068-libldap-dev_2.5.18+dfsg-3+b1_arm64.deb ... Unpacking libldap-dev:arm64 (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../069-libpkgconf3_1.8.1-4_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../070-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../071-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Selecting previously unselected package libnghttp2-dev:arm64. Preparing to unpack .../072-libnghttp2-dev_1.64.0-1_arm64.deb ... Unpacking libnghttp2-dev:arm64 (1.64.0-1) ... Selecting previously unselected package libpsl-dev:arm64. Preparing to unpack .../073-libpsl-dev_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl-dev:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package libgmpxx4ldbl:arm64. Preparing to unpack .../074-libgmpxx4ldbl_2%3a6.3.0+dfsg-2+b2_arm64.deb ... Unpacking libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-2+b2) ... Selecting previously unselected package libgmp-dev:arm64. Preparing to unpack .../075-libgmp-dev_2%3a6.3.0+dfsg-2+b2_arm64.deb ... Unpacking libgmp-dev:arm64 (2:6.3.0+dfsg-2+b2) ... Selecting previously unselected package libevent-2.1-7t64:arm64. Preparing to unpack .../076-libevent-2.1-7t64_2.1.12-stable-10+b1_arm64.deb ... Unpacking libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:arm64. Preparing to unpack .../077-libunbound8_1.22.0-1_arm64.deb ... Unpacking libunbound8:arm64 (1.22.0-1) ... Selecting previously unselected package libgnutls-dane0t64:arm64. Preparing to unpack .../078-libgnutls-dane0t64_3.8.8-2_arm64.deb ... 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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 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. 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CMakeFiles/MindTheGap.dir/build.make CMakeFiles/MindTheGap.dir/build make[3]: Entering directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' [ 20%] Building CXX object CMakeFiles/MindTheGap.dir/src/Filler.cpp.o [ 20%] Building CXX object CMakeFiles/MindTheGap.dir/src/main.cpp.o [ 30%] 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/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 [ 40%] Building CXX object CMakeFiles/MindTheGap.dir/src/GraphAnalysis.cpp.o [ 50%] Building CXX object CMakeFiles/nwalign.dir/src/nwAlign/nwalign.cpp.o [ 60%] 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/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/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 /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 /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/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 [ 70%] Building CXX object CMakeFiles/MindTheGap.dir/src/GraphOutputDot.cpp.o [ 80%] Building CXX object CMakeFiles/MindTheGap.dir/src/Finder.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/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 -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 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 | ^~~~~~~~~~~~~~ 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> | ^~~~~~~~~~~~~~ /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 | ^~~~~~~~~~~~~~ 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: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 | ^~~~~~~~~~~~~~ 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.103 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'mindthegap' in '../mindthegap_2.3.0-4_arm64.deb'. dpkg-deb: building package 'mindthegap-dbgsym' in '../mindthegap-dbgsym_2.3.0-4_arm64.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_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: 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/1006890 and its subdirectories I: Current time: Mon Nov 25 21:09:32 -12 2024 I: pbuilder-time-stamp: 1732612172 Tue Nov 26 09:09:32 UTC 2024 I: Signing ./b1/mindthegap_2.3.0-4_arm64.buildinfo as mindthegap_2.3.0-4_arm64.buildinfo.asc Tue Nov 26 09:09:32 UTC 2024 I: Signed ./b1/mindthegap_2.3.0-4_arm64.buildinfo as ./b1/mindthegap_2.3.0-4_arm64.buildinfo.asc Tue Nov 26 09:09:32 UTC 2024 - build #1 for mindthegap/unstable/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Tue Nov 26 09:09:32 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-81Jmelqw, removing. /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 26 09:09 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 26 09:08 b2 -rw-r--r-- 1 jenkins jenkins 2441 Sep 6 19:41 mindthegap_2.3.0-4.dsc -rw------- 1 jenkins jenkins 3572 Nov 26 09:08 rbuildlog.7j86bIK /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem/b1: total 4324 -rw-r--r-- 1 jenkins jenkins 112873 Nov 26 09:09 build.log -rw-r--r-- 1 jenkins jenkins 3390600 Nov 26 09:09 mindthegap-dbgsym_2.3.0-4_arm64.deb -rw-r--r-- 1 jenkins jenkins 648276 Nov 26 09:09 mindthegap-examples_2.3.0-4_all.deb -rw-r--r-- 1 jenkins jenkins 8148 Nov 26 09:09 mindthegap_2.3.0-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2441 Nov 26 09:09 mindthegap_2.3.0-4.dsc -rw-r--r-- 1 jenkins jenkins 7933 Nov 26 09:09 mindthegap_2.3.0-4_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8815 Nov 26 09:09 mindthegap_2.3.0-4_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2020 Nov 26 09:09 mindthegap_2.3.0-4_arm64.changes -rw-r--r-- 1 jenkins jenkins 226728 Nov 26 09:09 mindthegap_2.3.0-4_arm64.deb -rw-r--r-- 1 jenkins jenkins 1463 Nov 26 09:09 mindthegap_2.3.0-4_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem/b2: total 0 Tue Nov 26 09:09:35 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Nov 25 21:08:34 -12 2024 I: pbuilder-time-stamp: 1732612114 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 gpgv: Signature made Fri Sep 6 19:33:27 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mindthegap_2.3.0-4.dsc: no acceptable signature found 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/1006890/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='d6e76ddf703a4fcca27efabb22419cb2' 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='1006890' 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.r3lD5Jem/pbuilderrc_Ux50 --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.r3lD5Jem/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' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1006890/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 ... 20083 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} 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} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-103-1t64{a} libhdf5-cpp-103-1t64{a} libhdf5-dev{a} libhdf5-fortran-102t64{a} libhdf5-hl-100t64{a} libhdf5-hl-cpp-100t64{a} libhdf5-hl-fortran-100t64{a} libicu72{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} 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-dev{a} libtool{a} libuchardet0{a} libunbound8{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, 103 newly installed, 0 to remove and 0 not upgraded. Need to get 68.7 MB of archives. After unpacking 457 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 0.22.5-2 [198 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 1.23.0-5 [1129 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 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 1.4.19-4 [277 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 0.22.5-2 [723 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.1-1 [2267 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [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 1.21.3-3 [32.1 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 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 1.21.3-3 [310 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.11.0-1 [322 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.1-1 [9873 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.1-1+b1 [55.1 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 hdf5-helpers arm64 1.10.10+repack-4 [23.5 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-3 [56.7 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-3 [40.3 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-3 [40.8 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-3 [52.2 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-3 [126 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B] Get: 63 http://deb.debian.org/debian unstable/main arm64 libaec-dev arm64 1.1.3-1+b1 [20.2 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-3.2+b1 [10.6 MB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 66 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-3 [15.8 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.5.18+dfsg-3+b1 [300 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-2+b2 [329 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-2+b2 [621 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.22.0-1 [553 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.8-2 [446 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.8-2 [446 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.5-2+b1 [208 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.8-2 [1404 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.6+dfsg-1+b1 [329 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libcurl4-openssl-dev arm64 8.11.0-1 [447 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libgatbcore3 arm64 1.4.2+dfsg-13+b2 [1617 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libgatbcore-dev arm64 1.4.2+dfsg-13+b2 [3989 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4 [1050 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libhdf5-cpp-103-1t64 arm64 1.10.10+repack-4 [118 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libhdf5-fortran-102t64 arm64 1.10.10+repack-4 [88.1 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4 [60.9 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-fortran-100t64 arm64 1.10.10+repack-4 [39.0 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-cpp-100t64 arm64 1.10.10+repack-4 [21.4 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-3+b1 [293 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libjpeg-dev arm64 1:2.1.5-3+b1 [72.2 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libhdf5-dev arm64 1.10.10+repack-4 [2697 kB] Fetched 68.7 MB in 0s (147 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 20083 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. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../004-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../007-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../010-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../012-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../013-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../014-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../015-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../016-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package cmake-data. Preparing to unpack .../017-cmake-data_3.31.1-1_all.deb ... Unpacking cmake-data (3.31.1-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../018-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../019-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package libarchive13t64:arm64. Preparing to unpack .../020-libarchive13t64_3.7.4-1.1_arm64.deb ... Unpacking libarchive13t64:arm64 (3.7.4-1.1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../021-libbrotli1_1.1.0-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b6) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../022-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../023-libcom-err2_1.47.1-1+b1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../024-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../025-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../026-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../027-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../028-libsasl2-modules-db_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../029-libsasl2-2_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../030-libldap-2.5-0_2.5.18+dfsg-3+b1_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../031-libnghttp2-14_1.64.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../032-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../033-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../034-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:arm64. Preparing to unpack .../035-libcurl4t64_8.11.0-1_arm64.deb ... Unpacking libcurl4t64:arm64 (8.11.0-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../036-libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package libjsoncpp26:arm64. Preparing to unpack .../037-libjsoncpp26_1.9.6-3_arm64.deb ... Unpacking libjsoncpp26:arm64 (1.9.6-3) ... Selecting previously unselected package librhash1:arm64. Preparing to unpack .../038-librhash1_1.4.5-1_arm64.deb ... Unpacking librhash1:arm64 (1.4.5-1) ... Selecting previously unselected package libuv1t64:arm64. Preparing to unpack .../039-libuv1t64_1.48.0-7_arm64.deb ... Unpacking libuv1t64:arm64 (1.48.0-7) ... Selecting previously unselected package cmake. Preparing to unpack .../040-cmake_3.31.1-1_arm64.deb ... Unpacking cmake (3.31.1-1) ... Selecting previously unselected package comerr-dev:arm64. Preparing to unpack .../041-comerr-dev_2.1-1.47.1-1+b1_arm64.deb ... Unpacking comerr-dev:arm64 (2.1-1.47.1-1+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../042-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../043-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../044-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../045-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../046-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../047-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../048-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../049-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../050-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../051-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../052-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../053-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../054-hdf5-helpers_1.10.10+repack-4_arm64.deb ... Unpacking hdf5-helpers (1.10.10+repack-4) ... Selecting previously unselected package libgssrpc4t64:arm64. Preparing to unpack .../055-libgssrpc4t64_1.21.3-3_arm64.deb ... Unpacking libgssrpc4t64:arm64 (1.21.3-3) ... Selecting previously unselected package libkadm5clnt-mit12:arm64. Preparing to unpack .../056-libkadm5clnt-mit12_1.21.3-3_arm64.deb ... Unpacking libkadm5clnt-mit12:arm64 (1.21.3-3) ... Selecting previously unselected package libkdb5-10t64:arm64. Preparing to unpack .../057-libkdb5-10t64_1.21.3-3_arm64.deb ... Unpacking libkdb5-10t64:arm64 (1.21.3-3) ... Selecting previously unselected package libkadm5srv-mit12:arm64. Preparing to unpack .../058-libkadm5srv-mit12_1.21.3-3_arm64.deb ... Unpacking libkadm5srv-mit12:arm64 (1.21.3-3) ... Selecting previously unselected package krb5-multidev:arm64. Preparing to unpack .../059-krb5-multidev_1.21.3-3_arm64.deb ... Unpacking krb5-multidev:arm64 (1.21.3-3) ... Selecting previously unselected package libaec0:arm64. Preparing to unpack .../060-libaec0_1.1.3-1+b1_arm64.deb ... Unpacking libaec0:arm64 (1.1.3-1+b1) ... Selecting previously unselected package libsz2:arm64. Preparing to unpack .../061-libsz2_1.1.3-1+b1_arm64.deb ... Unpacking libsz2:arm64 (1.1.3-1+b1) ... Selecting previously unselected package libaec-dev:arm64. Preparing to unpack .../062-libaec-dev_1.1.3-1+b1_arm64.deb ... Unpacking libaec-dev:arm64 (1.1.3-1+b1) ... Selecting previously unselected package libboost1.83-dev:arm64. Preparing to unpack .../063-libboost1.83-dev_1.83.0-3.2+b1_arm64.deb ... Unpacking libboost1.83-dev:arm64 (1.83.0-3.2+b1) ... Selecting previously unselected package libboost-dev:arm64. Preparing to unpack .../064-libboost-dev_1.83.0.2+b2_arm64.deb ... Unpacking libboost-dev:arm64 (1.83.0.2+b2) ... Selecting previously unselected package libbrotli-dev:arm64. Preparing to unpack .../065-libbrotli-dev_1.1.0-2+b6_arm64.deb ... Unpacking libbrotli-dev:arm64 (1.1.0-2+b6) ... Selecting previously unselected package libidn2-dev:arm64. Preparing to unpack .../066-libidn2-dev_2.3.7-2+b1_arm64.deb ... Unpacking libidn2-dev:arm64 (2.3.7-2+b1) ... Selecting previously unselected package libkrb5-dev:arm64. Preparing to unpack .../067-libkrb5-dev_1.21.3-3_arm64.deb ... Unpacking libkrb5-dev:arm64 (1.21.3-3) ... Selecting previously unselected package libldap-dev:arm64. Preparing to unpack .../068-libldap-dev_2.5.18+dfsg-3+b1_arm64.deb ... Unpacking libldap-dev:arm64 (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../069-libpkgconf3_1.8.1-4_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../070-pkgconf-bin_1.8.1-4_arm64.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../071-pkgconf_1.8.1-4_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-4) ... Selecting previously unselected package libnghttp2-dev:arm64. Preparing to unpack .../072-libnghttp2-dev_1.64.0-1_arm64.deb ... Unpacking libnghttp2-dev:arm64 (1.64.0-1) ... Selecting previously unselected package libpsl-dev:arm64. Preparing to unpack .../073-libpsl-dev_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl-dev:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package libgmpxx4ldbl:arm64. Preparing to unpack .../074-libgmpxx4ldbl_2%3a6.3.0+dfsg-2+b2_arm64.deb ... Unpacking libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-2+b2) ... Selecting previously unselected package libgmp-dev:arm64. Preparing to unpack .../075-libgmp-dev_2%3a6.3.0+dfsg-2+b2_arm64.deb ... Unpacking libgmp-dev:arm64 (2:6.3.0+dfsg-2+b2) ... Selecting previously unselected package libevent-2.1-7t64:arm64. Preparing to unpack .../076-libevent-2.1-7t64_2.1.12-stable-10+b1_arm64.deb ... Unpacking libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:arm64. Preparing to unpack .../077-libunbound8_1.22.0-1_arm64.deb ... Unpacking libunbound8:arm64 (1.22.0-1) ... Selecting previously unselected package libgnutls-dane0t64:arm64. Preparing to unpack .../078-libgnutls-dane0t64_3.8.8-2_arm64.deb ... 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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 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. 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CMakeFiles/MindTheGap.dir/build.make CMakeFiles/MindTheGap.dir/build make[3]: Entering directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' [ 20%] Building CXX object CMakeFiles/MindTheGap.dir/src/Filler.cpp.o [ 20%] Building CXX object CMakeFiles/MindTheGap.dir/src/main.cpp.o [ 30%] 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/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 [ 40%] Building CXX object CMakeFiles/MindTheGap.dir/src/GraphAnalysis.cpp.o [ 50%] Building CXX object CMakeFiles/nwalign.dir/src/nwAlign/nwalign.cpp.o [ 60%] 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/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/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 /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 /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/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 [ 70%] Building CXX object CMakeFiles/MindTheGap.dir/src/GraphOutputDot.cpp.o [ 80%] Building CXX object CMakeFiles/MindTheGap.dir/src/Finder.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/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 -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 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 | ^~~~~~~~~~~~~~ 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> | ^~~~~~~~~~~~~~ /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 | ^~~~~~~~~~~~~~ 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: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 | ^~~~~~~~~~~~~~ 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.103 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'mindthegap' in '../mindthegap_2.3.0-4_arm64.deb'. dpkg-deb: building package 'mindthegap-dbgsym' in '../mindthegap-dbgsym_2.3.0-4_arm64.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_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: 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/1006890 and its subdirectories I: Current time: Mon Nov 25 21:09:32 -12 2024 I: pbuilder-time-stamp: 1732612172 Tue Nov 26 09:09:36 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Tue Nov 26 09:09:36 UTC 2024 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Tue Nov 26 09:09:36 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Tue Nov 26 09:09:36 UTC 2024 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-qYxpmV' ==================================================================================== Mon Dec 29 15:32:38 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "2 mindthegap unstable /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem 2.3.0-4" as arguments. Mon Dec 29 15:32:38 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-3d1s8x2N" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Dec 29 15:32:38 UTC 2025 I: Downloading source for unstable/mindthegap=2.3.0-4 Reading package lists... NOTICE: 'mindthegap' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/mindthegap.git Please use: git clone https://salsa.debian.org/med-team/mindthegap.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 788 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main mindthegap 2.3.0-4 (dsc) [2441 B] Get:2 http://deb.debian.org/debian unstable/main mindthegap 2.3.0-4 (tar) [778 kB] Get:3 http://deb.debian.org/debian unstable/main mindthegap 2.3.0-4 (diff) [8148 B] Fetched 788 kB in 0s (33.0 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'mindthegap' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/mindthegap.git Please use: git clone https://salsa.debian.org/med-team/mindthegap.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 788 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main mindthegap 2.3.0-4 (dsc) [2441 B] Get:2 http://deb.debian.org/debian unstable/main mindthegap 2.3.0-4 (tar) [778 kB] Get:3 http://deb.debian.org/debian unstable/main mindthegap 2.3.0-4 (diff) [8148 B] Fetched 788 kB in 0s (33.0 MB/s) Download complete and in download only mode ============================================================================= Re-Building mindthegap in unstable on arm64 on codethink03-arm64 now. Date: Mon Dec 29 15:32:38 GMT 2025 Date UTC: Mon Dec 29 15:32:38 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem/pbuilderrc_miux + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' mindthegap = debian-installer -o mindthegap = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' mindthegap = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo 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.r3lD5Jem/pbuilderrc_miux --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.r3lD5Jem/b2 --logfile b2/build.log mindthegap_2.3.0-4.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Dec 30 05:32:38 +14 2025 I: pbuilder-time-stamp: 1767022358 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 gpgv: Signature made Fri Sep 6 19:33:27 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mindthegap_2.3.0-4.dsc: no acceptable signature found 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/654773/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 Dec 29 15:32 /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/654773/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/654773/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]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(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=7b813ed704204277b1363c9e72385355 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=654773 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.r3lD5Jem/pbuilderrc_miux --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.r3lD5Jem/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 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/654773/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 ... 20083 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} 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} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-103-1t64{a} libhdf5-cpp-103-1t64{a} libhdf5-dev{a} libhdf5-fortran-102t64{a} libhdf5-hl-100t64{a} libhdf5-hl-cpp-100t64{a} libhdf5-hl-fortran-100t64{a} libicu72{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} 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-dev{a} libtool{a} libuchardet0{a} libunbound8{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, 103 newly installed, 0 to remove and 0 not upgraded. Need to get 68.7 MB of archives. After unpacking 457 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 0.22.5-2 [198 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 1.23.0-5 [1129 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 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 1.4.19-4 [277 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 0.22.5-2 [723 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.1-1 [2267 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [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 1.21.3-3 [32.1 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 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 1.21.3-3 [310 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.11.0-1 [322 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.1-1 [9873 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.1-1+b1 [55.1 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 hdf5-helpers arm64 1.10.10+repack-4 [23.5 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-3 [56.7 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-3 [40.3 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-3 [40.8 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-3 [52.2 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-3 [126 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B] Get: 63 http://deb.debian.org/debian unstable/main arm64 libaec-dev arm64 1.1.3-1+b1 [20.2 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-3.2+b1 [10.6 MB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 66 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-3 [15.8 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.5.18+dfsg-3+b1 [300 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-2+b2 [329 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-2+b2 [621 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.22.0-1 [553 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.8-2 [446 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.8-2 [446 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.5-2+b1 [208 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.8-2 [1404 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.6+dfsg-1+b1 [329 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libcurl4-openssl-dev arm64 8.11.0-1 [447 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libgatbcore3 arm64 1.4.2+dfsg-13+b2 [1617 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libgatbcore-dev arm64 1.4.2+dfsg-13+b2 [3989 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-8 [361 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4 [1050 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libhdf5-cpp-103-1t64 arm64 1.10.10+repack-4 [118 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libhdf5-fortran-102t64 arm64 1.10.10+repack-4 [88.1 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4 [60.9 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-fortran-100t64 arm64 1.10.10+repack-4 [39.0 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-cpp-100t64 arm64 1.10.10+repack-4 [21.4 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-3+b1 [293 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libjpeg-dev arm64 1:2.1.5-3+b1 [72.2 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libhdf5-dev arm64 1.10.10+repack-4 [2697 kB] Fetched 68.7 MB in 1s (133 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 20083 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. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../004-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../007-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../010-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../012-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../013-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../014-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../015-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../016-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package cmake-data. Preparing to unpack .../017-cmake-data_3.31.1-1_all.deb ... Unpacking cmake-data (3.31.1-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../018-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../019-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package libarchive13t64:arm64. Preparing to unpack .../020-libarchive13t64_3.7.4-1.1_arm64.deb ... Unpacking libarchive13t64:arm64 (3.7.4-1.1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../021-libbrotli1_1.1.0-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b6) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../022-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../023-libcom-err2_1.47.1-1+b1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../024-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../025-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../026-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../027-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../028-libsasl2-modules-db_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../029-libsasl2-2_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../030-libldap-2.5-0_2.5.18+dfsg-3+b1_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../031-libnghttp2-14_1.64.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../032-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../033-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../034-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:arm64. Preparing to unpack .../035-libcurl4t64_8.11.0-1_arm64.deb ... Unpacking libcurl4t64:arm64 (8.11.0-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../036-libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package libjsoncpp26:arm64. Preparing to unpack .../037-libjsoncpp26_1.9.6-3_arm64.deb ... Unpacking libjsoncpp26:arm64 (1.9.6-3) ... Selecting previously unselected package librhash1:arm64. Preparing to unpack .../038-librhash1_1.4.5-1_arm64.deb ... Unpacking librhash1:arm64 (1.4.5-1) ... Selecting previously unselected package libuv1t64:arm64. Preparing to unpack .../039-libuv1t64_1.48.0-7_arm64.deb ... Unpacking libuv1t64:arm64 (1.48.0-7) ... Selecting previously unselected package cmake. Preparing to unpack .../040-cmake_3.31.1-1_arm64.deb ... Unpacking cmake (3.31.1-1) ... Selecting previously unselected package comerr-dev:arm64. Preparing to unpack .../041-comerr-dev_2.1-1.47.1-1+b1_arm64.deb ... Unpacking comerr-dev:arm64 (2.1-1.47.1-1+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../042-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../043-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../044-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../045-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../046-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../047-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../048-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../049-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../050-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../051-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../052-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../053-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../054-hdf5-helpers_1.10.10+repack-4_arm64.deb ... Unpacking hdf5-helpers (1.10.10+repack-4) ... Selecting previously unselected package libgssrpc4t64:arm64. Preparing to unpack .../055-libgssrpc4t64_1.21.3-3_arm64.deb ... Unpacking libgssrpc4t64:arm64 (1.21.3-3) ... Selecting previously unselected package libkadm5clnt-mit12:arm64. Preparing to unpack .../056-libkadm5clnt-mit12_1.21.3-3_arm64.deb ... Unpacking libkadm5clnt-mit12:arm64 (1.21.3-3) ... Selecting previously unselected package libkdb5-10t64:arm64. Preparing to unpack .../057-libkdb5-10t64_1.21.3-3_arm64.deb ... Unpacking libkdb5-10t64:arm64 (1.21.3-3) ... Selecting previously unselected package libkadm5srv-mit12:arm64. Preparing to unpack .../058-libkadm5srv-mit12_1.21.3-3_arm64.deb ... Unpacking libkadm5srv-mit12:arm64 (1.21.3-3) ... Selecting previously unselected package krb5-multidev:arm64. Preparing to unpack .../059-krb5-multidev_1.21.3-3_arm64.deb ... Unpacking krb5-multidev:arm64 (1.21.3-3) ... Selecting previously unselected package libaec0:arm64. Preparing to unpack .../060-libaec0_1.1.3-1+b1_arm64.deb ... Unpacking libaec0:arm64 (1.1.3-1+b1) ... Selecting previously unselected package libsz2:arm64. Preparing to unpack .../061-libsz2_1.1.3-1+b1_arm64.deb ... 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Setting up cmake (3.31.1-1) ... Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4) ... Setting up libkadm5clnt-mit12:arm64 (1.21.3-3) ... Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-4) ... Setting up libkdb5-10t64:arm64 (1.21.3-3) ... Setting up libhdf5-cpp-103-1t64:arm64 (1.10.10+repack-4) ... Setting up libhdf5-fortran-102t64:arm64 (1.10.10+repack-4) ... Setting up debhelper (13.20) ... Setting up libkadm5srv-mit12:arm64 (1.21.3-3) ... Setting up libhdf5-hl-cpp-100t64:arm64 (1.10.10+repack-4) ... Setting up krb5-multidev:arm64 (1.21.3-3) ... Setting up libhdf5-hl-fortran-100t64:arm64 (1.10.10+repack-4) ... Setting up libkrb5-dev:arm64 (1.21.3-3) ... Setting up libcurl4-openssl-dev:arm64 (8.11.0-1) ... Setting up libhdf5-dev (1.10.10+repack-4) ... 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 (2.40-4) ... 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/654773/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/654773/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 (1.1s) -- 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 -B/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' make -f CMakeFiles/MindTheGap.dir/build.make CMakeFiles/MindTheGap.dir/depend make -f CMakeFiles/nwalign.dir/build.make CMakeFiles/nwalign.dir/depend make[3]: Entering directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/mindthegap-2.3.0 /build/reproducible-path/mindthegap-2.3.0 /build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu /build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu /build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu/CMakeFiles/MindTheGap.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' cd /build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/mindthegap-2.3.0 /build/reproducible-path/mindthegap-2.3.0 /build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu /build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu /build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu/CMakeFiles/nwalign.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' make -f CMakeFiles/nwalign.dir/build.make CMakeFiles/nwalign.dir/build make[3]: Leaving directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' make -f CMakeFiles/MindTheGap.dir/build.make CMakeFiles/MindTheGap.dir/build make[3]: Entering directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' [ 30%] Building CXX object CMakeFiles/MindTheGap.dir/src/Filler.cpp.o [ 30%] Building CXX object CMakeFiles/nwalign.dir/src/nwAlign/nwalign.cpp.o [ 30%] Building CXX object CMakeFiles/MindTheGap.dir/src/main.cpp.o [ 40%] Building CXX object CMakeFiles/MindTheGap.dir/src/GraphAnalysis.cpp.o [ 50%] Building CXX object CMakeFiles/MindTheGap.dir/src/Finder.cpp.o [ 60%] Building CXX object CMakeFiles/MindTheGap.dir/src/GraphOutputDot.cpp.o [ 70%] Building CXX object CMakeFiles/MindTheGap.dir/src/IGraphOutput.cpp.o [ 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/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 /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/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/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 -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 /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 /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/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/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/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/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.103 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'mindthegap' in '../mindthegap_2.3.0-4_arm64.deb'. dpkg-deb: building package 'mindthegap-dbgsym' in '../mindthegap-dbgsym_2.3.0-4_arm64.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_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/654773/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/654773/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/654773 and its subdirectories I: Current time: Tue Dec 30 05:33:43 +14 2025 I: pbuilder-time-stamp: 1767022423 + false + set +x Mon Dec 29 15:33:43 UTC 2025 I: Signing ./b2/mindthegap_2.3.0-4_arm64.buildinfo as mindthegap_2.3.0-4_arm64.buildinfo.asc Mon Dec 29 15:33:43 UTC 2025 I: Signed ./b2/mindthegap_2.3.0-4_arm64.buildinfo as ./b2/mindthegap_2.3.0-4_arm64.buildinfo.asc Mon Dec 29 15:33:43 UTC 2025 - build #2 for mindthegap/unstable/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Mon Dec 29 15:33:43 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-3d1s8x2N, removing. /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem: total 132 drwxr-xr-x 2 jenkins jenkins 4096 Nov 26 09:09 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 26 09:10 b2 -rw-r--r-- 1 jenkins jenkins 2441 Sep 6 19:41 mindthegap_2.3.0-4.dsc -rw------- 1 jenkins jenkins 116746 Nov 26 09:09 rbuildlog.7j86bIK /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem/b1: total 4340 -rw-r--r-- 1 jenkins jenkins 112873 Nov 26 09:09 build.log -rw-r--r-- 1 jenkins jenkins 3390600 Nov 26 09:09 mindthegap-dbgsym_2.3.0-4_arm64.deb -rw-r--r-- 1 jenkins jenkins 648276 Nov 26 09:09 mindthegap-examples_2.3.0-4_all.deb -rw-r--r-- 1 jenkins jenkins 8148 Nov 26 09:09 mindthegap_2.3.0-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2441 Nov 26 09:09 mindthegap_2.3.0-4.dsc -rw-r--r-- 1 jenkins jenkins 7933 Nov 26 09:09 mindthegap_2.3.0-4_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8815 Nov 26 09:09 mindthegap_2.3.0-4_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2020 Nov 26 09:09 mindthegap_2.3.0-4_arm64.changes -rw-r--r-- 1 jenkins jenkins 226728 Nov 26 09:09 mindthegap_2.3.0-4_arm64.deb -rw-r--r-- 1 jenkins jenkins 1463 Nov 26 09:09 mindthegap_2.3.0-4_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem/b2: total 4336 -rw-r--r-- 1 jenkins jenkins 114808 Nov 26 09:10 build.log -rw-r--r-- 1 jenkins jenkins 3390600 Nov 26 09:10 mindthegap-dbgsym_2.3.0-4_arm64.deb -rw-r--r-- 1 jenkins jenkins 648276 Nov 26 09:10 mindthegap-examples_2.3.0-4_all.deb -rw-r--r-- 1 jenkins jenkins 8148 Nov 26 09:10 mindthegap_2.3.0-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2441 Nov 26 09:10 mindthegap_2.3.0-4.dsc -rw-r--r-- 1 jenkins jenkins 7933 Nov 26 09:10 mindthegap_2.3.0-4_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8815 Nov 26 09:10 mindthegap_2.3.0-4_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2020 Nov 26 09:10 mindthegap_2.3.0-4_arm64.changes -rw-r--r-- 1 jenkins jenkins 226728 Nov 26 09:10 mindthegap_2.3.0-4_arm64.deb -rw-r--r-- 1 jenkins jenkins 1463 Nov 26 09:10 mindthegap_2.3.0-4_source.changes Tue Nov 26 09:10:48 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Tue Nov 26 09:10:49 UTC 2024 I: mindthegap_2.3.0-4_arm64.changes: Format: 1.8 Date: Fri, 06 Sep 2024 21:01:08 +0200 Source: mindthegap Binary: mindthegap mindthegap-dbgsym mindthegap-examples Architecture: arm64 all Version: 2.3.0-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: mindthegap - performs detection and assembly of DNA insertion variants in NGS mindthegap-examples - optional scripts and example resources for mindthegap Closes: 1075273 Changes: mindthegap (2.3.0-4) unstable; urgency=medium . * fix-use-as-function.patch: new: fix build failure with gcc-14. (Closes: #1075273) * d/control: declare compliance to standards version 4.7.0. * d/control: add myself to uploaders. * d/salsa-ci.yml: do not test build on i386 due to missing dependency. Checksums-Sha1: c3a8e608e3975752c2d8f50e77a12ce9ff466467 3390600 mindthegap-dbgsym_2.3.0-4_arm64.deb bd6e650030c21585c03d2ead646af29d6a732584 648276 mindthegap-examples_2.3.0-4_all.deb 85141e04a88708b3345dce85bd1034baab8e7014 7933 mindthegap_2.3.0-4_arm64.buildinfo 9484825c5d0a9f49fbc40325ea3b19a323332245 226728 mindthegap_2.3.0-4_arm64.deb Checksums-Sha256: b3e766012a75c0ac84826093a331f12b4f3fca01ed809159b2c46715ca73a17d 3390600 mindthegap-dbgsym_2.3.0-4_arm64.deb 91afe02e9a4f7a4d8c3a77f1492d181c74f2a1ff9d4a8f72381aa88283ea7410 648276 mindthegap-examples_2.3.0-4_all.deb 9230400241a0002ad2b5cc33e1ded589aa0f07b0933f09fa4ed034fd58512ff5 7933 mindthegap_2.3.0-4_arm64.buildinfo d88b815c2e2ed13af3bcbd7b57b037e124220580297813ed6b519b3528aa5f09 226728 mindthegap_2.3.0-4_arm64.deb Files: d5fa84e1039d38d201cc0a275336bd63 3390600 debug optional mindthegap-dbgsym_2.3.0-4_arm64.deb cb4567b8aa22f9ec02901cd3f6ae793b 648276 science optional mindthegap-examples_2.3.0-4_all.deb 01dac9a0cd15e9b959f399a9303a3ba2 7933 science optional mindthegap_2.3.0-4_arm64.buildinfo c931cf24a624fcc608eb18fe776683b1 226728 science optional mindthegap_2.3.0-4_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/mindthegap_2.3.0-4.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/mindthegap_2.3.0-4.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/mindthegap_2.3.0-4.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/mindthegap_2.3.0-4.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/mindthegap_2.3.0-4_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/mindthegap_2.3.0-4.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-11-26 09:09:33.491345607 +0000 +++ b2/build.log 2024-11-26 09:10:45.148109855 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Nov 25 21:08:34 -12 2024 -I: pbuilder-time-stamp: 1732612114 +I: Current time: Tue Dec 30 05:32:38 +14 2025 +I: pbuilder-time-stamp: 1767022358 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ 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/1006890/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/654773/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 Dec 29 15:32 /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/654773/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/654773/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(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 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + 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='d6e76ddf703a4fcca27efabb22419cb2' - 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='1006890' - PS1='# ' - PS2='> ' + INVOCATION_ID=7b813ed704204277b1363c9e72385355 + 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=654773 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.r3lD5Jem/pbuilderrc_Ux50 --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.r3lD5Jem/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' - http_proxy='http://192.168.101.4:3128' + 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.r3lD5Jem/pbuilderrc_miux --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.r3lD5Jem/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 codethink04-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1006890/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/654773/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -226,7 +258,7 @@ Get: 101 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-3+b1 [293 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libjpeg-dev arm64 1:2.1.5-3+b1 [72.2 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libhdf5-dev arm64 1.10.10+repack-4 [2697 kB] -Fetched 68.7 MB in 0s (147 MB/s) +Fetched 68.7 MB in 1s (133 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 20083 files and directories currently installed.) @@ -654,7 +686,11 @@ 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 +I: user script /srv/workspace/pbuilder/654773/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/654773/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 @@ -710,7 +746,7 @@ -- 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 (1.2s) +-- Configuring done (1.1s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -741,31 +777,34 @@ make -f CMakeFiles/MindTheGap.dir/build.make CMakeFiles/MindTheGap.dir/build make[3]: Entering directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/mindthegap-2.3.0/obj-aarch64-linux-gnu' -[ 20%] Building CXX object CMakeFiles/MindTheGap.dir/src/Filler.cpp.o -[ 20%] Building CXX object CMakeFiles/MindTheGap.dir/src/main.cpp.o -[ 30%] 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/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 +[ 30%] Building CXX object CMakeFiles/MindTheGap.dir/src/Filler.cpp.o +[ 30%] Building CXX object CMakeFiles/nwalign.dir/src/nwAlign/nwalign.cpp.o +[ 30%] Building CXX object CMakeFiles/MindTheGap.dir/src/main.cpp.o [ 40%] Building CXX object CMakeFiles/MindTheGap.dir/src/GraphAnalysis.cpp.o -[ 50%] Building CXX object CMakeFiles/nwalign.dir/src/nwAlign/nwalign.cpp.o -[ 60%] Building CXX object CMakeFiles/MindTheGap.dir/src/IGraphOutput.cpp.o +[ 50%] Building CXX object CMakeFiles/MindTheGap.dir/src/Finder.cpp.o +[ 60%] Building CXX object CMakeFiles/MindTheGap.dir/src/GraphOutputDot.cpp.o +[ 70%] Building CXX object CMakeFiles/MindTheGap.dir/src/IGraphOutput.cpp.o +[ 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/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 /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/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 -/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 /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/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 -[ 70%] Building CXX object CMakeFiles/MindTheGap.dir/src/GraphOutputDot.cpp.o -[ 80%] Building CXX object CMakeFiles/MindTheGap.dir/src/Finder.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/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 -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 /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 -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: +/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 +/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/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/string:49, - from /build/reproducible-path/mindthegap-2.3.0/src/GraphAnalysis.hpp:20: +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 | ^~~~~~~~~~~~~~ @@ -789,7 +828,7 @@ | ^~~~~~~~~~~~~~ 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: + 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> | ^~~~~~~~~~~~~~ @@ -800,8 +839,7 @@ 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: + 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 | ^~~~~~~~~~~~~~ @@ -825,18 +863,13 @@ | ^~~~~~~~~~~~~~ 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: + 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/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: +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 | ^~~~~~~~~~~~~~ @@ -846,16 +879,24 @@ /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> - | ^~~~~~~~~~~~~~ /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, @@ -863,7 +904,8 @@ 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: + 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 | ^~~~~~~~~~~~~~ @@ -873,12 +915,6 @@ /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> | ^~~~~~~~~~~~~~ @@ -1365,12 +1401,14 @@ 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/654773/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/654773/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/1006890 and its subdirectories -I: Current time: Mon Nov 25 21:09:32 -12 2024 -I: pbuilder-time-stamp: 1732612172 +I: removing directory /srv/workspace/pbuilder/654773 and its subdirectories +I: Current time: Tue Dec 30 05:33:43 +14 2025 +I: pbuilder-time-stamp: 1767022423 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/mindthegap_2.3.0-4.diff: 83.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/mindthegap_2.3.0-4.diff.gz b2/build.log: 87.3% -- replaced with stdout Compressing the 1st log... b1/build.log: 87.7% -- replaced with stdout Tue Nov 26 09:10:50 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_mindthegap_unstable_arm64_1732612250 + touch /var/log/reproducible-builds/diffoscope_stamp_mindthegap_unstable_arm64_1732612250 + RESULT=0 + systemd-run '--description=diffoscope on mindthegap/2.3.0-4 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_12-70470 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem --run-session -c jenkins-reproducible-unstable-diffoscope-de1988b9-b462-4311-a87a-c62a2dea31c8 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem/dbd-tmp-aL56QgZ ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem/mindthegap_2.3.0-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem/mindthegap_2.3.0-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem/mindthegap_2.3.0-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem/b1/mindthegap_2.3.0-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem/b2/mindthegap_2.3.0-4_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_12-70470.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem/mindthegap_2.3.0-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem/mindthegap_2.3.0-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem/mindthegap_2.3.0-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem/b1/mindthegap_2.3.0-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.r3lD5Jem/b2/mindthegap_2.3.0-4_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.381s) 0.381s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.053s) 0.053s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 690ms CPU time consumed: 691ms _ _ _ _ _ __ ___ (_)_ __ __| | |_| |__ ___ __ _ __ _ _ __ | '_ ` _ \| | '_ \ / _` | __| '_ \ / _ \/ _` |/ _` | '_ \ | | | | | | | | | | (_| | |_| | | | __/ (_| | (_| | |_) | |_| |_| |_|_|_| |_|\__,_|\__|_| |_|\___|\__, |\__,_| .__/ |___/ |_| Tue Nov 26 09:10:51 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Tue Nov 26 09:10:51 UTC 2024 I: mindthegap from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-26 09:10:51] INFO: Starting at 2024-11-26 09:10:51.633944 [2024-11-26 09:10:51] INFO: Generating the pages of 1 package(s) [2024-11-26 09:10:52] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/mindthegap didn't produce a buildlog, even though it has been built. [2024-11-26 09:10:52] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/mindthegap_2.3.0-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/mindthegap_2.3.0-4.diff.gz is missing [2024-11-26 09:10:52] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/mindthegap_2.3.0-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/mindthegap_2.3.0-4.diff.gz is missing [2024-11-26 09:10:52] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/mindthegap_2.3.0-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/mindthegap_2.3.0-2.diff.gz is missing [2024-11-26 09:10:52] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/mindthegap_2.3.0-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/mindthegap_2.3.0-2.diff.gz is missing [2024-11-26 09:10:52] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/armhf/mindthegap_2.2.2-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/armhf/mindthegap_2.2.2-2.diff.gz is missing [2024-11-26 09:10:52] INFO: Finished at 2024-11-26 09:10:52.097012, took: 0:00:00.463072 Tue Nov 26 09:10:52 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/mindthegap.html Tue Nov 26 09:10:52 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Nov 26 09:10:52 UTC 2024 I: Submitting 12K b1/mindthegap_2.3.0-4_arm64.buildinfo.asc https://buildinfo.debian.net/85141e04a88708b3345dce85bd1034baab8e7014/mindthegap_2.3.0-4_all Tue Nov 26 09:10:52 UTC 2024 I: Submitting 12K b2/mindthegap_2.3.0-4_arm64.buildinfo.asc https://buildinfo.debian.net/0c02bdbc96313e86d5500365b670a82172f6235d/mindthegap_2.3.0-4_all Tue Nov 26 09:10:54 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Nov 26 09:10:54 UTC 2024 I: Done submitting .buildinfo files. Tue Nov 26 09:10:54 UTC 2024 I: Removing signed mindthegap_2.3.0-4_arm64.buildinfo.asc files: removed './b1/mindthegap_2.3.0-4_arm64.buildinfo.asc' removed './b2/mindthegap_2.3.0-4_arm64.buildinfo.asc' 1732612254 arm64 unstable mindthegap Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/mindthegap_2.3.0-4.rbuild.log: 85.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/mindthegap_2.3.0-4.rbuild.log.gz [2024-11-26 09:10:54] INFO: Starting at 2024-11-26 09:10:54.549604 [2024-11-26 09:10:54] INFO: Generating the pages of 1 package(s) [2024-11-26 09:10:54] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/armhf/mindthegap_2.3.0-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/armhf/mindthegap_2.3.0-4.diff.gz is missing [2024-11-26 09:10:54] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/mindthegap_2.3.0-4.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/mindthegap_2.3.0-4.diff.gz is missing [2024-11-26 09:10:54] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/armhf/mindthegap_2.3.0-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/armhf/mindthegap_2.3.0-2.diff.gz is missing [2024-11-26 09:10:54] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bookworm/i386/mindthegap_2.3.0-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bookworm/i386/mindthegap_2.3.0-2.diff.gz is missing [2024-11-26 09:10:54] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/bullseye/armhf/mindthegap_2.2.2-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/bullseye/armhf/mindthegap_2.2.2-2.diff.gz is missing [2024-11-26 09:10:54] INFO: Finished at 2024-11-26 09:10:54.997942, took: 0:00:00.448341 All cleanup done. Tue Nov 26 09:10:55 UTC 2024 - total duration: 0h 2m 36s. Tue Nov 26 09:10:55 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-hb2G47Wb, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 2min 40.111s CPU time consumed: 7.216s