Tue Apr 9 14:29:08 UTC 2024 I: starting to build hilive/unstable/armhf on jenkins on '2024-04-09 14:28' Tue Apr 9 14:29:08 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_6/2669/console.log Tue Apr 9 14:29:08 UTC 2024 I: Downloading source for unstable/hilive=2.0a-3 --2024-04-09 14:29:08-- http://deb.debian.org/debian/pool/main/h/hilive/hilive_2.0a-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2118 (2.1K) [text/prs.lines.tag] Saving to: ‘hilive_2.0a-3.dsc’ 0K .. 100% 310M=0s 2024-04-09 14:29:08 (310 MB/s) - ‘hilive_2.0a-3.dsc’ saved [2118/2118] Tue Apr 9 14:29:08 UTC 2024 I: hilive_2.0a-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: hilive Binary: hilive Architecture: any Version: 2.0a-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://gitlab.com/rki_bioinformatics/HiLive2 Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/hilive Vcs-Git: https://salsa.debian.org/med-team/hilive.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12), cmake, libboost-system-dev, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libhts-dev, libseqan2-dev, zlib1g-dev, liblz4-dev, chrpath, markdown Package-List: hilive deb science optional arch=any Checksums-Sha1: 5705773f60eef87916fe3612b26df04ae3959d32 161788 hilive_2.0a.orig.tar.gz fbe1ef06642fafe9547758eff3f8dde6ad874e66 9000 hilive_2.0a-3.debian.tar.xz Checksums-Sha256: a60e7675988b35d9ebf9472ca7515b40f790654c04e67d35fabf069d91d73bf6 161788 hilive_2.0a.orig.tar.gz 8da7ff9f1fa24befc2a2f14c190da2c1d1f0e924908adcd42710f8a53d97a4db 9000 hilive_2.0a-3.debian.tar.xz Files: 8d393041a814071b4ac6a3db1f1f10e6 161788 hilive_2.0a.orig.tar.gz 455831bc062fe258d0d11b61f583b0d9 9000 hilive_2.0a-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl4gRlURHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEMpA/+JEf5qZaIMlzreWMDxFW+4eCcMvjA18X6 TAv5/xgdu9iQl1B31zkHw8SXon1Tg2kYbc4A2MvP8iRiHMpEvbAO9B3z+NuIlX4P g2WXlplC05XtuYtUXRnQVbZJ74xdfm9OuCkz2EfRsdOFET2mp3W985VWpgFLulA9 R/qPQBAIJACDNL7t/9TweOj/ZTN5eu/lxZewZVHAZLiFrQDB9LQ/2O9RnSzje/cF dBHmLqGJsXzkw/JqU3WfgaAXhTbf3OU/CcR7Ks5nKFP85HvPPM23UnbgzcMhBIZQ F8bl4lEj1lrZ3hhbHtHo3J7Ar5iNuFqd7SrBNPMRAcVqjYZLHIzNcbNGfyGfglc8 hcfV3Xh7cICvJ3xfIAHoCyGGi8fXwviSDnZdNAmdgma+4HkKdikYe9mQ7Ty4SGY6 p6aNWL+X8dJc15MBQ2kg8yN/Oxzh+RLUtG6GdRY6ijHRmZLSkCHO1ppmQph6WlaT JXwic4L0d89wWO29DlLxC6LO7XWbOiToWSAmqA16EvA/MwJGvsHQNgfP855KNIVD 3J6TWteifJ7azGGNle9K64Xh5023JuajXaNMVE4+LIaYnxIaai8pDfBVRo+ABm0G tZwApDo1RS/nh9F6GqyjmcpG2faaUavQgrUoLsiQr1wRdmJrgCD1jD/sVjsUdMkM ITZHcB+VeOg= =0BPt -----END PGP SIGNATURE----- Tue Apr 9 14:29:08 UTC 2024 I: Checking whether the package is not for us Tue Apr 9 14:29:08 UTC 2024 I: Starting 1st build on remote node virt64b-armhf-rb.debian.net. Tue Apr 9 14:29:08 UTC 2024 I: Preparing to do remote build '1' on virt64b-armhf-rb.debian.net. Tue Apr 9 14:37:58 UTC 2024 I: Deleting $TMPDIR on virt64b-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Apr 9 02:29:14 -12 2024 I: pbuilder-time-stamp: 1712672954 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 [hilive_2.0a-3.dsc] I: copying [./hilive_2.0a.orig.tar.gz] I: copying [./hilive_2.0a-3.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Jan 16 11:17:41 2020 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./hilive_2.0a-3.dsc: no acceptable signature found dpkg-source: info: extracting hilive in hilive-2.0a dpkg-source: info: unpacking hilive_2.0a.orig.tar.gz dpkg-source: info: unpacking hilive_2.0a-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying do_not_set_rpath.patch dpkg-source: info: applying use_FindSeQan.patch dpkg-source: info: applying use_dynamic_linking.patch dpkg-source: info: applying remove_march_native.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/25229/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='b5d12e8f6b94455084134b21ebe0e22f' 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='25229' 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.wtKPGz9M/pbuilderrc_agy7 --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.wtKPGz9M/b1 --logfile b1/build.log hilive_2.0a-3.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64b 6.1.0-18-arm64 #1 SMP Debian 6.1.76-1 (2024-02-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 7 07:43 /bin -> usr/bin I: user script /srv/workspace/pbuilder/25229/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12), cmake, libboost-system-dev, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libhts-dev, libseqan2-dev, zlib1g-dev, liblz4-dev, chrpath, markdown dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19442 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libboost-system-dev; however: Package libboost-system-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-filesystem-dev; however: Package libboost-filesystem-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libseqan2-dev; however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on liblz4-dev; however: Package liblz4-dev is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on markdown; however: Package markdown 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} chrpath{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-system-dev{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost1.83-dev{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu-dev{a} libicu72{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblz4-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash0{a} librtmp1{a} libseqan2-dev{a} libssh2-1t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} markdown{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 libltdl-dev libmail-sendmail-perl libssl3 lynx psmisc publicsuffix wget 0 packages upgraded, 82 newly installed, 0 to remove and 0 not upgraded. Need to get 58.3 MB of archives. After unpacking 366 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf libproc2-0 armhf 2:4.0.4-4 [55.7 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf procps armhf 2:4.0.4-4 [864 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-3+b1 [1091 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40-5 [85.1 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.12.1-1 [1375 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf autopoint all 0.21-14 [496 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf chrpath armhf 0.16-2+b1 [15.9 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b2 [599 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf libarchive13t64 armhf 3.7.2-2 [304 kB] Get: 22 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b3 [284 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.20.1-6+b1 [30.6 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.0-2.4 [19.5 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.20.1-6+b1 [75.5 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-3 [7908 B] Get: 27 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.20.1-6+b1 [290 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.20.1-6+b1 [112 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf libnghttp2-14 armhf 1.61.0-1 [63.0 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf libpsl5t64 armhf 0.21.2-1.1 [55.6 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b4 [53.2 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf libssh2-1t64 armhf 1.11.0-4.1+b2 [198 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf libcurl4t64 armhf 8.7.1-2 [391 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf libexpat1 armhf 2.6.2-1 [83.5 kB] Get: 35 http://deb.debian.org/debian unstable/main armhf libjsoncpp25 armhf 1.9.5-6+b2 [69.9 kB] Get: 36 http://deb.debian.org/debian unstable/main armhf librhash0 armhf 1.4.3-3+b1 [143 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf libuv1t64 armhf 1.48.0-1.1 [134 kB] Get: 38 http://deb.debian.org/debian unstable/main armhf cmake-data all 3.28.3-1 [2128 kB] Get: 39 http://deb.debian.org/debian unstable/main armhf cmake armhf 3.28.3-1+b2 [5115 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 41 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-7 [517 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 44 http://deb.debian.org/debian unstable/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 47 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.191-1+b1 [183 kB] Get: 48 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf debhelper all 13.15.3 [901 kB] Get: 53 http://deb.debian.org/debian unstable/main armhf icu-devtools armhf 72.1-4+b1 [185 kB] Get: 54 http://deb.debian.org/debian unstable/main armhf libboost1.83-dev armhf 1.83.0-2.1+b1 [10.6 MB] Get: 55 http://deb.debian.org/debian unstable/main armhf libboost-atomic1.83.0 armhf 1.83.0-2.1+b1 [233 kB] Get: 56 http://deb.debian.org/debian unstable/main armhf libboost-atomic1.83-dev armhf 1.83.0-2.1+b1 [234 kB] Get: 57 http://deb.debian.org/debian unstable/main armhf libboost-filesystem1.83.0 armhf 1.83.0-2.1+b1 [270 kB] Get: 58 http://deb.debian.org/debian unstable/main armhf libboost-system1.83.0 armhf 1.83.0-2.1+b1 [230 kB] Get: 59 http://deb.debian.org/debian unstable/main armhf libboost-system1.83-dev armhf 1.83.0-2.1+b1 [231 kB] Get: 60 http://deb.debian.org/debian unstable/main armhf libboost-filesystem1.83-dev armhf 1.83.0-2.1+b1 [284 kB] Get: 61 http://deb.debian.org/debian unstable/main armhf libboost-filesystem-dev armhf 1.83.0.2+b2 [3616 B] Get: 62 http://deb.debian.org/debian unstable/main armhf libboost-regex1.83.0 armhf 1.83.0-2.1+b1 [307 kB] Get: 63 http://deb.debian.org/debian unstable/main armhf libicu-dev armhf 72.1-4+b1 [10.1 MB] Get: 64 http://deb.debian.org/debian unstable/main armhf libboost-regex1.83-dev armhf 1.83.0-2.1+b1 [335 kB] Get: 65 http://deb.debian.org/debian unstable/main armhf libboost-iostreams1.83-dev armhf 1.83.0-2.1+b1 [260 kB] Get: 66 http://deb.debian.org/debian unstable/main armhf libboost-iostreams-dev armhf 1.83.0.2+b2 [3568 B] Get: 67 http://deb.debian.org/debian unstable/main armhf libboost-program-options1.83.0 armhf 1.83.0-2.1+b1 [327 kB] Get: 68 http://deb.debian.org/debian unstable/main armhf libboost-program-options1.83-dev armhf 1.83.0-2.1+b1 [370 kB] Get: 69 http://deb.debian.org/debian unstable/main armhf libboost-program-options-dev armhf 1.83.0.2+b2 [3604 B] Get: 70 http://deb.debian.org/debian unstable/main armhf libboost-system-dev armhf 1.83.0.2+b2 [3724 B] Get: 71 http://deb.debian.org/debian unstable/main armhf libcurl3t64-gnutls armhf 8.7.1-2 [383 kB] Get: 72 http://deb.debian.org/debian unstable/main armhf libcurl4-gnutls-dev armhf 8.7.1-2 [498 kB] Get: 73 http://deb.debian.org/debian unstable/main armhf libdeflate0 armhf 1.20-1 [35.9 kB] Get: 74 http://deb.debian.org/debian unstable/main armhf libdeflate-dev armhf 1.20-1 [44.0 kB] Get: 75 http://deb.debian.org/debian unstable/main armhf libhtscodecs2 armhf 1.6.0-1+b1 [61.3 kB] Get: 76 http://deb.debian.org/debian unstable/main armhf libhts3t64 armhf 1.19+ds-1.1+b1 [395 kB] Get: 77 http://deb.debian.org/debian unstable/main armhf liblzma-dev armhf 5.6.1+really5.4.5-1 [281 kB] Get: 78 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg-3.1 [904 kB] Get: 79 http://deb.debian.org/debian unstable/main armhf libhts-dev armhf 1.19+ds-1.1+b1 [1598 kB] Get: 80 http://deb.debian.org/debian unstable/main armhf liblz4-dev armhf 1.9.4-2 [75.0 kB] Get: 81 http://deb.debian.org/debian unstable/main armhf libseqan2-dev all 2.4.0+dfsg-16 [1216 kB] Get: 82 http://deb.debian.org/debian unstable/main armhf markdown all 1.0.1-12 [17.7 kB] Fetched 58.3 MB in 16s (3624 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:armhf. 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Setting up libboost-filesystem1.83-dev:armhf (1.83.0-2.1+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:armhf (1.20.1-6+b1) ... Setting up libboost-regex1.83-dev:armhf (1.83.0-2.1+b1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up libarchive13t64:armhf (3.7.2-2) ... Setting up libboost-filesystem-dev:armhf (1.83.0.2+b2) ... Setting up libcurl4t64:armhf (8.7.1-2) ... Setting up libboost-iostreams1.83-dev:armhf (1.83.0-2.1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:armhf (8.7.1-2) ... Setting up libboost-iostreams-dev:armhf (1.83.0.2+b2) ... Setting up libcurl4-gnutls-dev:armhf (8.7.1-2) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up cmake (3.28.3-1+b2) ... Setting up libhts3t64:armhf (1.19+ds-1.1+b1) ... Setting up libhts-dev:armhf (1.19+ds-1.1+b1) ... Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.37-15.1) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.33-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/hilive-2.0a/ && 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 > ../hilive_2.0a-3_source.changes dpkg-buildpackage: info: source package hilive dpkg-buildpackage: info: source version 2.0a-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/hilive-2.0a' dh_auto_configure -- -DSEQAN_PATH=/usr/lib/seqan/ cd obj-arm-linux-gnueabihf && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DSEQAN_PATH=/usr/lib/seqan/ .. -- The CXX compiler identification is GNU 13.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/lib/arm-linux-gnueabihf/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") found components: system filesystem program_options iostreams -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.3") -- Performing Test CXX14_BUILTIN -- Performing Test CXX14_BUILTIN - Success CMake Warning (dev) at /usr/share/cmake/seqan/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): CMakeLists.txt:102 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Looking for C++ include execinfo.h -- Looking for C++ include execinfo.h - found -- Found Seqan: /usr/include (found version "2.4.0") -- Configuring done (1.9s) -- 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_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf make[1]: Leaving directory '/build/reproducible-path/hilive-2.0a' dh_auto_build cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/hilive-2.0a -B/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf/CMakeFiles /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' make -f CMakeFiles/HiLiveLibs.dir/build.make CMakeFiles/HiLiveLibs.dir/depend make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' cd /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hilive-2.0a /build/reproducible-path/hilive-2.0a /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf/CMakeFiles/HiLiveLibs.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' make -f CMakeFiles/HiLiveLibs.dir/build.make CMakeFiles/HiLiveLibs.dir/build make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' [ 12%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o [ 12%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o -c /build/reproducible-path/hilive-2.0a/lib/tools_static.cpp /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o -c /build/reproducible-path/hilive-2.0a/lib/alnread.cpp [ 18%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o -c /build/reproducible-path/hilive-2.0a/lib/tools.cpp In file included from /build/reproducible-path/hilive-2.0a/lib/tools.h:11, from /build/reproducible-path/hilive-2.0a/lib/tools.cpp:1: /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/hilive-2.0a/lib/headers.h:1, from /build/reproducible-path/hilive-2.0a/lib/tools_static.h:10: /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 314 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ In file included from /build/reproducible-path/hilive-2.0a/lib/tools_static.cpp:1: /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/hilive-2.0a/lib/headers.h:1, from /build/reproducible-path/hilive-2.0a/lib/tools_static.h:10: /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 314 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ In file included from /build/reproducible-path/hilive-2.0a/lib/tools.h:11, from /build/reproducible-path/hilive-2.0a/lib/kindex.h:7, from /build/reproducible-path/hilive-2.0a/lib/alnread.h:6, from /build/reproducible-path/hilive-2.0a/lib/alnread.cpp:1: /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/hilive-2.0a/lib/headers.h:1, from /build/reproducible-path/hilive-2.0a/lib/alnread.h:4: /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 314 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ [ 25%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/alnstream.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/alnstream.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/alnstream.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/alnstream.cpp.o -c /build/reproducible-path/hilive-2.0a/lib/alnstream.cpp [ 31%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o -c /build/reproducible-path/hilive-2.0a/lib/alnout.cpp In file included from /build/reproducible-path/hilive-2.0a/lib/tools.h:11, from /build/reproducible-path/hilive-2.0a/lib/kindex.h:7, from /build/reproducible-path/hilive-2.0a/lib/alnstream.h:7, from /build/reproducible-path/hilive-2.0a/lib/alnstream.cpp:1: /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/hilive-2.0a/lib/headers.h:1, from /build/reproducible-path/hilive-2.0a/lib/alnstream.h:4: /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 314 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/reproducible-path/hilive-2.0a/lib/alnstream.cpp: In member function 'uint64_t oAlnStream::lz4write(const char*, uint64_t)': /build/reproducible-path/hilive-2.0a/lib/alnstream.cpp:23:43: warning: 'int LZ4_compress(const char*, char*, int)' is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations] 23 | uint32_t compressed_size = LZ4_compress (source, buf.data(), size); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/hilive-2.0a/lib/headers.h:5: /usr/include/lz4.h:765:75: note: declared here 765 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize); | ^~~~~~~~~~~~ In file included from /build/reproducible-path/hilive-2.0a/lib/tools.h:11, from /build/reproducible-path/hilive-2.0a/lib/kindex.h:7, from /build/reproducible-path/hilive-2.0a/lib/alnout.h:7, from /build/reproducible-path/hilive-2.0a/lib/alnout.cpp:1: /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/hilive-2.0a/lib/headers.h:1, from /build/reproducible-path/hilive-2.0a/lib/alnout.h:4: /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 314 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/reproducible-path/hilive-2.0a/lib/alnstream.cpp: In member function 'ReadAlignment* iAlnStream::get_alignment()': /build/reproducible-path/hilive-2.0a/lib/alnstream.cpp:359:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 359 | fread(buffer.data(),1,buf_size,fstream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/hilive-2.0a/lib/alnstream.cpp:389:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 389 | fread(buffer.data(),1,buf_size,fstream); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 37%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o -c /build/reproducible-path/hilive-2.0a/lib/illumina_parsers.cpp In file included from /build/reproducible-path/hilive-2.0a/lib/tools.h:11, from /build/reproducible-path/hilive-2.0a/lib/illumina_parsers.h:6, from /build/reproducible-path/hilive-2.0a/lib/illumina_parsers.cpp:1: /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/hilive-2.0a/lib/headers.h:1, from /build/reproducible-path/hilive-2.0a/lib/illumina_parsers.h:4: /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 314 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ [ 43%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/kindex.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/kindex.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/kindex.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/kindex.cpp.o -c /build/reproducible-path/hilive-2.0a/lib/kindex.cpp [ 50%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o -c /build/reproducible-path/hilive-2.0a/lib/parallel.cpp In file included from /build/reproducible-path/hilive-2.0a/lib/tools.h:11, from /build/reproducible-path/hilive-2.0a/lib/kindex.h:7, from /build/reproducible-path/hilive-2.0a/lib/kindex.cpp:1: /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/hilive-2.0a/lib/headers.h:1, from /build/reproducible-path/hilive-2.0a/lib/kindex.h:4: /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 314 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ In file included from /build/reproducible-path/hilive-2.0a/lib/tools.h:11, from /build/reproducible-path/hilive-2.0a/lib/parallel.h:6, from /build/reproducible-path/hilive-2.0a/lib/parallel.cpp:1: /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/hilive-2.0a/lib/headers.h:1, from /build/reproducible-path/hilive-2.0a/lib/parallel.h:4: /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 314 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ [ 56%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/argument_parser.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/argument_parser.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/argument_parser.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/argument_parser.cpp.o -c /build/reproducible-path/hilive-2.0a/lib/argument_parser.cpp In file included from /build/reproducible-path/hilive-2.0a/lib/tools.h:11, from /build/reproducible-path/hilive-2.0a/lib/parallel.h:6, from /build/reproducible-path/hilive-2.0a/lib/argument_parser.h:5, from /build/reproducible-path/hilive-2.0a/lib/argument_parser.cpp:1: /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from /build/reproducible-path/hilive-2.0a/lib/argument_parser.h:1: /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/reproducible-path/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)': /build/reproducible-path/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 314 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ [ 62%] Linking CXX static library libHiLiveLibs.a /usr/bin/cmake -P CMakeFiles/HiLiveLibs.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/HiLiveLibs.dir/link.txt --verbose=1 /usr/bin/ar qc libHiLiveLibs.a CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o CMakeFiles/HiLiveLibs.dir/lib/alnstream.cpp.o CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o CMakeFiles/HiLiveLibs.dir/lib/kindex.cpp.o CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o CMakeFiles/HiLiveLibs.dir/lib/argument_parser.cpp.o /usr/bin/ranlib libHiLiveLibs.a make[3]: Leaving directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' [ 62%] Built target HiLiveLibs make -f CMakeFiles/hilive.dir/build.make CMakeFiles/hilive.dir/depend make -f CMakeFiles/hilive-build.dir/build.make CMakeFiles/hilive-build.dir/depend make -f CMakeFiles/hilive-out.dir/build.make CMakeFiles/hilive-out.dir/depend make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' cd /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hilive-2.0a /build/reproducible-path/hilive-2.0a /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf/CMakeFiles/hilive-out.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' cd /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hilive-2.0a /build/reproducible-path/hilive-2.0a /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf/CMakeFiles/hilive.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' cd /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hilive-2.0a /build/reproducible-path/hilive-2.0a /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf/CMakeFiles/hilive-build.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' make -f CMakeFiles/hilive.dir/build.make CMakeFiles/hilive.dir/build make -f CMakeFiles/hilive-out.dir/build.make CMakeFiles/hilive-out.dir/build make[3]: Leaving directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' make -f CMakeFiles/hilive-build.dir/build.make CMakeFiles/hilive-build.dir/build make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' [ 75%] Building CXX object CMakeFiles/hilive.dir/tools/hilive.cpp.o [ 75%] Building CXX object CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -MD -MT CMakeFiles/hilive.dir/tools/hilive.cpp.o -MF CMakeFiles/hilive.dir/tools/hilive.cpp.o.d -o CMakeFiles/hilive.dir/tools/hilive.cpp.o -c /build/reproducible-path/hilive-2.0a/tools/hilive.cpp /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -MD -MT CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o -MF CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o.d -o CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o -c /build/reproducible-path/hilive-2.0a/tools/hilive_out.cpp [ 81%] Building CXX object CMakeFiles/hilive-build.dir/tools/build_index.cpp.o /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf -I/build/reproducible-path/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -MD -MT CMakeFiles/hilive-build.dir/tools/build_index.cpp.o -MF CMakeFiles/hilive-build.dir/tools/build_index.cpp.o.d -o CMakeFiles/hilive-build.dir/tools/build_index.cpp.o -c /build/reproducible-path/hilive-2.0a/tools/build_index.cpp In file included from /build/reproducible-path/hilive-2.0a/tools/../lib/tools.h:11, from /build/reproducible-path/hilive-2.0a/tools/../lib/kindex.h:7, from /build/reproducible-path/hilive-2.0a/tools/hilive.cpp:4: /build/reproducible-path/hilive-2.0a/tools/../lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/tools/../lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/hilive-2.0a/tools/../lib/headers.h:1, from /build/reproducible-path/hilive-2.0a/tools/hilive.cpp:1: /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ In file included from /build/reproducible-path/hilive-2.0a/tools/../lib/tools.h:11, from /build/reproducible-path/hilive-2.0a/tools/../lib/kindex.h:7, from /build/reproducible-path/hilive-2.0a/tools/build_index.cpp:5: /build/reproducible-path/hilive-2.0a/tools/../lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/tools/../lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from /build/reproducible-path/hilive-2.0a/tools/build_index.cpp:1: /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/reproducible-path/hilive-2.0a/tools/../lib/tools_static.h: In function 'void rtrim(std::string&)': /build/reproducible-path/hilive-2.0a/tools/../lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 314 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/reproducible-path/hilive-2.0a/tools/../lib/tools_static.h: In function 'void rtrim(std::string&)': /build/reproducible-path/hilive-2.0a/tools/../lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 314 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ In file included from /build/reproducible-path/hilive-2.0a/tools/../lib/tools.h:11, from /build/reproducible-path/hilive-2.0a/tools/../lib/kindex.h:7, from /build/reproducible-path/hilive-2.0a/tools/hilive_out.cpp:5: /build/reproducible-path/hilive-2.0a/tools/../lib/tools_static.h: In function 'void ltrim(std::string&)': /build/reproducible-path/hilive-2.0a/tools/../lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 304 | std::not1(std::ptr_fun(std::isspace)))); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from /build/reproducible-path/hilive-2.0a/tools/hilive_out.cpp:1: /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/reproducible-path/hilive-2.0a/tools/../lib/tools_static.h: In function 'void rtrim(std::string&)': /build/reproducible-path/hilive-2.0a/tools/../lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 314 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ [ 87%] Linking CXX executable hilive-build /usr/bin/cmake -E cmake_link_script CMakeFiles/hilive-build.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive "CMakeFiles/hilive-build.dir/tools/build_index.cpp.o" -o hilive-build libHiLiveLibs.a /usr/lib/arm-linux-gnueabihf/libz.so -llz4 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.83.0 /usr/lib/arm-linux-gnueabihf/libboost_filesystem.so.1.83.0 /usr/lib/arm-linux-gnueabihf/libboost_program_options.so.1.83.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.83.0 -lrt /usr/lib/arm-linux-gnueabihf/libz.so -llz4 -lrt /usr/lib/arm-linux-gnueabihf/libboost_atomic.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' [ 87%] Built target hilive-build [ 93%] Linking CXX executable hilive-out /usr/bin/cmake -E cmake_link_script CMakeFiles/hilive-out.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive "CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o" -o hilive-out libHiLiveLibs.a /usr/lib/arm-linux-gnueabihf/libz.so -llz4 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.83.0 /usr/lib/arm-linux-gnueabihf/libboost_filesystem.so.1.83.0 /usr/lib/arm-linux-gnueabihf/libboost_program_options.so.1.83.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.83.0 -lrt /usr/lib/arm-linux-gnueabihf/libz.so -llz4 -lrt /usr/lib/arm-linux-gnueabihf/libboost_atomic.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' [ 93%] Built target hilive-out [100%] Linking CXX executable hilive /usr/bin/cmake -E cmake_link_script CMakeFiles/hilive.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hilive-2.0a=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive CMakeFiles/hilive.dir/tools/hilive.cpp.o -o hilive libHiLiveLibs.a /usr/lib/arm-linux-gnueabihf/libz.so -llz4 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.83.0 /usr/lib/arm-linux-gnueabihf/libboost_filesystem.so.1.83.0 /usr/lib/arm-linux-gnueabihf/libboost_program_options.so.1.83.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.83.0 -lrt /usr/lib/arm-linux-gnueabihf/libz.so -llz4 -lrt /usr/lib/arm-linux-gnueabihf/libboost_atomic.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' [100%] Built target hilive make[2]: Leaving directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/hilive-2.0a/obj-arm-linux-gnueabihf' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install --destdir=debian/hilive/ debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/hilive-2.0a' chrpath --delete obj-arm-linux-gnueabihf/hilive* dh_install make[1]: Leaving directory '/build/reproducible-path/hilive-2.0a' debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/hilive-2.0a' markdown README.md > README.html dh_installdocs rm README.html make[1]: Leaving directory '/build/reproducible-path/hilive-2.0a' dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: debian/hilive/usr/bin/hilive-build contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hilive/usr/bin/hilive contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'hilive' in '../hilive_2.0a-3_armhf.deb'. dpkg-deb: building package 'hilive-dbgsym' in '../hilive-dbgsym_2.0a-3_armhf.deb'. dpkg-genbuildinfo --build=binary -O../hilive_2.0a-3_armhf.buildinfo dpkg-genchanges --build=binary -O../hilive_2.0a-3_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/25229 and its subdirectories I: Current time: Tue Apr 9 02:37:29 -12 2024 I: pbuilder-time-stamp: 1712673449 Tue Apr 9 14:38:01 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt32z-armhf-rb.debian.net. Tue Apr 9 14:38:01 UTC 2024 I: Preparing to do remote build '2' on virt32z-armhf-rb.debian.net. Tue Apr 9 14:44:16 UTC 2024 I: Deleting $TMPDIR on virt32z-armhf-rb.debian.net. Tue Apr 9 14:44:19 UTC 2024 I: hilive_2.0a-3_armhf.changes: Format: 1.8 Date: Thu, 16 Jan 2020 11:56:44 +0100 Source: hilive Binary: hilive hilive-dbgsym Architecture: armhf Version: 2.0a-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: hilive - realtime alignment of Illumina reads Changes: hilive (2.0a-3) unstable; urgency=medium . [ Andreas Tille ] * Really install documentation . [ Juhani Numminen ] * Remove undesired build flag -march=native . [ Andreas Tille ] * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. * Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright). Checksums-Sha1: 485256fb4c9e5d944fc92bfa52b4a37bc679eaef 9120660 hilive-dbgsym_2.0a-3_armhf.deb b58f9b52203cff79c7cae3b3d6138249ecac4e35 6999 hilive_2.0a-3_armhf.buildinfo 9cba85e677b5f4229c7d3891fdbebd0ec0d59ce2 468344 hilive_2.0a-3_armhf.deb Checksums-Sha256: 5490dbce4b24109731a4968acd4065934ffd42f6cd8e22626bc6e6f2084fb97d 9120660 hilive-dbgsym_2.0a-3_armhf.deb 9f8d198e295d7ba4d57cdb2e73ba555a2bddcad158c158165ee272cfb3670ce5 6999 hilive_2.0a-3_armhf.buildinfo 730ee4dca0938047c1804d972bea5d8e86f3d7f832831bfb9defa2e3ae299582 468344 hilive_2.0a-3_armhf.deb Files: c41cd71ee2843d838913b0f110b14d6f 9120660 debug optional hilive-dbgsym_2.0a-3_armhf.deb 441f29c49a9c516e0bae5ab8c0328a04 6999 science optional hilive_2.0a-3_armhf.buildinfo 230330fe2b3cec9353d5ac2a35207b8d 468344 science optional hilive_2.0a-3_armhf.deb Tue Apr 9 14:44:20 UTC 2024 I: diffoscope 263 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_6-2669.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.wtKPGz9M/hilive_2.0a-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.wtKPGz9M/hilive_2.0a-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.wtKPGz9M/hilive_2.0a-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.wtKPGz9M/b1/hilive_2.0a-3_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.wtKPGz9M/b2/hilive_2.0a-3_armhf.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: 0.486s) 0.486s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.120s) 0.120s 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: 837ms CPU time consumed: 837ms Tue Apr 9 14:44:21 UTC 2024 I: diffoscope 263 found no differences in the changes files, and a .buildinfo file also exists. Tue Apr 9 14:44:21 UTC 2024 I: hilive from unstable built successfully and reproducibly on armhf. Tue Apr 9 14:44:23 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Apr 9 14:44:23 UTC 2024 I: Submitting 8.0K b1/hilive_2.0a-3_armhf.buildinfo.asc Tue Apr 9 14:44:24 UTC 2024 I: Submitting 8.0K b2/hilive_2.0a-3_armhf.buildinfo.asc Tue Apr 9 14:44:25 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 9 14:44:25 UTC 2024 I: Done submitting .buildinfo files. Tue Apr 9 14:44:25 UTC 2024 I: Removing signed hilive_2.0a-3_armhf.buildinfo.asc files: removed './b1/hilive_2.0a-3_armhf.buildinfo.asc' removed './b2/hilive_2.0a-3_armhf.buildinfo.asc'