Mon May 8 19:25:29 UTC 2023 I: starting to build hilive/bookworm/amd64 on jenkins on '2023-05-08 19:25' Mon May 8 19:25:29 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_26/11799/console.log Mon May 8 19:25:29 UTC 2023 I: Downloading source for bookworm/hilive=2.0a-3 --2023-05-08 19:25:29-- http://cdn-fastly.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% 152M=0s 2023-05-08 19:25:29 (152 MB/s) - ‘hilive_2.0a-3.dsc’ saved [2118/2118] Mon May 8 19:25:29 UTC 2023 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----- Mon May 8 19:25:29 UTC 2023 I: Checking whether the package is not for us Mon May 8 19:25:29 UTC 2023 I: Starting 1st build on remote node ionos5-amd64.debian.net. Mon May 8 19:25:29 UTC 2023 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Mon May 8 19:28:00 UTC 2023 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 9 13:48:32 -12 2024 I: pbuilder-time-stamp: 1717984112 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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 Wed Jan 15 23:17:41 2020 -12 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/3460713/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='1ac63cadd9dd494896806032d3433322' 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='3460713' 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.Bs9UV585/pbuilderrc_8qLQ --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Bs9UV585/b1 --logfile b1/build.log hilive_2.0a-3.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos5-amd64 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 2023 more -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/3460713/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 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 ... 19596 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} libarchive13{a} libboost-filesystem-dev{a} libboost-filesystem1.74-dev{a} libboost-filesystem1.74.0{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-system-dev{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost1.74-dev{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu-dev{a} libicu72{a} libjsoncpp25{a} libldap-2.5-0{a} liblz4-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libseqan2-dev{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1{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 libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 77 newly installed, 0 to remove and 0 not upgraded. Need to get 60.9 MB of archives. After unpacking 364 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libarchive13 amd64 3.6.2-1 [343 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-9 [386 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libjsoncpp25 amd64 1.9.5-4 [78.6 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 librhash0 amd64 1.4.3-3 [134 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libuv1 amd64 1.44.2-1 [140 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 cmake-data all 3.25.1-1 [2026 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 cmake amd64 3.25.1-1 [8692 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 icu-devtools amd64 72.1-3 [206 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-20 [9510 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libboost-filesystem1.74.0 amd64 1.74.0+ds1-20 [258 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libboost-system1.74.0 amd64 1.74.0+ds1-20 [218 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libboost-system1.74-dev amd64 1.74.0+ds1-20 [219 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libboost-filesystem1.74-dev amd64 1.74.0+ds1-20 [279 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libboost-filesystem-dev amd64 1.74.0.3 [4368 B] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libboost-regex1.74.0 amd64 1.74.0+ds1-20 [487 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libicu-dev amd64 72.1-3 [10.3 MB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libboost-regex1.74-dev amd64 1.74.0+ds1-20 [558 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libboost-iostreams1.74-dev amd64 1.74.0+ds1-20 [248 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libboost-iostreams-dev amd64 1.74.0.3 [4316 B] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options1.74.0 amd64 1.74.0+ds1-20 [328 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options1.74-dev amd64 1.74.0+ds1-20 [358 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options-dev amd64 1.74.0.3 [4340 B] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libboost-system-dev amd64 1.74.0.3 [4468 B] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-9 [381 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libcurl4-gnutls-dev amd64 7.88.1-9 [481 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libdeflate-dev amd64 1.14-1 [53.3 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libhts-dev amd64 1.16+ds-3 [1601 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 liblz4-dev amd64 1.9.4-1 [84.3 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libseqan2-dev all 2.4.0+dfsg-15 [1215 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 markdown all 1.0.1-12 [17.7 kB] Fetched 60.9 MB in 1s (80.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.2-3_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../01-procps_2%3a4.0.2-3_amd64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../04-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../07-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../10-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package chrpath. Preparing to unpack .../17-chrpath_0.16-2+b1_amd64.deb ... Unpacking chrpath (0.16-2+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../18-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../19-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../20-libarchive13_3.6.2-1_amd64.deb ... Unpacking libarchive13:amd64 (3.6.2-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../21-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../22-libsasl2-modules-db_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../23-libsasl2-2_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../24-libldap-2.5-0_2.5.13+dfsg-5_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../25-libnghttp2-14_1.52.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.52.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../26-libpsl5_0.21.2-1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.2-1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../27-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../28-libssh2-1_1.10.0-3+b1_amd64.deb ... Unpacking libssh2-1:amd64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../29-libcurl4_7.88.1-9_amd64.deb ... Unpacking libcurl4:amd64 (7.88.1-9) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../30-libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package libjsoncpp25:amd64. Preparing to unpack .../31-libjsoncpp25_1.9.5-4_amd64.deb ... Unpacking libjsoncpp25:amd64 (1.9.5-4) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../32-librhash0_1.4.3-3_amd64.deb ... Unpacking librhash0:amd64 (1.4.3-3) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../33-libuv1_1.44.2-1_amd64.deb ... Unpacking libuv1:amd64 (1.44.2-1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../34-cmake-data_3.25.1-1_all.deb ... Unpacking cmake-data (3.25.1-1) ... Selecting previously unselected package cmake. Preparing to unpack .../35-cmake_3.25.1-1_amd64.deb ... Unpacking cmake (3.25.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../36-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../37-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../38-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../39-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../40-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../41-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../42-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../43-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../44-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package gettext. Preparing to unpack .../45-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../46-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 .../47-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../48-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../49-icu-devtools_72.1-3_amd64.deb ... Unpacking icu-devtools (72.1-3) ... Selecting previously unselected package libboost1.74-dev:amd64. Preparing to unpack .../50-libboost1.74-dev_1.74.0+ds1-20_amd64.deb ... Unpacking libboost1.74-dev:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-filesystem1.74.0:amd64. Preparing to unpack .../51-libboost-filesystem1.74.0_1.74.0+ds1-20_amd64.deb ... Unpacking libboost-filesystem1.74.0:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-system1.74.0:amd64. Preparing to unpack .../52-libboost-system1.74.0_1.74.0+ds1-20_amd64.deb ... Unpacking libboost-system1.74.0:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-system1.74-dev:amd64. Preparing to unpack .../53-libboost-system1.74-dev_1.74.0+ds1-20_amd64.deb ... Unpacking libboost-system1.74-dev:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-filesystem1.74-dev:amd64. Preparing to unpack .../54-libboost-filesystem1.74-dev_1.74.0+ds1-20_amd64.deb ... Unpacking libboost-filesystem1.74-dev:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-filesystem-dev:amd64. Preparing to unpack .../55-libboost-filesystem-dev_1.74.0.3_amd64.deb ... Unpacking libboost-filesystem-dev:amd64 (1.74.0.3) ... Selecting previously unselected package libboost-regex1.74.0:amd64. Preparing to unpack .../56-libboost-regex1.74.0_1.74.0+ds1-20_amd64.deb ... Unpacking libboost-regex1.74.0:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libicu-dev:amd64. Preparing to unpack .../57-libicu-dev_72.1-3_amd64.deb ... Unpacking libicu-dev:amd64 (72.1-3) ... Selecting previously unselected package libboost-regex1.74-dev:amd64. Preparing to unpack .../58-libboost-regex1.74-dev_1.74.0+ds1-20_amd64.deb ... Unpacking libboost-regex1.74-dev:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-iostreams1.74-dev:amd64. Preparing to unpack .../59-libboost-iostreams1.74-dev_1.74.0+ds1-20_amd64.deb ... Unpacking libboost-iostreams1.74-dev:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-iostreams-dev:amd64. Preparing to unpack .../60-libboost-iostreams-dev_1.74.0.3_amd64.deb ... Unpacking libboost-iostreams-dev:amd64 (1.74.0.3) ... Selecting previously unselected package libboost-program-options1.74.0:amd64. Preparing to unpack .../61-libboost-program-options1.74.0_1.74.0+ds1-20_amd64.deb ... Unpacking libboost-program-options1.74.0:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-program-options1.74-dev:amd64. Preparing to unpack .../62-libboost-program-options1.74-dev_1.74.0+ds1-20_amd64.deb ... Unpacking libboost-program-options1.74-dev:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-program-options-dev:amd64. Preparing to unpack .../63-libboost-program-options-dev_1.74.0.3_amd64.deb ... Unpacking libboost-program-options-dev:amd64 (1.74.0.3) ... Selecting previously unselected package libboost-system-dev:amd64. Preparing to unpack .../64-libboost-system-dev_1.74.0.3_amd64.deb ... Unpacking libboost-system-dev:amd64 (1.74.0.3) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../65-libcurl3-gnutls_7.88.1-9_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.88.1-9) ... Selecting previously unselected package libcurl4-gnutls-dev:amd64. Preparing to unpack .../66-libcurl4-gnutls-dev_7.88.1-9_amd64.deb ... Unpacking libcurl4-gnutls-dev:amd64 (7.88.1-9) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../67-libdeflate0_1.14-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.14-1) ... Selecting previously unselected package libdeflate-dev:amd64. Preparing to unpack .../68-libdeflate-dev_1.14-1_amd64.deb ... Unpacking libdeflate-dev:amd64 (1.14-1) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../69-libhtscodecs2_1.3.0-4_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.3.0-4) ... Selecting previously unselected package libhts3:amd64. Preparing to unpack .../70-libhts3_1.16+ds-3_amd64.deb ... Unpacking libhts3:amd64 (1.16+ds-3) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../71-liblzma-dev_5.4.1-0.2_amd64.deb ... Unpacking liblzma-dev:amd64 (5.4.1-0.2) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../72-zlib1g-dev_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Selecting previously unselected package libhts-dev:amd64. Preparing to unpack .../73-libhts-dev_1.16+ds-3_amd64.deb ... Unpacking libhts-dev:amd64 (1.16+ds-3) ... Selecting previously unselected package liblz4-dev:amd64. Preparing to unpack .../74-liblz4-dev_1.9.4-1_amd64.deb ... Unpacking liblz4-dev:amd64 (1.9.4-1) ... Selecting previously unselected package libseqan2-dev. Preparing to unpack .../75-libseqan2-dev_2.4.0+dfsg-15_all.deb ... Unpacking libseqan2-dev (2.4.0+dfsg-15) ... Selecting previously unselected package markdown. Preparing to unpack .../76-markdown_1.0.1-12_all.deb ... Unpacking markdown (1.0.1-12) ... Setting up libhtscodecs2:amd64 (1.3.0-4) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libboost-system1.74.0:amd64 (1.74.0+ds1-20) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libboost1.74-dev:amd64 (1.74.0+ds1-20) ... Setting up libicu72:amd64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libboost-program-options1.74.0:amd64 (1.74.0+ds1-20) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libnghttp2-14:amd64 (1.52.0-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libboost-filesystem1.74.0:amd64 (1.74.0+ds1-20) ... Setting up file (1:5.44-3) ... Setting up libboost-program-options1.74-dev:amd64 (1.74.0+ds1-20) ... Setting up libseqan2-dev (2.4.0+dfsg-15) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libuv1:amd64 (1.44.2-1) ... Setting up libboost-program-options-dev:amd64 (1.74.0.3) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libboost-system1.74-dev:amd64 (1.74.0+ds1-20) ... Setting up libboost-regex1.74.0:amd64 (1.74.0+ds1-20) ... Setting up libproc2-0:amd64 (2:4.0.2-3) ... Setting up autopoint (0.21-12) ... Setting up libjsoncpp25:amd64 (1.9.5-4) ... Setting up icu-devtools (72.1-3) ... Setting up liblz4-dev:amd64 (1.9.4-1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:amd64 (5.4.1-0.2) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up librhash0:amd64 (1.4.3-3) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up cmake-data (3.25.1-1) ... Setting up libboost-filesystem1.74-dev:amd64 (1.74.0+ds1-20) ... Setting up libdeflate-dev:amd64 (1.14-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libicu-dev:amd64 (72.1-3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up libboost-filesystem-dev:amd64 (1.74.0.3) ... Setting up chrpath (0.16-2+b1) ... Setting up markdown (1.0.1-12) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:amd64 (3.6.2-1) ... Setting up libboost-system-dev:amd64 (1.74.0.3) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libboost-regex1.74-dev:amd64 (1.74.0+ds1-20) ... Setting up groff-base (1.22.4-10) ... Setting up libcurl4:amd64 (7.88.1-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-9) ... Setting up libcurl4-gnutls-dev:amd64 (7.88.1-9) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libboost-iostreams1.74-dev:amd64 (1.74.0+ds1-20) ... Setting up cmake (3.25.1-1) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libhts-dev:amd64 (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Setting up libboost-iostreams-dev:amd64 (1.74.0.3) ... Processing triggers for libc-bin (2.36-9) ... 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 (1.31-1.2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/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 amd64 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/hilive-2.0a' dh_auto_configure -- -DSEQAN_PATH=/usr/lib/seqan/ cd obj-x86_64-linux-gnu && 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/x86_64-linux-gnu -DSEQAN_PATH=/usr/lib/seqan/ .. -- The CXX compiler identification is GNU 12.2.0 -- 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/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: system filesystem program_options iostreams -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.13") -- Performing Test CXX14_BUILTIN -- Performing Test CXX14_BUILTIN - Success -- Looking for C++ include execinfo.h -- Looking for C++ include execinfo.h - found -- Found Seqan: /usr/include (found version "2.4.0") -- Configuring done -- Generating done 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/hilive-2.0a/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/hilive-2.0a' dh_auto_build cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/hilive-2.0a/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/hilive-2.0a -B/build/hilive-2.0a/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hilive-2.0a/obj-x86_64-linux-gnu/CMakeFiles /build/hilive-2.0a/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/hilive-2.0a/obj-x86_64-linux-gnu' make -f CMakeFiles/HiLiveLibs.dir/build.make CMakeFiles/HiLiveLibs.dir/depend make[3]: Entering directory '/build/hilive-2.0a/obj-x86_64-linux-gnu' cd /build/hilive-2.0a/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hilive-2.0a /build/hilive-2.0a /build/hilive-2.0a/obj-x86_64-linux-gnu /build/hilive-2.0a/obj-x86_64-linux-gnu /build/hilive-2.0a/obj-x86_64-linux-gnu/CMakeFiles/HiLiveLibs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hilive-2.0a/obj-x86_64-linux-gnu' make -f CMakeFiles/HiLiveLibs.dir/build.make CMakeFiles/HiLiveLibs.dir/build make[3]: Entering directory '/build/hilive-2.0a/obj-x86_64-linux-gnu' [ 6%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o [ 12%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o [ 18%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/alnstream.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-x86_64-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -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/hilive-2.0a/lib/tools_static.cpp [ 25%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-x86_64-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -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/hilive-2.0a/lib/tools.cpp [ 31%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o [ 37%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/argument_parser.cpp.o [ 43%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/kindex.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-x86_64-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -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/hilive-2.0a/lib/alnstream.cpp [ 50%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o [ 56%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-x86_64-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -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/hilive-2.0a/lib/alnread.cpp /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-x86_64-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -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/hilive-2.0a/lib/alnout.cpp /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-x86_64-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -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/hilive-2.0a/lib/kindex.cpp /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-x86_64-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -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/hilive-2.0a/lib/parallel.cpp /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-x86_64-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -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/hilive-2.0a/lib/illumina_parsers.cpp /usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-x86_64-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -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/hilive-2.0a/lib/argument_parser.cpp In file included from /build/hilive-2.0a/lib/tools_static.cpp:1: /build/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/hilive-2.0a/lib/headers.h:1, from /build/hilive-2.0a/lib/tools_static.h:10: /usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)': /build/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++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ In file included from /build/hilive-2.0a/lib/tools.h:11, from /build/hilive-2.0a/lib/tools.cpp:1: /build/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/hilive-2.0a/lib/headers.h:1, from /build/hilive-2.0a/lib/tools_static.h:10: /usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)': /build/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++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ In file included from /build/hilive-2.0a/lib/tools.h:11, from /build/hilive-2.0a/lib/illumina_parsers.h:6, from /build/hilive-2.0a/lib/illumina_parsers.cpp:1: /build/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/hilive-2.0a/lib/headers.h:1, from /build/hilive-2.0a/lib/illumina_parsers.h:4: /usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)': /build/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++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ In file included from /build/hilive-2.0a/lib/tools.h:11, from /build/hilive-2.0a/lib/kindex.h:7, from /build/hilive-2.0a/lib/alnstream.h:7, from /build/hilive-2.0a/lib/alnstream.cpp:1: /build/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/hilive-2.0a/lib/headers.h:1, from /build/hilive-2.0a/lib/alnstream.h:4: /usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)': /build/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++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ In file included from /build/hilive-2.0a/lib/tools.h:11, from /build/hilive-2.0a/lib/kindex.h:7, from /build/hilive-2.0a/lib/alnout.h:7, from /build/hilive-2.0a/lib/alnout.cpp:1: /build/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/hilive-2.0a/lib/headers.h:1, from /build/hilive-2.0a/lib/alnout.h:4: /usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)': /build/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++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ In file included from /build/hilive-2.0a/lib/tools.h:11, from /build/hilive-2.0a/lib/parallel.h:6, from /build/hilive-2.0a/lib/parallel.cpp:1: /build/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/hilive-2.0a/lib/headers.h:1, from /build/hilive-2.0a/lib/parallel.h:4: /usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)': /build/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++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ In file included from /build/hilive-2.0a/lib/tools.h:11, from /build/hilive-2.0a/lib/parallel.h:6, from /build/hilive-2.0a/lib/argument_parser.h:5, from /build/hilive-2.0a/lib/argument_parser.cpp:1: /build/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/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++/12/string:48, 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/hilive-2.0a/lib/argument_parser.h:1: /usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)': /build/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++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ In file included from /build/hilive-2.0a/lib/tools.h:11, from /build/hilive-2.0a/lib/kindex.h:7, from /build/hilive-2.0a/lib/kindex.cpp:1: /build/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/hilive-2.0a/lib/headers.h:1, from /build/hilive-2.0a/lib/kindex.h:4: /usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)': /build/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++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ In file included from /build/hilive-2.0a/lib/tools.h:11, from /build/hilive-2.0a/lib/kindex.h:7, from /build/hilive-2.0a/lib/alnread.h:6, from /build/hilive-2.0a/lib/alnread.cpp:1: /build/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)': /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/hilive-2.0a/lib/headers.h:1, from /build/hilive-2.0a/lib/alnread.h:4: /usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)': /build/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++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/hilive-2.0a/lib/alnstream.cpp: In member function 'uint64_t oAlnStream::lz4write(const char*, uint64_t)': /build/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/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); | ^~~~~~~~~~~~ /build/hilive-2.0a/lib/alnstream.cpp: In member function 'ReadAlignment* iAlnStream::get_alignment()': /build/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/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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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/hilive-2.0a/obj-x86_64-linux-gnu' [ 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/hilive-2.0a/obj-x86_64-linux-gnu' cd /build/hilive-2.0a/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hilive-2.0a /build/hilive-2.0a /build/hilive-2.0a/obj-x86_64-linux-gnu /build/hilive-2.0a/obj-x86_64-linux-gnu /build/hilive-2.0a/obj-x86_64-linux-gnu/CMakeFiles/hilive.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hilive-2.0a/obj-x86_64-linux-gnu' cd /build/hilive-2.0a/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hilive-2.0a /build/hilive-2.0a /build/hilive-2.0a/obj-x86_64-linux-gnu /build/hilive-2.0a/obj-x86_64-linux-gnu /build/hilive-2.0a/obj-x86_64-linux-gnu/CMakeFiles/hilive-build.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hilive-2.0a/obj-x86_64-linux-gnu' cd /build/hilive-2.0a/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hilive-2.0a /build/hilive-2.0a /build/hilive-2.0a/obj-x86_64-linux-gnu /build/hilive-2.0a/obj-x86_64-linux-gnu /build/hilive-2.0a/obj-x86_64-linux-gnu/CMakeFiles/hilive-out.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hilive-2.0a/obj-x86_64-linux-gnu' make -f CMakeFiles/hilive.dir/build.make CMakeFiles/hilive.dir/build make[3]: Leaving directory '/build/hilive-2.0a/obj-x86_64-linux-gnu' make -f CMakeFiles/hilive-out.dir/build.make CMakeFiles/hilive-out.dir/build make[3]: Entering directory '/build/hilive-2.0a/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hilive-2.0a/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/hilive-2.0a/obj-x86_64-linux-gnu' make -f CMakeFiles/hilive-build.dir/build.make CMakeFiles/hilive-build.dir/build make[3]: Entering directory '/build/hilive-2.0a/obj-x86_64-linux-gnu' [ 68%] 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_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-x86_64-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -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/hilive-2.0a/tools/hilive.cpp [ 81%] Building CXX object CMakeFiles/hilive-build.dir/tools/build_index.cpp.o /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-x86_64-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -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/hilive-2.0a/tools/hilive_out.cpp /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-x86_64-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -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/hilive-2.0a/tools/build_index.cpp In file included from /build/hilive-2.0a/tools/../lib/tools.h:11, from /build/hilive-2.0a/tools/../lib/kindex.h:7, from /build/hilive-2.0a/tools/hilive.cpp:4: /build/hilive-2.0a/tools/../lib/tools_static.h: In function 'void ltrim(std::string&)': /build/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++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/hilive-2.0a/tools/../lib/headers.h:1, from /build/hilive-2.0a/tools/hilive.cpp:1: /usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/hilive-2.0a/tools/../lib/tools_static.h: In function 'void rtrim(std::string&)': /build/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++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ In file included from /build/hilive-2.0a/tools/../lib/tools.h:11, from /build/hilive-2.0a/tools/../lib/kindex.h:7, from /build/hilive-2.0a/tools/hilive_out.cpp:5: /build/hilive-2.0a/tools/../lib/tools_static.h: In function 'void ltrim(std::string&)': /build/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++/12/string:48, 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/hilive-2.0a/tools/hilive_out.cpp:1: /usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/hilive-2.0a/tools/../lib/tools_static.h: In function 'void rtrim(std::string&)': /build/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++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ In file included from /build/hilive-2.0a/tools/../lib/tools.h:11, from /build/hilive-2.0a/tools/../lib/kindex.h:7, from /build/hilive-2.0a/tools/build_index.cpp:5: /build/hilive-2.0a/tools/../lib/tools_static.h: In function 'void ltrim(std::string&)': /build/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++/12/string:48, 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/hilive-2.0a/tools/build_index.cpp:1: /usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ /build/hilive-2.0a/tools/../lib/tools_static.h: In function 'void rtrim(std::string&)': /build/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++/12/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/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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/x86_64-linux-gnu/libz.so -llz4 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 -lrt /usr/lib/x86_64-linux-gnu/libz.so -llz4 -lrt make[3]: Leaving directory '/build/hilive-2.0a/obj-x86_64-linux-gnu' [ 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/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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/x86_64-linux-gnu/libz.so -llz4 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 -lrt /usr/lib/x86_64-linux-gnu/libz.so -llz4 -lrt make[3]: Leaving directory '/build/hilive-2.0a/obj-x86_64-linux-gnu' [ 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/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -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/x86_64-linux-gnu/libz.so -llz4 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 -lrt /usr/lib/x86_64-linux-gnu/libz.so -llz4 -lrt make[3]: Leaving directory '/build/hilive-2.0a/obj-x86_64-linux-gnu' [100%] Built target hilive make[2]: Leaving directory '/build/hilive-2.0a/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/hilive-2.0a/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/hilive-2.0a/obj-x86_64-linux-gnu' 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/hilive-2.0a' chrpath --delete obj-x86_64-linux-gnu/hilive* dh_install make[1]: Leaving directory '/build/hilive-2.0a' debian/rules override_dh_installdocs make[1]: Entering directory '/build/hilive-2.0a' markdown README.md > README.html dh_installdocs rm README.html make[1]: Leaving directory '/build/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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'hilive' in '../hilive_2.0a-3_amd64.deb'. dpkg-deb: building package 'hilive-dbgsym' in '../hilive-dbgsym_2.0a-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../hilive_2.0a-3_amd64.buildinfo dpkg-genchanges --build=binary -O../hilive_2.0a-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3460713 and its subdirectories I: Current time: Sun Jun 9 13:51:01 -12 2024 I: pbuilder-time-stamp: 1717984261 Mon May 8 19:28:00 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Mon May 8 19:28:00 UTC 2023 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Mon May 8 19:34:05 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Mon May 8 19:34:05 UTC 2023 I: hilive_2.0a-3_amd64.changes: Format: 1.8 Date: Thu, 16 Jan 2020 11:56:44 +0100 Source: hilive Binary: hilive hilive-dbgsym Architecture: amd64 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: 5d6444250ae25801e9f5a8153376e8de9be655d9 10221764 hilive-dbgsym_2.0a-3_amd64.deb f46bf16d7fac7b0b1012c2992cc415143e1335d0 6881 hilive_2.0a-3_amd64.buildinfo 7df365db69c8a3718f887fa77d59bd32a3feeb05 529076 hilive_2.0a-3_amd64.deb Checksums-Sha256: cb281c183ba048cc8573f49069d3c1c1e70b81a00e12960fc165b7bb29c5811a 10221764 hilive-dbgsym_2.0a-3_amd64.deb d0e4f8dc476d440dbd67409bfc4960a31ee50847e6bf24def2f5f7fabd5fee93 6881 hilive_2.0a-3_amd64.buildinfo ae29da9150ad18c32e092406784011f8d676b53866ee125fad48ec133dbb724a 529076 hilive_2.0a-3_amd64.deb Files: fff076c9ed6a7c21726fe2e6caa1d8df 10221764 debug optional hilive-dbgsym_2.0a-3_amd64.deb 6a42c2735cfd94fc233aee6233f7cc77 6881 science optional hilive_2.0a-3_amd64.buildinfo 82be74afdeac9d0eb8ffa58fae75df9d 529076 science optional hilive_2.0a-3_amd64.deb Mon May 8 19:34:06 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Bs9UV585/hilive_2.0a-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Bs9UV585/hilive_2.0a-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Bs9UV585/hilive_2.0a-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Bs9UV585/b1/hilive_2.0a-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Bs9UV585/b2/hilive_2.0a-3_amd64.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: 0.414s) 0.414s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.125s) 0.125s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Mon May 8 19:36:52 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Mon May 8 19:36:52 UTC 2023 I: hilive from bookworm built successfully and reproducibly on amd64. Mon May 8 19:36:55 UTC 2023 I: Submitting .buildinfo files to external archives: Mon May 8 19:36:55 UTC 2023 I: Submitting 8.0K b1/hilive_2.0a-3_amd64.buildinfo.asc Mon May 8 19:36:59 UTC 2023 I: Submitting 8.0K b2/hilive_2.0a-3_amd64.buildinfo.asc Mon May 8 19:37:03 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon May 8 19:37:03 UTC 2023 I: Done submitting .buildinfo files. Mon May 8 19:37:03 UTC 2023 I: Removing signed hilive_2.0a-3_amd64.buildinfo.asc files: removed './b1/hilive_2.0a-3_amd64.buildinfo.asc' removed './b2/hilive_2.0a-3_amd64.buildinfo.asc'