Sat Aug 21 16:48:35 UTC 2021 I: starting to build racon/bullseye/arm64 on jenkins on '2021-08-21 16:48' Sat Aug 21 16:48:35 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_1/3255/console.log Sat Aug 21 16:48:35 UTC 2021 I: Downloading source for bullseye/racon=1.4.20-1 --2021-08-21 16:48:35-- http://cdn-fastly.deb.debian.org/debian/pool/main/r/racon/racon_1.4.20-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2083 (2.0K) Saving to: ‘racon_1.4.20-1.dsc’ 0K .. 100% 96.0M=0s 2021-08-21 16:48:35 (96.0 MB/s) - ‘racon_1.4.20-1.dsc’ saved [2083/2083] Sat Aug 21 16:48:35 UTC 2021 I: racon_1.4.20-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: racon Binary: racon Architecture: any Version: 1.4.20-1 Maintainer: Debian Med Packaging Team Uploaders: Cédric Lood , Andreas Tille Homepage: https://github.com/lbcb-sci/racon Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/racon Vcs-Git: https://salsa.debian.org/med-team/racon.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), cmake, libgtest-dev, libbioparser-dev (>= 3.0.12), libcereal-dev, libedlib-dev, libspoa-dev, libthread-pool-dev (>= 3.0.2), rampler Package-List: racon deb science optional arch=any Checksums-Sha1: 85c544087652aa62fa1ee8e52fcf9fe9352d73b5 3083388 racon_1.4.20.orig.tar.gz 7f8899b51881dbb6f2e7e7fe24c4e57502f133f8 6268 racon_1.4.20-1.debian.tar.xz Checksums-Sha256: 50c22e66a1141c865b70917eecf34155b9ab3a4642765381c30f64557bdb2a9f 3083388 racon_1.4.20.orig.tar.gz ea85a7a999ef7a76ce036f0685f1f08303643335a6afb61c974aab009e4569c4 6268 racon_1.4.20-1.debian.tar.xz Files: e6300df6ac01cea7e6b175b48281c3f4 3083388 racon_1.4.20.orig.tar.gz 2cc7de1761aed4e11cb09431b27adaae 6268 racon_1.4.20-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmAGrsgACgkQPCZ2P2xn 5uIEbRAAqXCb8Numg38VrZG3rCk9sc3OQA1jUtCgLzFkdpaF5KKLxg1BRZSUntx8 X5a+uM6GOPBwotO32y75AdF0rQzkS/NbJxwN5xK5W8cezTTlAGjdwVlzcHwNDtuo yR2x8IgZJatcUiTomagKwZY/g+5uwFUyKNmPLFYqTnCl2hM4nu9bZklnHyoy2/FK DMUyALAIWcVfQ/VR7fp2DAMy5Pcro8XrzQvTlQKe5eM7SzydKETmgaj+gja5bkTd 1e3/X4WEhfzjjqT5DHKXOHvFimANpk1xUps3C/O7PIkZSmyw+zmeI4EIZPLWW7tk lsRHSixX63tH/SM2QW5JB+UKU0F52T8OkCrhr3/UpICI3T7y1cHGB50dRfD/aDh5 iP9CecAmCciX0rNRfuxhkzSQ8hTN7T3A7klBow9J94uJUd1RHIDj/WLkeIh/TU7c mTL3kcBQC/GmA7rxxyM6aAijHpS6S63npZgQJGTc0zu0odbbLL3vJPkHg0D9pyAl DbVQUI54KdrrOmKEn79HL2HOmuGLIgfUhjc6uE0WakR3nFF4WFrYF9mlCslBzVDR f/EVdfAKmZM2s/8TdeFVXxMWhX37vU+7dnop0attm+QA9zy1MDtFfhe32ysv17yl yLe0FmZZK0kW9xTIIQmFkx4ClDt1ZA4FNwdWsDOrXEi/cnuZ0ME= =vHWr -----END PGP SIGNATURE----- Sat Aug 21 16:48:35 UTC 2021 I: Checking whether the package is not for us Sat Aug 21 16:48:35 UTC 2021 I: Starting 1st build on remote node codethink9-arm64.debian.net. Sat Aug 21 16:48:35 UTC 2021 I: Preparing to do remote build '1' on codethink9-arm64.debian.net. Sat Aug 21 16:56:33 UTC 2021 I: Deleting $TMPDIR on codethink9-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Sep 23 11:11:41 -12 2022 I: pbuilder-time-stamp: 1663974701 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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 [racon_1.4.20-1.dsc] I: copying [./racon_1.4.20.orig.tar.gz] I: copying [./racon_1.4.20-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.FyUM74M1/trustedkeys.kbx': General error gpgv: Signature made Mon Jan 18 22:04:56 2021 -12 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./racon_1.4.20-1.dsc dpkg-source: info: extracting racon in racon-1.4.20 dpkg-source: info: unpacking racon_1.4.20.orig.tar.gz dpkg-source: info: unpacking racon_1.4.20-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying remove_buildpath dpkg-source: info: applying py3 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/26276/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='26276' 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/tmp.KqRd9dJF08/pbuilderrc_4Vgo --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.KqRd9dJF08/b1 --logfile b1/build.log racon_1.4.20-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink9-arm64 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Aug 4 2021 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Jul 28 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Jul 28 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 93744 Mar 2 2021 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Jul 28 2021 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Jul 28 2021 more -rwsr-xr-x 1 root root 51360 Jul 28 2021 mount -rwxr-xr-x 1 root root 14496 Jul 28 2021 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Sep 23 03:48 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Jul 28 2021 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Jul 28 2021 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Jul 28 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/26276/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cmake, libgtest-dev, libbioparser-dev (>= 3.0.12), libcereal-dev, libedlib-dev, libspoa-dev, libthread-pool-dev (>= 3.0.2), rampler dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19646 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libgtest-dev; however: Package libgtest-dev is not installed. pbuilder-satisfydepends-dummy depends on libbioparser-dev (>= 3.0.12); however: Package libbioparser-dev is not installed. pbuilder-satisfydepends-dummy depends on libcereal-dev; however: Package libcereal-dev is not installed. pbuilder-satisfydepends-dummy depends on libedlib-dev; however: Package libedlib-dev is not installed. pbuilder-satisfydepends-dummy depends on libspoa-dev; however: Package libspoa-dev is not installed. pbuilder-satisfydepends-dummy depends on libthread-pool-dev (>= 3.0.2); however: Package libthread-pool-dev is not installed. pbuilder-satisfydepends-dummy depends on rampler; however: Package rampler is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} googletest{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libbioparser-dev{a} libbrotli1{a} libcereal-dev{a} libcurl4{a} libdebhelper-perl{a} libedlib-dev{a} libedlib0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgtest-dev{a} libicu67{a} libjsoncpp24{a} libldap-2.4-2{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libprocps8{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libspoa-dev{a} libspoa7.0.0{a} libssh2-1{a} libsub-override-perl{a} libthread-pool-dev{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} po-debconf{a} procps{a} rampler{a} rapidjson-dev{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 27.5 MB of archives. After unpacking 112 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-8 [142 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 libncurses6 arm64 6.2+20201114-2 [93.2 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libprocps8 arm64 2:3.3.17-5 [61.9 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 procps arm64 2:3.3.17-5 [497 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 cmake-data all 3.18.4-2 [1725 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libarchive13 arm64 3.4.3-2+b1 [320 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 libcurl4 arm64 7.74.0-1.3+b1 [321 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libjsoncpp24 arm64 1.9.4-4 [72.5 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 librhash0 arm64 1.4.1-2 [127 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libuv1 arm64 1.40.0-2 [126 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 cmake arm64 3.18.4-2 [3673 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 googletest all 1.10.0.20201025-1.1 [629 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libbioparser-dev all 3.0.12-1 [7168 B] Get: 54 http://deb.debian.org/debian bullseye/main arm64 rapidjson-dev all 1.1.0+dfsg2-7 [98.9 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 libcereal-dev all 1.3.0+dfsg-1 [210 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 libedlib0 arm64 1.2.6-1 [15.2 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 libedlib-dev arm64 1.2.6-1 [17.5 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 libgtest-dev arm64 1.10.0.20201025-1.1 [221 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 libspoa7.0.0 arm64 4.0.7+ds-1+b1 [46.4 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 libspoa-dev arm64 4.0.7+ds-1+b1 [6992 B] Get: 61 http://deb.debian.org/debian bullseye/main arm64 libthread-pool-dev all 3.0.2-1 [4376 B] Get: 62 http://deb.debian.org/debian bullseye/main arm64 rampler arm64 2.0.0-1 [20.5 kB] Fetched 27.5 MB in 4s (6791 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19646 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_arm64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_arm64.deb ... 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Selecting previously unselected package libmagic-mgc. Preparing to unpack .../09-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../10-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../11-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../12-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../13-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../14-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../15-autoconf_2.69-14_all.deb ... 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Selecting previously unselected package libarchive13:arm64. Preparing to unpack .../22-libarchive13_3.4.3-2+b1_arm64.deb ... Unpacking libarchive13:arm64 (3.4.3-2+b1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../23-libbrotli1_1.0.9-2+b2_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b2) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../24-libsasl2-modules-db_2.1.27+dfsg-2.1_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../25-libsasl2-2_2.1.27+dfsg-2.1_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libldap-2.4-2:arm64. Preparing to unpack .../26-libldap-2.4-2_2.4.57+dfsg-3_arm64.deb ... Unpacking libldap-2.4-2:arm64 (2.4.57+dfsg-3) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../27-libnghttp2-14_1.43.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.43.0-1) ... Selecting previously unselected package libpsl5:arm64. Preparing to unpack .../28-libpsl5_0.21.0-1.2_arm64.deb ... Unpacking libpsl5:arm64 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../29-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:arm64. Preparing to unpack .../30-libssh2-1_1.9.0-2_arm64.deb ... Unpacking libssh2-1:arm64 (1.9.0-2) ... Selecting previously unselected package libcurl4:arm64. Preparing to unpack .../31-libcurl4_7.74.0-1.3+b1_arm64.deb ... Unpacking libcurl4:arm64 (7.74.0-1.3+b1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../32-libexpat1_2.2.10-2_arm64.deb ... Unpacking libexpat1:arm64 (2.2.10-2) ... 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Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:arm64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b2) ... Setting up libnghttp2-14:arm64 (1.43.0-1) ... Setting up libmagic1:arm64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up googletest (1.10.0.20201025-1.1) ... Setting up rapidjson-dev (1.1.0+dfsg2-7) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libuv1:arm64 (1.40.0-2) ... Setting up rampler (2.0.0-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:arm64 (6.2+20201114-2) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up libthread-pool-dev (3.0.2-1) ... Setting up libspoa7.0.0:arm64 (4.0.7+ds-1+b1) ... Setting up autopoint (0.21-4) ... Setting up libedlib0 (1.2.6-1) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2.1) ... Setting up libjsoncpp24:arm64 (1.9.4-4) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libbioparser-dev (3.0.12-1) ... Setting up librhash0:arm64 (1.4.1-2) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:arm64 (1.9.0-2) ... Setting up cmake-data (3.18.4-2) ... Setting up libelf1:arm64 (0.183-1) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... Setting up libprocps8:arm64 (2:3.3.17-5) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libgtest-dev:arm64 (1.10.0.20201025-1.1) ... Setting up libtool (2.4.6-15) ... Setting up libarchive13:arm64 (3.4.3-2+b1) ... Setting up libcereal-dev (1.3.0+dfsg-1) ... Setting up libldap-2.4-2:arm64 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libedlib-dev (1.2.6-1) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up procps (2:3.3.17-5) ... Setting up libcurl4:arm64 (7.74.0-1.3+b1) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libspoa-dev:arm64 (4.0.7+ds-1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up cmake (3.18.4-2) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/racon-1.4.20/ && 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 > ../racon_1.4.20-1_source.changes dpkg-buildpackage: info: source package racon dpkg-buildpackage: info: source version 1.4.20-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=cmake dh_auto_clean -O--buildsystem=cmake dh_autoreconf_clean -O--buildsystem=cmake dh_clean -O--buildsystem=cmake debian/rules binary dh binary --buildsystem=cmake dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/racon-1.4.20' dh_auto_configure -- -Dracon_build_tests=ON -Dracon_build_wrapper=ON cd obj-aarch64-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_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -Dracon_build_tests=ON -Dracon_build_wrapper=ON .. -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found GTest: /usr/lib/aarch64-linux-gnu/libgtest.a -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/racon-1.4.20/obj-aarch64-linux-gnu # Somehow the means in the patch for CMakeLists.txt to replace -lpthread by -pthread to not work # Just hack it here sed -i 's/-lpthread/-pthread/' obj-*/CMakeFiles/racon_test.dir/link.txt make[1]: Leaving directory '/build/racon-1.4.20' dh_auto_build -O--buildsystem=cmake cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/racon-1.4.20/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/racon-1.4.20 -B/build/racon-1.4.20/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/racon-1.4.20/obj-aarch64-linux-gnu/CMakeFiles /build/racon-1.4.20/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/racon-1.4.20/obj-aarch64-linux-gnu' make -f CMakeFiles/racon_test.dir/build.make CMakeFiles/racon_test.dir/depend make[3]: Entering directory '/build/racon-1.4.20/obj-aarch64-linux-gnu' cd /build/racon-1.4.20/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/racon-1.4.20 /build/racon-1.4.20 /build/racon-1.4.20/obj-aarch64-linux-gnu /build/racon-1.4.20/obj-aarch64-linux-gnu /build/racon-1.4.20/obj-aarch64-linux-gnu/CMakeFiles/racon_test.dir/DependInfo.cmake --color= make -f CMakeFiles/racon.dir/build.make CMakeFiles/racon.dir/depend make[3]: Entering directory '/build/racon-1.4.20/obj-aarch64-linux-gnu' cd /build/racon-1.4.20/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/racon-1.4.20 /build/racon-1.4.20 /build/racon-1.4.20/obj-aarch64-linux-gnu /build/racon-1.4.20/obj-aarch64-linux-gnu /build/racon-1.4.20/obj-aarch64-linux-gnu/CMakeFiles/racon.dir/DependInfo.cmake --color= Dependee "/build/racon-1.4.20/obj-aarch64-linux-gnu/CMakeFiles/racon_test.dir/DependInfo.cmake" is newer than depender "/build/racon-1.4.20/obj-aarch64-linux-gnu/CMakeFiles/racon_test.dir/depend.internal". 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CMakeFiles/racon.dir/src/overlap.cpp.o CMakeFiles/racon.dir/src/sequence.cpp.o CMakeFiles/racon.dir/src/window.cpp.o -o bin/racon -lspoa -ledlib -lz [100%] Linking CXX executable bin/racon_test /usr/bin/cmake -E cmake_link_script CMakeFiles/racon_test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/racon-1.4.20=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/racon_test.dir/test/racon_test.cpp.o CMakeFiles/racon_test.dir/src/logger.cpp.o CMakeFiles/racon_test.dir/src/polisher.cpp.o CMakeFiles/racon_test.dir/src/overlap.cpp.o CMakeFiles/racon_test.dir/src/sequence.cpp.o CMakeFiles/racon_test.dir/src/window.cpp.o -o bin/racon_test -lspoa -ledlib /usr/lib/aarch64-linux-gnu/libgtest_main.a -lz /usr/lib/aarch64-linux-gnu/libgtest.a -pthread make[3]: Leaving directory '/build/racon-1.4.20/obj-aarch64-linux-gnu' [100%] Built target racon make[3]: Leaving directory '/build/racon-1.4.20/obj-aarch64-linux-gnu' [100%] Built target racon_test make[2]: Leaving directory '/build/racon-1.4.20/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/racon-1.4.20/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/racon-1.4.20/obj-aarch64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/racon-1.4.20' cd test && ../obj-*/bin/racon_test Running main() from /build/googletest-GKBoPn/googletest-1.10.0.20201025/googletest/src/gtest_main.cc [==========] Running 15 tests from 2 test suites. [----------] Global test environment set-up. [----------] 5 tests from RaconInitializeTest [ RUN ] RaconInitializeTest.PolisherTypeError [ OK ] RaconInitializeTest.PolisherTypeError (5 ms) [ RUN ] RaconInitializeTest.WindowLengthError [ OK ] RaconInitializeTest.WindowLengthError (7 ms) [ RUN ] RaconInitializeTest.SequencesPathExtensionError [ OK ] RaconInitializeTest.SequencesPathExtensionError (8 ms) [ RUN ] RaconInitializeTest.OverlapsPathExtensionError [ OK ] RaconInitializeTest.OverlapsPathExtensionError (6 ms) [ RUN ] RaconInitializeTest.TargetPathExtensionError [ OK ] RaconInitializeTest.TargetPathExtensionError (6 ms) [----------] 5 tests from RaconInitializeTest (32 ms total) [----------] 10 tests from RaconPolishingTest [ RUN ] RaconPolishingTest.ConsensusWithQualities [racon::Polisher::initialize] loaded target sequences 0.001082 s [racon::Polisher::initialize] loaded sequences 0.193621 s [racon::Polisher::initialize] loaded overlaps 0.008955 s [racon::Polisher::initialize] aligning overlaps [=> ] 0.150353 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.187345 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.227327 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.287359 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.323332 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.347321 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.423315 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.451326 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.487324 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.555332 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.579335 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.623329 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.655322 s [racon::Polisher::initialize] aligning overlaps [==============> ] 0.695335 s [racon::Polisher::initialize] aligning overlaps [===============> ] 0.723336 s [racon::Polisher::initialize] aligning overlaps [================> ] 0.763324 s [racon::Polisher::initialize] aligning overlaps [=================> ] 0.787322 s [racon::Polisher::initialize] aligning overlaps [==================> ] 0.827337 s [racon::Polisher::initialize] aligning overlaps [===================>] 0.867328 s [racon::Polisher::initialize] aligning overlaps [====================] 0.915338 s [racon::Polisher::initialize] transformed data into windows 0.004851 s [racon::Polisher::polish] generating consensus [=> ] 0.170866 s [racon::Polisher::polish] generating consensus [==> ] 0.318903 s [racon::Polisher::polish] generating consensus [===> ] 0.462889 s [racon::Polisher::polish] generating consensus [====> ] 0.550910 s [racon::Polisher::polish] generating consensus [=====> ] 0.635002 s [racon::Polisher::polish] generating consensus [======> ] 0.714891 s [racon::Polisher::polish] generating consensus [=======> ] 0.758882 s [racon::Polisher::polish] generating consensus [========> ] 0.866921 s [racon::Polisher::polish] generating consensus [=========> ] 0.946877 s [racon::Polisher::polish] generating consensus [==========> ] 1.078875 s [racon::Polisher::polish] generating consensus [===========> ] 1.306878 s [racon::Polisher::polish] generating consensus [============> ] 1.466887 s [racon::Polisher::polish] generating consensus [=============> ] 1.802874 s [racon::Polisher::polish] generating consensus [==============> ] 2.058882 s [racon::Polisher::polish] generating consensus [===============> ] 2.258889 s [racon::Polisher::polish] generating consensus [================> ] 2.398873 s [racon::Polisher::polish] generating consensus [=================> ] 2.630873 s [racon::Polisher::polish] generating consensus [==================> ] 2.786882 s [racon::Polisher::polish] generating consensus [===================>] 2.958874 s [racon::Polisher::polish] generating consensus [====================] 3.546343 s [racon::Polisher::] total = 4.714170 s [ OK ] RaconPolishingTest.ConsensusWithQualities (4723 ms) [ RUN ] RaconPolishingTest.ConsensusWithoutQualities [racon::Polisher::initialize] loaded target sequences 0.001007 s [racon::Polisher::initialize] loaded sequences 0.051205 s [racon::Polisher::initialize] loaded overlaps 0.000592 s [racon::Polisher::initialize] aligning overlaps [=> ] 0.083087 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.131068 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.167081 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.211084 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.247080 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.271072 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.323084 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.371073 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.391073 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.439075 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.467076 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.503099 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.559087 s [racon::Polisher::initialize] aligning overlaps [==============> ] 0.575055 s [racon::Polisher::initialize] aligning overlaps [===============> ] 0.627072 s [racon::Polisher::initialize] aligning overlaps [================> ] 0.687087 s [racon::Polisher::initialize] aligning overlaps [=================> ] 0.707091 s [racon::Polisher::initialize] aligning overlaps [==================> ] 0.747070 s [racon::Polisher::initialize] aligning overlaps [===================>] 0.795079 s [racon::Polisher::initialize] aligning overlaps [====================] 0.855095 s [racon::Polisher::initialize] transformed data into windows 0.001041 s [racon::Polisher::polish] generating consensus [=> ] 0.206706 s [racon::Polisher::polish] generating consensus [==> ] 0.406655 s [racon::Polisher::polish] generating consensus [===> ] 0.558670 s [racon::Polisher::polish] generating consensus [====> ] 0.642699 s [racon::Polisher::polish] generating consensus [=====> ] 0.706656 s [racon::Polisher::polish] generating consensus [======> ] 0.778660 s [racon::Polisher::polish] generating consensus [=======> ] 0.866678 s [racon::Polisher::polish] generating consensus [========> ] 1.006657 s [racon::Polisher::polish] generating consensus [=========> ] 1.078657 s [racon::Polisher::polish] generating consensus [==========> ] 1.242659 s [racon::Polisher::polish] generating consensus [===========> ] 1.482673 s [racon::Polisher::polish] generating consensus [============> ] 1.718659 s [racon::Polisher::polish] generating consensus [=============> ] 2.110663 s [racon::Polisher::polish] generating consensus [==============> ] 2.274673 s [racon::Polisher::polish] generating consensus [===============> ] 2.602662 s [racon::Polisher::polish] generating consensus [================> ] 2.838647 s [racon::Polisher::polish] generating consensus [=================> ] 3.070668 s [racon::Polisher::polish] generating consensus [==================> ] 3.154648 s [racon::Polisher::polish] generating consensus [===================>] 3.378669 s [racon::Polisher::polish] generating consensus [====================] 4.350808 s [racon::Polisher::] total = 5.300224 s [ OK ] RaconPolishingTest.ConsensusWithoutQualities (5314 ms) [ RUN ] RaconPolishingTest.ConsensusWithQualitiesAndAlignments [racon::Polisher::initialize] loaded target sequences 0.001004 s [racon::Polisher::initialize] loaded sequences 0.127355 s [racon::Polisher::initialize] loaded overlaps 0.060035 s [racon::Polisher::initialize] aligning overlaps [=> ] 0.022580 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.023384 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.024204 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.024973 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.025231 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.025565 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.026058 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.026391 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.026812 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.027182 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.027641 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.028129 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.028706 s [racon::Polisher::initialize] aligning overlaps [==============> ] 0.031868 s [racon::Polisher::initialize] aligning overlaps [===============> ] 0.031908 s [racon::Polisher::initialize] aligning overlaps [================> ] 0.031927 s [racon::Polisher::initialize] aligning overlaps [=================> ] 0.031945 s [racon::Polisher::initialize] aligning overlaps [==================> ] 0.031963 s [racon::Polisher::initialize] aligning overlaps [===================>] 0.031979 s [racon::Polisher::initialize] aligning overlaps [====================] 0.031996 s [racon::Polisher::initialize] transformed data into windows 0.004465 s [racon::Polisher::polish] generating consensus [=> ] 0.271753 s [racon::Polisher::polish] generating consensus [==> ] 0.361770 s [racon::Polisher::polish] generating consensus [===> ] 0.543712 s [racon::Polisher::polish] generating consensus [====> ] 0.615762 s [racon::Polisher::polish] generating consensus [=====> ] 0.679710 s [racon::Polisher::polish] generating consensus [======> ] 0.751702 s [racon::Polisher::polish] generating consensus [=======> ] 0.815699 s [racon::Polisher::polish] generating consensus [========> ] 0.919766 s [racon::Polisher::polish] generating consensus [=========> ] 0.951715 s [racon::Polisher::polish] generating consensus [==========> ] 1.051739 s [racon::Polisher::polish] generating consensus [===========> ] 1.203730 s [racon::Polisher::polish] generating consensus [============> ] 1.355718 s [racon::Polisher::polish] generating consensus [=============> ] 1.599722 s [racon::Polisher::polish] generating consensus [==============> ] 1.827724 s [racon::Polisher::polish] generating consensus [===============> ] 1.983716 s [racon::Polisher::polish] generating consensus [================> ] 2.115702 s [racon::Polisher::polish] generating consensus [=================> ] 2.291729 s [racon::Polisher::polish] generating consensus [==================> ] 2.395713 s [racon::Polisher::polish] generating consensus [===================>] 2.503712 s [racon::Polisher::polish] generating consensus [====================] 3.047853 s [racon::Polisher::] total = 3.303248 s [ OK ] RaconPolishingTest.ConsensusWithQualitiesAndAlignments (3313 ms) [ RUN ] RaconPolishingTest.ConsensusWithoutQualitiesAndWithAlignments [racon::Polisher::initialize] loaded target sequences 0.000969 s [racon::Polisher::initialize] loaded sequences 0.051086 s [racon::Polisher::initialize] loaded overlaps 0.063151 s [racon::Polisher::initialize] aligning overlaps [=> ] 0.011810 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.012117 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.012311 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.012625 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.012810 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.013054 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.013352 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.013620 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.013848 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.014085 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.014423 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.014759 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.015079 s [racon::Polisher::initialize] aligning overlaps [==============> ] 0.017205 s [racon::Polisher::initialize] aligning overlaps [===============> ] 0.017240 s [racon::Polisher::initialize] aligning overlaps [================> ] 0.017257 s [racon::Polisher::initialize] aligning overlaps [=================> ] 0.017275 s [racon::Polisher::initialize] aligning overlaps [==================> ] 0.017290 s [racon::Polisher::initialize] aligning overlaps [===================>] 0.017306 s [racon::Polisher::initialize] aligning overlaps [====================] 0.017322 s [racon::Polisher::initialize] transformed data into windows 0.000959 s [racon::Polisher::polish] generating consensus [=> ] 0.212904 s [racon::Polisher::polish] generating consensus [==> ] 0.351976 s [racon::Polisher::polish] generating consensus [===> ] 0.464839 s [racon::Polisher::polish] generating consensus [====> ] 0.592903 s [racon::Polisher::polish] generating consensus [=====> ] 0.616853 s [racon::Polisher::polish] generating consensus [======> ] 0.676845 s [racon::Polisher::polish] generating consensus [=======> ] 0.736835 s [racon::Polisher::polish] generating consensus [========> ] 0.848916 s [racon::Polisher::polish] generating consensus [=========> ] 0.940852 s [racon::Polisher::polish] generating consensus [==========> ] 1.100847 s [racon::Polisher::polish] generating consensus [===========> ] 1.264845 s [racon::Polisher::polish] generating consensus [============> ] 1.488859 s [racon::Polisher::polish] generating consensus [=============> ] 1.820847 s [racon::Polisher::polish] generating consensus [==============> ] 2.040848 s [racon::Polisher::polish] generating consensus [===============> ] 2.308842 s [racon::Polisher::polish] generating consensus [================> ] 2.424847 s [racon::Polisher::polish] generating consensus [=================> ] 2.632858 s [racon::Polisher::polish] generating consensus [==================> ] 2.732850 s [racon::Polisher::polish] generating consensus [===================>] 2.860846 s [racon::Polisher::polish] generating consensus [====================] 3.704966 s [racon::Polisher::] total = 3.864685 s [ OK ] RaconPolishingTest.ConsensusWithoutQualitiesAndWithAlignments (3868 ms) [ RUN ] RaconPolishingTest.ConsensusWithQualitiesLargerWindow [racon::Polisher::initialize] loaded target sequences 0.000997 s [racon::Polisher::initialize] loaded sequences 0.122516 s [racon::Polisher::initialize] loaded overlaps 0.000591 s [racon::Polisher::initialize] aligning overlaps [=> ] 0.060238 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.098269 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.130272 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.172702 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.205435 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.230266 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.294267 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.338273 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.372044 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.414280 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.462268 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.494275 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.558264 s [racon::Polisher::initialize] aligning overlaps [==============> ] 0.593394 s [racon::Polisher::initialize] aligning overlaps [===============> ] 0.618275 s [racon::Polisher::initialize] aligning overlaps [================> ] 0.666262 s [racon::Polisher::initialize] aligning overlaps [=================> ] 0.690262 s [racon::Polisher::initialize] aligning overlaps [==================> ] 0.728075 s [racon::Polisher::initialize] aligning overlaps [===================>] 0.762254 s [racon::Polisher::initialize] aligning overlaps [====================] 0.814275 s [racon::Polisher::initialize] transformed data into windows 0.004438 s [racon::Polisher::polish] generating consensus [=> ] 0.455343 s [racon::Polisher::polish] generating consensus [==> ] 0.455408 s [racon::Polisher::polish] generating consensus [===> ] 0.763310 s [racon::Polisher::polish] generating consensus [====> ] 0.763394 s [racon::Polisher::polish] generating consensus [=====> ] 0.891313 s [racon::Polisher::polish] generating consensus [======> ] 0.935303 s [racon::Polisher::polish] generating consensus [=======> ] 1.059298 s [racon::Polisher::polish] generating consensus [========> ] 1.159342 s [racon::Polisher::polish] generating consensus [=========> ] 1.315326 s [racon::Polisher::polish] generating consensus [==========> ] 1.547318 s [racon::Polisher::polish] generating consensus [===========> ] 1.783311 s [racon::Polisher::polish] generating consensus [============> ] 2.199311 s [racon::Polisher::polish] generating consensus [=============> ] 2.611315 s [racon::Polisher::polish] generating consensus [==============> ] 2.907308 s [racon::Polisher::polish] generating consensus [===============> ] 3.175312 s [racon::Polisher::polish] generating consensus [================> ] 3.355378 s [racon::Polisher::polish] generating consensus [=================> ] 3.735321 s [racon::Polisher::polish] generating consensus [==================> ] 3.735378 s [racon::Polisher::polish] generating consensus [===================>] 4.143308 s [racon::Polisher::polish] generating consensus [====================] 4.983411 s [racon::Polisher::] total = 5.958938 s [ OK ] RaconPolishingTest.ConsensusWithQualitiesLargerWindow (5969 ms) [ RUN ] RaconPolishingTest.ConsensusWithQualitiesEditDistance [racon::Polisher::initialize] loaded target sequences 0.005345 s [racon::Polisher::initialize] loaded sequences 0.106273 s [racon::Polisher::initialize] loaded overlaps 0.000597 s [racon::Polisher::initialize] aligning overlaps [=> ] 0.068445 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.108428 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.136427 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.180428 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.212419 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.232439 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.276427 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.332428 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.368436 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.404426 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.448429 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.480437 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.532433 s [racon::Polisher::initialize] aligning overlaps [==============> ] 0.560423 s [racon::Polisher::initialize] aligning overlaps [===============> ] 0.612421 s [racon::Polisher::initialize] aligning overlaps [================> ] 0.644437 s [racon::Polisher::initialize] aligning overlaps [=================> ] 0.676466 s [racon::Polisher::initialize] aligning overlaps [==================> ] 0.724437 s [racon::Polisher::initialize] aligning overlaps [===================>] 0.764438 s [racon::Polisher::initialize] aligning overlaps [====================] 0.796434 s [racon::Polisher::initialize] transformed data into windows 0.004688 s [racon::Polisher::polish] generating consensus [=> ] 0.223106 s [racon::Polisher::polish] generating consensus [==> ] 0.315064 s [racon::Polisher::polish] generating consensus [===> ] 0.411073 s [racon::Polisher::polish] generating consensus [====> ] 0.483092 s [racon::Polisher::polish] generating consensus [=====> ] 0.515076 s [racon::Polisher::polish] generating consensus [======> ] 0.543075 s [racon::Polisher::polish] generating consensus [=======> ] 0.599068 s [racon::Polisher::polish] generating consensus [========> ] 0.655121 s [racon::Polisher::polish] generating consensus [=========> ] 0.735052 s [racon::Polisher::polish] generating consensus [==========> ] 0.827058 s [racon::Polisher::polish] generating consensus [===========> ] 1.043056 s [racon::Polisher::polish] generating consensus [============> ] 1.199061 s [racon::Polisher::polish] generating consensus [=============> ] 1.491075 s [racon::Polisher::polish] generating consensus [==============> ] 1.639063 s [racon::Polisher::polish] generating consensus [===============> ] 1.779072 s [racon::Polisher::polish] generating consensus [================> ] 1.923068 s [racon::Polisher::polish] generating consensus [=================> ] 2.059077 s [racon::Polisher::polish] generating consensus [==================> ] 2.155052 s [racon::Polisher::polish] generating consensus [===================>] 2.283063 s [racon::Polisher::polish] generating consensus [====================] 2.831594 s [racon::Polisher::] total = 3.773190 s [ OK ] RaconPolishingTest.ConsensusWithQualitiesEditDistance (3779 ms) [ RUN ] RaconPolishingTest.FragmentCorrectionWithQualities [racon::Polisher::initialize] loaded target sequences 0.098171 s [racon::Polisher::initialize] loaded sequences 0.098284 s [racon::Polisher::initialize] loaded overlaps 0.022306 s [racon::Polisher::initialize] aligning overlaps [=> ] 0.071738 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.111734 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.155719 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.195719 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.231726 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.255741 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.299728 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.311730 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.355737 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.395715 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.427727 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.467729 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.511732 s [racon::Polisher::initialize] aligning overlaps [==============> ] 0.555720 s [racon::Polisher::initialize] aligning overlaps [===============> ] 0.599709 s [racon::Polisher::initialize] aligning overlaps [================> ] 0.643721 s [racon::Polisher::initialize] aligning overlaps [=================> ] 0.671726 s [racon::Polisher::initialize] aligning overlaps [==================> ] 0.731733 s [racon::Polisher::initialize] aligning overlaps [===================>] 0.767724 s [racon::Polisher::initialize] aligning overlaps [====================] 0.875726 s [racon::Polisher::initialize] transformed data into windows 0.009665 s [racon::Polisher::polish] generating consensus [=> ] 0.110161 s [racon::Polisher::polish] generating consensus [==> ] 0.226309 s [racon::Polisher::polish] generating consensus [===> ] 0.334270 s [racon::Polisher::polish] generating consensus [====> ] 0.334652 s [racon::Polisher::polish] generating consensus [=====> ] 0.414264 s [racon::Polisher::polish] generating consensus [======> ] 0.462336 s [racon::Polisher::polish] generating consensus [=======> ] 0.542475 s [racon::Polisher::polish] generating consensus [========> ] 0.546123 s [racon::Polisher::polish] generating consensus [=========> ] 0.690076 s [racon::Polisher::polish] generating consensus [==========> ] 0.750063 s [racon::Polisher::polish] generating consensus [===========> ] 0.798294 s [racon::Polisher::polish] generating consensus [============> ] 0.834237 s [racon::Polisher::polish] generating consensus [=============> ] 0.894325 s [racon::Polisher::polish] generating consensus [==============> ] 0.894744 s [racon::Polisher::polish] generating consensus [===============> ] 1.042323 s [racon::Polisher::polish] generating consensus [================> ] 1.054141 s [racon::Polisher::polish] generating consensus [=================> ] 1.326269 s [racon::Polisher::polish] generating consensus [==================> ] 1.442280 s [racon::Polisher::polish] generating consensus [===================>] 1.566366 s [racon::Polisher::polish] generating consensus [====================] 1.622322 s [racon::Polisher::] total = 2.727980 s [ OK ] RaconPolishingTest.FragmentCorrectionWithQualities (2735 ms) [ RUN ] RaconPolishingTest.FragmentCorrectionWithQualitiesFull [racon::Polisher::initialize] loaded target sequences 0.137245 s [racon::Polisher::initialize] loaded sequences 0.097031 s [racon::Polisher::initialize] loaded overlaps 0.033821 s [racon::Polisher::initialize] aligning overlaps [=> ] 0.926729 s [racon::Polisher::initialize] aligning overlaps [==> ] 1.482730 s [racon::Polisher::initialize] aligning overlaps [===> ] 1.994725 s [racon::Polisher::initialize] aligning overlaps [====> ] 2.702731 s [racon::Polisher::initialize] aligning overlaps [=====> ] 3.270738 s [racon::Polisher::initialize] aligning overlaps [======> ] 3.794734 s [racon::Polisher::initialize] aligning overlaps [=======> ] 4.538728 s [racon::Polisher::initialize] aligning overlaps [========> ] 5.318739 s [racon::Polisher::initialize] aligning overlaps [=========> ] 6.110724 s [racon::Polisher::initialize] aligning overlaps [==========> ] 6.878727 s [racon::Polisher::initialize] aligning overlaps [===========> ] 7.494727 s [racon::Polisher::initialize] aligning overlaps [============> ] 8.314725 s [racon::Polisher::initialize] aligning overlaps [=============> ] 9.230727 s [racon::Polisher::initialize] aligning overlaps [==============> ] 10.070726 s [racon::Polisher::initialize] aligning overlaps [===============> ] 10.998715 s [racon::Polisher::initialize] aligning overlaps [================> ] 11.846720 s [racon::Polisher::initialize] aligning overlaps [=================> ] 12.718742 s [racon::Polisher::initialize] aligning overlaps [==================> ] 13.622737 s [racon::Polisher::initialize] aligning overlaps [===================>] 14.510737 s [racon::Polisher::initialize] aligning overlaps [====================] 15.458741 s [racon::Polisher::initialize] transformed data into windows 0.207640 s [racon::Polisher::polish] generating consensus [=> ] 4.644677 s [racon::Polisher::polish] generating consensus [==> ] 8.128674 s [racon::Polisher::polish] generating consensus [===> ] 11.992698 s [racon::Polisher::polish] generating consensus [====> ] 15.012788 s [racon::Polisher::polish] generating consensus [=====> ] 18.556761 s [racon::Polisher::polish] generating consensus [======> ] 22.520670 s [racon::Polisher::polish] generating consensus [=======> ] 26.380673 s [racon::Polisher::polish] generating consensus [========> ] 29.304674 s [racon::Polisher::polish] generating consensus [=========> ] 33.012696 s [racon::Polisher::polish] generating consensus [==========> ] 37.632716 s [racon::Polisher::polish] generating consensus [===========> ] 41.460808 s [racon::Polisher::polish] generating consensus [============> ] 45.756661 s [racon::Polisher::polish] generating consensus [=============> ] 49.320687 s [racon::Polisher::polish] generating consensus [==============> ] 53.420665 s [racon::Polisher::polish] generating consensus [===============> ] 57.336671 s [racon::Polisher::polish] generating consensus [================> ] 59.616776 s [racon::Polisher::polish] generating consensus [=================> ] 64.036673 s [racon::Polisher::polish] generating consensus [==================> ] 68.136751 s [racon::Polisher::polish] generating consensus [===================>] 72.128656 s [racon::Polisher::polish] generating consensus [====================] 76.008803 s [racon::Polisher::] total = 91.954614 s [ OK ] RaconPolishingTest.FragmentCorrectionWithQualitiesFull (91957 ms) [ RUN ] RaconPolishingTest.FragmentCorrectionWithoutQualitiesFull [racon::Polisher::initialize] loaded target sequences 0.047544 s [racon::Polisher::initialize] loaded sequences 0.051906 s [racon::Polisher::initialize] loaded overlaps 0.034673 s [racon::Polisher::initialize] aligning overlaps [=> ] 1.003622 s [racon::Polisher::initialize] aligning overlaps [==> ] 1.715617 s [racon::Polisher::initialize] aligning overlaps [===> ] 2.331607 s [racon::Polisher::initialize] aligning overlaps [====> ] 3.091605 s [racon::Polisher::initialize] aligning overlaps [=====> ] 3.691612 s [racon::Polisher::initialize] aligning overlaps [======> ] 4.179602 s [racon::Polisher::initialize] aligning overlaps [=======> ] 4.787592 s [racon::Polisher::initialize] aligning overlaps [========> ] 5.571593 s [racon::Polisher::initialize] aligning overlaps [=========> ] 6.383605 s [racon::Polisher::initialize] aligning overlaps [==========> ] 7.167607 s [racon::Polisher::initialize] aligning overlaps [===========> ] 7.771629 s [racon::Polisher::initialize] aligning overlaps [============> ] 8.761959 s [racon::Polisher::initialize] aligning overlaps [=============> ] 9.719618 s [racon::Polisher::initialize] aligning overlaps [==============> ] 10.523606 s [racon::Polisher::initialize] aligning overlaps [===============> ] 11.415601 s [racon::Polisher::initialize] aligning overlaps [================> ] 12.227597 s [racon::Polisher::initialize] aligning overlaps [=================> ] 13.075606 s [racon::Polisher::initialize] aligning overlaps [==================> ] 14.035617 s [racon::Polisher::initialize] aligning overlaps [===================>] 15.055620 s [racon::Polisher::initialize] aligning overlaps [====================] 15.923618 s [racon::Polisher::initialize] transformed data into windows 0.069935 s [racon::Polisher::polish] generating consensus [=> ] 6.670038 s [racon::Polisher::polish] generating consensus [==> ] 11.290051 s [racon::Polisher::polish] generating consensus [===> ] 16.414135 s [racon::Polisher::polish] generating consensus [====> ] 20.250154 s [racon::Polisher::polish] generating consensus [=====> ] 25.278073 s [racon::Polisher::polish] generating consensus [======> ] 30.602052 s [racon::Polisher::polish] generating consensus [=======> ] 35.946052 s [racon::Polisher::polish] generating consensus [========> ] 40.306048 s [racon::Polisher::polish] generating consensus [=========> ] 45.526057 s [racon::Polisher::polish] generating consensus [==========> ] 51.774106 s [racon::Polisher::polish] generating consensus [===========> ] 56.986168 s [racon::Polisher::polish] generating consensus [============> ] 62.702047 s [racon::Polisher::polish] generating consensus [=============> ] 67.846069 s [racon::Polisher::polish] generating consensus [==============> ] 73.382030 s [racon::Polisher::polish] generating consensus [===============> ] 78.670039 s [racon::Polisher::polish] generating consensus [================> ] 81.550162 s [racon::Polisher::polish] generating consensus [=================> ] 88.018056 s [racon::Polisher::polish] generating consensus [==================> ] 94.058156 s [racon::Polisher::polish] generating consensus [===================>] 99.694052 s [racon::Polisher::polish] generating consensus [====================] 105.112379 s [racon::Polisher::] total = 121.250471 s [ OK ] RaconPolishingTest.FragmentCorrectionWithoutQualitiesFull (121255 ms) [ RUN ] RaconPolishingTest.FragmentCorrectionWithQualitiesFullMhap [racon::Polisher::initialize] loaded target sequences 0.108434 s [racon::Polisher::initialize] loaded sequences 0.065841 s [racon::Polisher::initialize] loaded overlaps 0.019307 s [racon::Polisher::initialize] aligning overlaps [=> ] 1.052975 s [racon::Polisher::initialize] aligning overlaps [==> ] 1.740974 s [racon::Polisher::initialize] aligning overlaps [===> ] 2.356993 s [racon::Polisher::initialize] aligning overlaps [====> ] 3.136649 s [racon::Polisher::initialize] aligning overlaps [=====> ] 3.776984 s [racon::Polisher::initialize] aligning overlaps [======> ] 4.412981 s [racon::Polisher::initialize] aligning overlaps [=======> ] 5.232981 s [racon::Polisher::initialize] aligning overlaps [========> ] 6.220985 s [racon::Polisher::initialize] aligning overlaps [=========> ] 7.168980 s [racon::Polisher::initialize] aligning overlaps [==========> ] 7.920971 s [racon::Polisher::initialize] aligning overlaps [===========> ] 8.580990 s [racon::Polisher::initialize] aligning overlaps [============> ] 9.478257 s [racon::Polisher::initialize] aligning overlaps [=============> ] 10.368984 s [racon::Polisher::initialize] aligning overlaps [==============> ] 11.161195 s [racon::Polisher::initialize] aligning overlaps [===============> ] 12.132982 s [racon::Polisher::initialize] aligning overlaps [================> ] 13.176992 s [racon::Polisher::initialize] aligning overlaps [=================> ] 14.161007 s [racon::Polisher::initialize] aligning overlaps [==================> ] 15.156995 s [racon::Polisher::initialize] aligning overlaps [===================>] 16.172993 s [racon::Polisher::initialize] aligning overlaps [====================] 17.201022 s [racon::Polisher::initialize] transformed data into windows 0.197982 s [racon::Polisher::polish] generating consensus [=> ] 5.502089 s [racon::Polisher::polish] generating consensus [==> ] 8.862088 s [racon::Polisher::polish] generating consensus [===> ] 13.322162 s [racon::Polisher::polish] generating consensus [====> ] 16.678144 s [racon::Polisher::polish] generating consensus [=====> ] 21.266152 s [racon::Polisher::polish] generating consensus [======> ] 26.126053 s [racon::Polisher::polish] generating consensus [=======> ] 30.946082 s [racon::Polisher::polish] generating consensus [========> ] 34.542174 s [racon::Polisher::polish] generating consensus [=========> ] 39.202078 s [racon::Polisher::polish] generating consensus [==========> ] 45.210139 s [racon::Polisher::polish] generating consensus [===========> ] 50.194202 s [racon::Polisher::polish] generating consensus [============> ] 55.994124 s [racon::Polisher::polish] generating consensus [=============> ] 60.718086 s [racon::Polisher::polish] generating consensus [==============> ] 66.130081 s [racon::Polisher::polish] generating consensus [===============> ] 71.702099 s [racon::Polisher::polish] generating consensus [================> ] 74.858188 s [racon::Polisher::polish] generating consensus [=================> ] 80.990073 s [racon::Polisher::polish] generating consensus [==================> ] 86.450202 s [racon::Polisher::polish] generating consensus [===================>] 90.918072 s [racon::Polisher::polish] generating consensus [====================] 95.502199 s [racon::Polisher::] total = 113.106170 s [ OK ] RaconPolishingTest.FragmentCorrectionWithQualitiesFullMhap (113112 ms) [----------] 10 tests from RaconPolishingTest (356027 ms total) [----------] Global test environment tear-down [==========] 15 tests from 2 test suites ran. (356059 ms total) [ PASSED ] 15 tests. make[1]: Leaving directory '/build/racon-1.4.20' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake cd obj-aarch64-linux-gnu && make -j8 install DESTDIR=/build/racon-1.4.20/debian/racon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/racon-1.4.20/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/racon-1.4.20 -B/build/racon-1.4.20/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/racon-1.4.20/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/racon-1.4.20/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/racon-1.4.20/debian/racon/usr/bin/racon make[1]: Leaving directory '/build/racon-1.4.20/obj-aarch64-linux-gnu' dh_install -O--buildsystem=cmake dh_installdocs -O--buildsystem=cmake dh_installchangelogs -O--buildsystem=cmake dh_installexamples -O--buildsystem=cmake dh_installman -O--buildsystem=cmake dh_installsystemduser -O--buildsystem=cmake dh_lintian -O--buildsystem=cmake dh_perl -O--buildsystem=cmake dh_link -O--buildsystem=cmake dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake dh_fixperms -O--buildsystem=cmake dh_missing -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'racon' in '../racon_1.4.20-1_arm64.deb'. dpkg-deb: building package 'racon-dbgsym' in '../racon-dbgsym_1.4.20-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../racon_1.4.20-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full 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/26276 and its subdirectories I: Current time: Fri Sep 23 11:19:31 -12 2022 I: pbuilder-time-stamp: 1663975171 Sat Aug 21 16:56:33 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink10-arm64.debian.net. Sat Aug 21 16:56:34 UTC 2021 I: Preparing to do remote build '2' on codethink10-arm64.debian.net. Sat Aug 21 17:05:48 UTC 2021 I: Deleting $TMPDIR on codethink10-arm64.debian.net. Sat Aug 21 17:05:49 UTC 2021 I: racon_1.4.20-1_arm64.changes: Format: 1.8 Date: Tue, 19 Jan 2021 08:11:15 +0100 Source: racon Binary: racon racon-dbgsym Architecture: arm64 Version: 1.4.20-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: racon - consensus module for raw de novo DNA assembly of long uncorrected Changes: racon (1.4.20-1) unstable; urgency=medium . * Team upload. . [ Andreas Tille ] * Add lintian-override * Standards-Version: 4.5.1 (routine-update) . [ Michael R. Crusoe ] * Update patches. * Build the wrapper script. * Bump libthread-pool-dev build-dep to be at least 3 * libthread-pool-dev is now header-only, update use_debian_packaged_libs.patch to reflect that. Checksums-Sha1: 8ef4d98df64a8f4ccefde586102485973a6998d2 2085928 racon-dbgsym_1.4.20-1_arm64.deb 6655bcee56ed790f8c420d74dfd319c69f372075 5956 racon_1.4.20-1_arm64.buildinfo cab0c1b180ca34d6d72b71666d1e58df6b1e9f89 3251636 racon_1.4.20-1_arm64.deb Checksums-Sha256: 99d85b5a810f680a3645bddcb8f1670af0bd4b41f8c06b6b6c1faa3db2cd50a9 2085928 racon-dbgsym_1.4.20-1_arm64.deb a92d58167bbea4cac6d4f107ae511ea694eb2aa1663311e05cb568c6be5a409f 5956 racon_1.4.20-1_arm64.buildinfo ba5a6600be886eb5daaedd9114550e12cab4e14327607fc9853dc16f2d6e3962 3251636 racon_1.4.20-1_arm64.deb Files: 97e0732f889919b21d0256c5697f491e 2085928 debug optional racon-dbgsym_1.4.20-1_arm64.deb c9497e1dbb3935c460081c87a1d02c26 5956 science optional racon_1.4.20-1_arm64.buildinfo 36e08a7de3d933c7352e63909e533c3a 3251636 science optional racon_1.4.20-1_arm64.deb Sat Aug 21 17:05:50 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.KqRd9dJF08/racon_1.4.20-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.KqRd9dJF08/racon_1.4.20-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.KqRd9dJF08/racon_1.4.20-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.KqRd9dJF08/b1/racon_1.4.20-1_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.KqRd9dJF08/b2/racon_1.4.20-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.484s) 0.484s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.096s) 0.096s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sat Aug 21 17:05:52 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Sat Aug 21 17:05:52 UTC 2021 I: racon from bullseye built successfully and reproducibly on arm64. Sat Aug 21 17:05:55 UTC 2021 I: Submitting .buildinfo files to external archives: Sat Aug 21 17:05:55 UTC 2021 I: Submitting 8.0K b1/racon_1.4.20-1_arm64.buildinfo.asc Sat Aug 21 17:05:56 UTC 2021 I: Submitting 8.0K b2/racon_1.4.20-1_arm64.buildinfo.asc Sat Aug 21 17:05:56 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Aug 21 17:05:56 UTC 2021 I: Done submitting .buildinfo files. Sat Aug 21 17:05:56 UTC 2021 I: Removing signed racon_1.4.20-1_arm64.buildinfo.asc files: removed './b1/racon_1.4.20-1_arm64.buildinfo.asc' removed './b2/racon_1.4.20-1_arm64.buildinfo.asc'