I: pbuilder: network access will be disabled during build I: Current time: Thu Aug 11 22:45:49 +14 2022 I: pbuilder-time-stamp: 1660207549 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 [freebayes_1.3.5-1.dsc] I: copying [./freebayes_1.3.5.orig.tar.gz] I: copying [./freebayes_1.3.5-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.mjtd3ieq/trustedkeys.kbx': General error gpgv: Signature made Thu Feb 11 00:31:15 2021 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./freebayes_1.3.5-1.dsc dpkg-source: info: extracting freebayes in freebayes-1.3.5 dpkg-source: info: unpacking freebayes_1.3.5.orig.tar.gz dpkg-source: info: unpacking freebayes_1.3.5-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/14298/tmp/hooks/D01_modify_environment starting debug: Running on codethink13-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/14298/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/14298/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=14298 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.ajnojZIIpn/pbuilderrc_uD47 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ajnojZIIpn/b2 --logfile b2/build.log --extrapackages usrmerge freebayes_1.3.5-1.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 22 2021 bash -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 23 2020 cat -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash -rwxr-xr-x 1 root root 101384 Sep 23 2020 date -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd -rwxr-xr-x 1 root root 89824 Sep 23 2020 df -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir -rwxr-xr-x 1 root root 76152 Feb 8 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 8 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 93744 Mar 3 2021 gzip -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln -rwxr-xr-x 1 root root 52720 Feb 8 2020 login -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls -rwxr-xr-x 1 root root 161960 Feb 8 2021 lsblk -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 8 2021 more -rwsr-xr-x 1 root root 51360 Feb 8 2021 mount -rwxr-xr-x 1 root root 14496 Feb 8 2021 mountpoint -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 2021 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Aug 11 22:46 sh -> bash lrwxrwxrwx 1 root root 4 Aug 10 05:48 sh.distrib -> dash -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty -rwsr-xr-x 1 root root 67776 Feb 8 2021 su -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync -rwxr-xr-x 1 root root 535768 Feb 17 2021 tar -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch -rwxr-xr-x 1 root root 31512 Sep 23 2020 true -rwxr-xr-x 1 root root 14264 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 8 2021 umount -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 8 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/14298/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), meson, ninja-build, pkg-config, python3, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, parallel, libvcflib-tools (>= 1.0.0~rc1+dfsg1-6) 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 meson; however: Package meson is not installed. pbuilder-satisfydepends-dummy depends on ninja-build; however: Package ninja-build is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libvcflib-dev (>= 1.0.0~rc2+dfsg-3~); however: Package libvcflib-dev is not installed. pbuilder-satisfydepends-dummy depends on libtabixpp-dev; however: Package libtabixpp-dev is not installed. pbuilder-satisfydepends-dummy depends on libseqlib-dev (>= 1.1.2+dfsg-5); however: Package libseqlib-dev is not installed. pbuilder-satisfydepends-dummy depends on bc; however: Package bc is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on parallel; however: Package parallel is not installed. pbuilder-satisfydepends-dummy depends on libvcflib-tools (>= 1.0.0~rc1+dfsg1-6); however: Package libvcflib-tools 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} bc{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.1{a} libblas3{a} libbrotli1{a} libbsd0{a} libbwa-dev{a} libcairo2{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdatrie1{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdisorder-dev{a} libdisorder0{a} libelf1{a} libexpat1{a} libfastahack-dev{a} libfastahack0{a} libfile-stripnondeterminism-perl{a} libfml-dev{a} libfml0{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhts-dev{a} libhts3{a} libice6{a} libicu67{a} libjbig0{a} libjpeg62-turbo{a} libjsoncpp-dev{a} libjsoncpp24{a} liblapack3{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{a} libncurses6{a} libnghttp2-14{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libprocps8{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libseqlib-dev{a} libseqlib2{a} libsigsegv2{a} libsm6{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libssh2-1{a} libssw-dev{a} libssw0{a} libsub-override-perl{a} libtabixpp-dev{a} libtabixpp0{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff5{a} libtk8.6{a} libtool{a} libuchardet0{a} libvcflib-dev{a} libvcflib-tools{a} libvcflib1{a} libwebp6{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxss1{a} libxt6{a} littler{a} m4{a} man-db{a} media-types{a} meson{a} ninja-build{a} openssl{a} parallel{a} pkg-config{a} po-debconf{a} procps{a} python3{a} python3-minimal{a} python3-pkg-resources{a} python3.9{a} python3.9-minimal{a} r-base-core{a} r-cran-assertthat{a} r-cran-brio{a} r-cran-callr{a} r-cran-cli{a} r-cran-colorspace{a} r-cran-crayon{a} r-cran-desc{a} r-cran-diffobj{a} r-cran-digest{a} r-cran-ellipsis{a} r-cran-evaluate{a} r-cran-fansi{a} r-cran-farver{a} r-cran-ggplot2{a} r-cran-glue{a} r-cran-gridbase{a} r-cran-gtable{a} r-cran-isoband{a} r-cran-jsonlite{a} r-cran-labeling{a} r-cran-lattice{a} r-cran-lifecycle{a} r-cran-littler{a} r-cran-magrittr{a} r-cran-mass{a} r-cran-matrix{a} r-cran-mgcv{a} r-cran-munsell{a} r-cran-nlme{a} r-cran-pillar{a} r-cran-pkgbuild{a} r-cran-pkgconfig{a} r-cran-pkgkitten{a} r-cran-pkgload{a} r-cran-plyr{a} r-cran-praise{a} r-cran-prettyunits{a} r-cran-processx{a} r-cran-ps{a} r-cran-r6{a} r-cran-rcolorbrewer{a} r-cran-rcpp{a} r-cran-rematch2{a} r-cran-rlang{a} r-cran-rprojroot{a} r-cran-rstudioapi{a} r-cran-scales{a} r-cran-testthat{a} r-cran-tibble{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{a} r-cran-waldo{a} r-cran-withr{a} readline-common{a} samtools{a} sensible-utils{a} sysstat{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bcron cron curl libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lynx psmisc publicsuffix r-base-dev r-cran-abind r-cran-bit64 r-cran-cliapp r-cran-codetools r-cran-curl r-cran-data.table r-cran-dbi r-cran-domc r-cran-dplyr r-cran-generics r-cran-hexbin r-cran-hms r-cran-knitr r-cran-lubridate r-cran-mapproj r-cran-mockery r-cran-mockr r-cran-quantreg r-cran-rmarkdown r-cran-rsqlite r-cran-sp r-cran-vdiffr r-cran-xml2 r-doc-html r-recommended shared-mime-info systemd systemd-cron wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 203 newly installed, 0 to remove and 0 not upgraded. Need to get 109 MB of archives. After unpacking 263 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 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 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libncurses6 arm64 6.2+20201114-2 [93.2 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libprocps8 arm64 2:3.3.17-5 [61.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 procps arm64 2:3.3.17-5 [497 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 openssl arm64 1.1.1k-1 [829 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 ca-certificates all 20210119 [158 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 ucf all 3.0043 [74.0 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 bc arm64 1.07.1-2+b2 [107 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 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 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 libpng16-16 arm64 1.6.37-3 [289 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libfreetype6 arm64 2.10.4+dfsg-1 [393 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 libfontconfig1 arm64 2.13.1-4.2 [344 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 fontconfig arm64 2.13.1-4.2 [416 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 libbamtools2.5.1 arm64 2.5.1+dfsg-9 [142 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 libbamtools-dev arm64 2.5.1+dfsg-9 [197 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 libblas3 arm64 3.9.0-3 [101 kB] Get: 61 http://deb.debian.org/debian bullseye/main arm64 libmd0 arm64 1.0.3-3 [27.9 kB] Get: 62 http://deb.debian.org/debian bullseye/main arm64 libbsd0 arm64 0.11.3-1 [106 kB] Get: 63 http://deb.debian.org/debian bullseye/main arm64 libbwa-dev arm64 0.7.17-6+b1 [138 kB] Get: 64 http://deb.debian.org/debian bullseye/main arm64 libpixman-1-0 arm64 0.40.0-1 [444 kB] Get: 65 http://deb.debian.org/debian bullseye/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 66 http://deb.debian.org/debian bullseye/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 67 http://deb.debian.org/debian bullseye/main arm64 libxcb1 arm64 1.14-3 [138 kB] Get: 68 http://deb.debian.org/debian bullseye/main arm64 libx11-data all 2:1.7.1-1 [310 kB] Get: 69 http://deb.debian.org/debian bullseye/main arm64 libx11-6 arm64 2:1.7.1-1 [747 kB] Get: 70 http://deb.debian.org/debian bullseye/main arm64 libxcb-render0 arm64 1.14-3 [111 kB] Get: 71 http://deb.debian.org/debian bullseye/main arm64 libxcb-shm0 arm64 1.14-3 [101 kB] Get: 72 http://deb.debian.org/debian bullseye/main arm64 libxext6 arm64 2:1.3.3-1.1 [51.6 kB] Get: 73 http://deb.debian.org/debian bullseye/main arm64 libxrender1 arm64 1:0.9.10-1 [30.4 kB] Get: 74 http://deb.debian.org/debian bullseye/main arm64 libcairo2 arm64 1.16.0-5 [648 kB] Get: 75 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 76 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 77 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 78 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 79 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 80 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 81 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 82 http://deb.debian.org/debian bullseye/main arm64 libcurl3-gnutls arm64 7.74.0-1.3+b1 [318 kB] Get: 83 http://deb.debian.org/debian bullseye/main arm64 libcurl4 arm64 7.74.0-1.3+b1 [321 kB] Get: 84 http://deb.debian.org/debian bullseye/main arm64 libcurl4-gnutls-dev arm64 7.74.0-1.3+b1 [419 kB] Get: 85 http://deb.debian.org/debian bullseye/main arm64 libdatrie1 arm64 0.2.13-1 [42.1 kB] Get: 86 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB] Get: 87 http://deb.debian.org/debian bullseye/main arm64 libdeflate-dev arm64 1.7-1 [44.5 kB] Get: 88 http://deb.debian.org/debian bullseye/main arm64 libdisorder0 arm64 0.0.2+git20130809.8062ee1-2 [4284 B] Get: 89 http://deb.debian.org/debian bullseye/main arm64 libdisorder-dev arm64 0.0.2+git20130809.8062ee1-2 [4348 B] Get: 90 http://deb.debian.org/debian bullseye/main arm64 libfastahack0 arm64 1.0.0+dfsg-7 [23.7 kB] Get: 91 http://deb.debian.org/debian bullseye/main arm64 libfastahack-dev arm64 1.0.0+dfsg-7 [26.0 kB] Get: 92 http://deb.debian.org/debian bullseye/main arm64 libfml0 arm64 0.1+git20190320.b499514-1+b1 [65.9 kB] Get: 93 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 94 http://deb.debian.org/debian bullseye/main arm64 libfml-dev arm64 0.1+git20190320.b499514-1+b1 [79.5 kB] Get: 95 http://deb.debian.org/debian bullseye/main arm64 libfribidi0 arm64 1.0.8-2 [64.8 kB] Get: 96 http://deb.debian.org/debian bullseye/main arm64 libgfortran5 arm64 10.2.1-6 [333 kB] Get: 97 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-0 arm64 2.66.8-1 [1286 kB] Get: 98 http://deb.debian.org/debian bullseye/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB] Get: 99 http://deb.debian.org/debian bullseye/main arm64 libharfbuzz0b arm64 2.7.4-1 [1445 kB] Get: 100 http://deb.debian.org/debian bullseye/main arm64 libhts3 arm64 1.11-4 [346 kB] Get: 101 http://deb.debian.org/debian bullseye/main arm64 liblzma-dev arm64 5.2.5-2 [227 kB] Get: 102 http://deb.debian.org/debian bullseye/main arm64 libhts-dev arm64 1.11-4 [3856 kB] Get: 103 http://deb.debian.org/debian bullseye/main arm64 x11-common all 1:7.7+22 [252 kB] Get: 104 http://deb.debian.org/debian bullseye/main arm64 libice6 arm64 2:1.0.10-1 [55.6 kB] Get: 105 http://deb.debian.org/debian bullseye/main arm64 libjbig0 arm64 2.1-3.1+b2 [27.8 kB] Get: 106 http://deb.debian.org/debian bullseye/main arm64 libjpeg62-turbo arm64 1:2.0.6-4 [133 kB] Get: 107 http://deb.debian.org/debian bullseye/main arm64 libjsoncpp24 arm64 1.9.4-4 [72.5 kB] Get: 108 http://deb.debian.org/debian bullseye/main arm64 libjsoncpp-dev arm64 1.9.4-4 [25.4 kB] Get: 109 http://deb.debian.org/debian bullseye/main arm64 liblapack3 arm64 3.9.0-3 [1541 kB] Get: 110 http://deb.debian.org/debian bullseye/main arm64 libthai-data all 0.1.28-3 [170 kB] Get: 111 http://deb.debian.org/debian bullseye/main arm64 libthai0 arm64 0.1.28-3 [53.0 kB] Get: 112 http://deb.debian.org/debian bullseye/main arm64 libpango-1.0-0 arm64 1.46.2-3 [183 kB] Get: 113 http://deb.debian.org/debian bullseye/main arm64 libpangoft2-1.0-0 arm64 1.46.2-3 [59.4 kB] Get: 114 http://deb.debian.org/debian bullseye/main arm64 libpangocairo-1.0-0 arm64 1.46.2-3 [48.6 kB] Get: 115 http://deb.debian.org/debian bullseye/main arm64 libpaper1 arm64 1.1.28+b1 [21.4 kB] Get: 116 http://deb.debian.org/debian bullseye/main arm64 libpaper-utils arm64 1.1.28+b1 [18.3 kB] Get: 117 http://deb.debian.org/debian bullseye/main arm64 libsensors-config all 1:3.6.0-7 [32.3 kB] Get: 118 http://deb.debian.org/debian bullseye/main arm64 libsensors5 arm64 1:3.6.0-7 [51.2 kB] Get: 119 http://deb.debian.org/debian bullseye/main arm64 libssw0 arm64 1.1-13 [18.5 kB] Get: 120 http://deb.debian.org/debian bullseye/main arm64 libseqlib2 arm64 1.2.0+dfsg-4 [148 kB] Get: 121 http://deb.debian.org/debian bullseye/main arm64 libssw-dev arm64 1.1-13 [21.9 kB] Get: 122 http://deb.debian.org/debian bullseye/main arm64 libseqlib-dev arm64 1.2.0+dfsg-4 [204 kB] Get: 123 http://deb.debian.org/debian bullseye/main arm64 libsm6 arm64 2:1.2.3-1 [34.0 kB] Get: 124 http://deb.debian.org/debian bullseye/main arm64 libsmithwaterman0 arm64 0.0+git20160702.2610e25-11 [32.8 kB] Get: 125 http://deb.debian.org/debian bullseye/main arm64 libsmithwaterman-dev arm64 0.0+git20160702.2610e25-11 [37.4 kB] Get: 126 http://deb.debian.org/debian bullseye/main arm64 libtabixpp0 arm64 1.1.0-4 [8788 B] Get: 127 http://deb.debian.org/debian bullseye/main arm64 libtabixpp-dev arm64 1.1.0-4 [8108 B] Get: 128 http://deb.debian.org/debian bullseye/main arm64 libtcl8.6 arm64 8.6.11+dfsg-1 [964 kB] Get: 129 http://deb.debian.org/debian bullseye/main arm64 libwebp6 arm64 0.6.1-2.1 [244 kB] Get: 130 http://deb.debian.org/debian bullseye/main arm64 libtiff5 arm64 4.2.0-1 [276 kB] Get: 131 http://deb.debian.org/debian bullseye/main arm64 libxft2 arm64 2.3.2-2 [51.3 kB] Get: 132 http://deb.debian.org/debian bullseye/main arm64 libxss1 arm64 1:1.2.3-1 [17.8 kB] Get: 133 http://deb.debian.org/debian bullseye/main arm64 libtk8.6 arm64 8.6.11-2 [738 kB] Get: 134 http://deb.debian.org/debian bullseye/main arm64 libvcflib1 arm64 1.0.2+dfsg-2 [133 kB] Get: 135 http://deb.debian.org/debian bullseye/main arm64 libvcflib-dev arm64 1.0.2+dfsg-2 [84.9 kB] Get: 136 http://deb.debian.org/debian bullseye/main arm64 zip arm64 3.0-12 [228 kB] Get: 137 http://deb.debian.org/debian bullseye/main arm64 unzip arm64 6.0-26 [165 kB] Get: 138 http://deb.debian.org/debian bullseye/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 139 http://deb.debian.org/debian bullseye/main arm64 libxt6 arm64 1:1.2.0-1 [176 kB] Get: 140 http://deb.debian.org/debian bullseye/main arm64 r-base-core arm64 4.0.4-1 [24.9 MB] Get: 141 http://deb.debian.org/debian bullseye/main arm64 r-cran-littler arm64 0.3.12-1 [95.1 kB] Get: 142 http://deb.debian.org/debian bullseye/main arm64 littler all 0.3.12-1 [15.6 kB] Get: 143 http://deb.debian.org/debian bullseye/main arm64 r-cran-pkgkitten all 0.2.1-1 [26.5 kB] Get: 144 http://deb.debian.org/debian bullseye/main arm64 r-cran-rcpp arm64 1.0.6-1 [2020 kB] Get: 145 http://deb.debian.org/debian bullseye/main arm64 r-cran-plyr arm64 1.8.6-2 [828 kB] Get: 146 http://deb.debian.org/debian bullseye/main arm64 r-cran-digest arm64 0.6.27-1 [185 kB] Get: 147 http://deb.debian.org/debian bullseye/main arm64 r-cran-glue arm64 1.4.2-1 [138 kB] Get: 148 http://deb.debian.org/debian bullseye/main arm64 r-cran-gtable all 0.3.0+dfsg-2 [163 kB] Get: 149 http://deb.debian.org/debian bullseye/main arm64 r-cran-brio arm64 1.1.1-1 [31.0 kB] Get: 150 http://deb.debian.org/debian bullseye/main arm64 r-cran-ps arm64 1.5.0-1 [275 kB] Get: 151 http://deb.debian.org/debian bullseye/main arm64 r-cran-r6 all 2.5.0-1 [104 kB] Get: 152 http://deb.debian.org/debian bullseye/main arm64 r-cran-processx arm64 3.4.5-1 [294 kB] Get: 153 http://deb.debian.org/debian bullseye/main arm64 r-cran-callr all 3.5.1-1 [386 kB] Get: 154 http://deb.debian.org/debian bullseye/main arm64 r-cran-assertthat all 0.2.1-2 [56.5 kB] Get: 155 http://deb.debian.org/debian bullseye/main arm64 r-cran-cli all 2.3.0-1 [480 kB] Get: 156 http://deb.debian.org/debian bullseye/main arm64 r-cran-crayon all 1.4.0-1 [143 kB] Get: 157 http://deb.debian.org/debian bullseye/main arm64 r-cran-rprojroot all 2.0.2-1 [114 kB] Get: 158 http://deb.debian.org/debian bullseye/main arm64 r-cran-desc all 1.2.0-3 [301 kB] Get: 159 http://deb.debian.org/debian bullseye/main arm64 r-cran-rlang arm64 0.4.10-1 [1177 kB] Get: 160 http://deb.debian.org/debian bullseye/main arm64 r-cran-ellipsis arm64 0.3.1-1 [31.7 kB] Get: 161 http://deb.debian.org/debian bullseye/main arm64 r-cran-evaluate all 0.14-2 [81.1 kB] Get: 162 http://deb.debian.org/debian bullseye/main arm64 r-cran-jsonlite arm64 1.7.2+dfsg-1 [445 kB] Get: 163 http://deb.debian.org/debian bullseye/main arm64 r-cran-lifecycle all 0.2.0-2 [93.2 kB] Get: 164 http://deb.debian.org/debian bullseye/main arm64 r-cran-magrittr arm64 2.0.1-1 [198 kB] Get: 165 http://deb.debian.org/debian bullseye/main arm64 r-cran-prettyunits all 1.1.1-2 [39.1 kB] Get: 166 http://deb.debian.org/debian bullseye/main arm64 r-cran-withr all 2.4.1-1 [210 kB] Get: 167 http://deb.debian.org/debian bullseye/main arm64 r-cran-pkgbuild all 1.2.0-1 [146 kB] Get: 168 http://deb.debian.org/debian bullseye/main arm64 r-cran-rstudioapi all 0.13-1 [262 kB] Get: 169 http://deb.debian.org/debian bullseye/main arm64 r-cran-pkgload arm64 1.1.0-1 [168 kB] Get: 170 http://deb.debian.org/debian bullseye/main arm64 r-cran-praise all 1.0.0-4 [20.1 kB] Get: 171 http://deb.debian.org/debian bullseye/main arm64 r-cran-diffobj arm64 0.3.2-1 [1069 kB] Get: 172 http://deb.debian.org/debian bullseye/main arm64 r-cran-fansi arm64 0.4.2-1 [340 kB] Get: 173 http://deb.debian.org/debian bullseye/main arm64 r-cran-utf8 arm64 1.1.4-2 [131 kB] Get: 174 http://deb.debian.org/debian bullseye/main arm64 r-cran-vctrs arm64 0.3.6-1 [1094 kB] Get: 175 http://deb.debian.org/debian bullseye/main arm64 r-cran-pillar all 1.4.7-1 [227 kB] Get: 176 http://deb.debian.org/debian bullseye/main arm64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB] Get: 177 http://deb.debian.org/debian bullseye/main arm64 r-cran-tibble arm64 3.0.6+dfsg-1 [416 kB] Get: 178 http://deb.debian.org/debian bullseye/main arm64 r-cran-rematch2 all 2.1.2-2 [46.3 kB] Get: 179 http://deb.debian.org/debian bullseye/main arm64 r-cran-waldo all 0.2.3-2 [79.3 kB] Get: 180 http://deb.debian.org/debian bullseye/main arm64 r-cran-testthat arm64 3.0.1-1 [1439 kB] Get: 181 http://deb.debian.org/debian bullseye/main arm64 r-cran-isoband arm64 0.2.3-2 [2062 kB] Get: 182 http://deb.debian.org/debian bullseye/main arm64 r-cran-mass arm64 7.3-53.1-1 [1114 kB] Get: 183 http://deb.debian.org/debian bullseye/main arm64 r-cran-lattice arm64 0.20-41-1+b1 [1164 kB] Get: 184 http://deb.debian.org/debian bullseye/main arm64 r-cran-nlme arm64 3.1.152-1 [2238 kB] Get: 185 http://deb.debian.org/debian bullseye/main arm64 r-cran-matrix arm64 1.3-2-1 [3559 kB] Get: 186 http://deb.debian.org/debian bullseye/main arm64 r-cran-mgcv arm64 1.8-34-1 [2978 kB] Get: 187 http://deb.debian.org/debian bullseye/main arm64 r-cran-farver arm64 2.0.3-1+b1 [1380 kB] Get: 188 http://deb.debian.org/debian bullseye/main arm64 r-cran-labeling all 0.4.2-1 [62.7 kB] Get: 189 http://deb.debian.org/debian bullseye/main arm64 r-cran-colorspace arm64 2.0-0+dfsg-1 [1683 kB] Get: 190 http://deb.debian.org/debian bullseye/main arm64 r-cran-munsell all 0.5.0-2 [236 kB] Get: 191 http://deb.debian.org/debian bullseye/main arm64 r-cran-rcolorbrewer all 1.1-2-3 [54.4 kB] Get: 192 http://deb.debian.org/debian bullseye/main arm64 r-cran-viridislite all 0.3.0-4 [59.2 kB] Get: 193 http://deb.debian.org/debian bullseye/main arm64 r-cran-scales all 1.1.1-1 [557 kB] Get: 194 http://deb.debian.org/debian bullseye/main arm64 r-cran-ggplot2 all 3.3.3+dfsg-1 [3158 kB] Get: 195 http://deb.debian.org/debian bullseye/main arm64 r-cran-gridbase all 0.4-7-5 [163 kB] Get: 196 http://deb.debian.org/debian bullseye/main arm64 libvcflib-tools arm64 1.0.2+dfsg-2 [657 kB] Get: 197 http://deb.debian.org/debian bullseye/main arm64 ninja-build arm64 1.10.1-1 [107 kB] Get: 198 http://deb.debian.org/debian bullseye/main arm64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 199 http://deb.debian.org/debian bullseye/main arm64 meson all 0.56.2-1 [437 kB] Get: 200 http://deb.debian.org/debian bullseye/main arm64 sysstat arm64 12.5.2-2 [581 kB] Get: 201 http://deb.debian.org/debian bullseye/main arm64 parallel all 20161222-1.1 [306 kB] Get: 202 http://deb.debian.org/debian bullseye/main arm64 pkg-config arm64 0.29.2-1 [63.6 kB] Get: 203 http://deb.debian.org/debian bullseye/main arm64 samtools arm64 1.11-1 [526 kB] Fetched 109 MB in 2s (50.5 MB/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 .../0-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... 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Setting up libcurl3-gnutls:arm64 (7.74.0-1.3+b1) ... Setting up libxcb-shm0:arm64 (1.14-3) ... Setting up libcurl4-gnutls-dev:arm64 (7.74.0-1.3+b1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libthai0:arm64 (0.1.28-3) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libfreetype6:arm64 (2.10.4+dfsg-1) ... Setting up libbamtools-dev:arm64 (2.5.1+dfsg-9) ... Setting up libsmithwaterman-dev (0.0+git20160702.2610e25-11) ... Setting up ucf (3.0043) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... 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 libx11-6:arm64 (2:1.7.1-1) ... Setting up libharfbuzz0b:arm64 (2.7.4-1) ... Setting up libsm6:arm64 (2:1.2.3-1) ... Setting up sysstat (12.5.2-2) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Setting up libpython3.9-stdlib:arm64 (3.9.2-1) ... Setting up libpython3-stdlib:arm64 (3.9.2-3) ... 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 libpaper1:arm64 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up libhts3:arm64 (1.11-4) ... Setting up libxrender1:arm64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:arm64 (2:1.3.3-1.1) ... Setting up libhts-dev:arm64 (1.11-4) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up samtools (1.11-1) ... Setting up dh-autoreconf (20) ... Setting up libxt6:arm64 (1:1.2.0-1) ... Setting up parallel (20161222-1.1) ... Setting up libtabixpp0:arm64 (1.1.0-4) ... Setting up libxss1:arm64 (1:1.2.3-1) ... Setting up libfontconfig1:arm64 (2.13.1-4.2) ... Setting up libseqlib2:arm64 (1.2.0+dfsg-4) ... Setting up python3.9 (3.9.2-1) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxft2:arm64 (2.3.2-2) ... Setting up libtk8.6:arm64 (8.6.11-2) ... Setting up libpango-1.0-0:arm64 (1.46.2-3) ... Setting up libseqlib-dev:arm64 (1.2.0+dfsg-4) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libcairo2:arm64 (1.16.0-5) ... Setting up libvcflib1:arm64 (1.0.2+dfsg-2) ... Setting up libtabixpp-dev:arm64 (1.1.0-4) ... Setting up libpangoft2-1.0-0:arm64 (1.46.2-3) ... Setting up libpangocairo-1.0-0:arm64 (1.46.2-3) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up libvcflib-dev:arm64 (1.0.2+dfsg-2) ... Setting up meson (0.56.2-1) ... Setting up r-base-core (4.0.4-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.4.0-1) ... Setting up r-cran-gtable (0.3.0+dfsg-2) ... Setting up r-cran-labeling (0.4.2-1) ... Setting up r-cran-lattice (0.20-41-1+b1) ... Setting up r-cran-ps (1.5.0-1) ... Setting up r-cran-nlme (3.1.152-1) ... Setting up r-cran-farver (2.0.3-1+b1) ... Setting up r-cran-viridislite (0.3.0-4) ... Setting up r-cran-r6 (2.5.0-1) ... Setting up r-cran-pkgkitten (0.2.1-1) ... Setting up r-cran-magrittr (2.0.1-1) ... Setting up r-cran-littler (0.3.12-1) ... Setting up r-cran-rcpp (1.0.6-1) ... Setting up r-cran-brio (1.1.1-1) ... Setting up r-cran-diffobj (0.3.2-1) ... Setting up r-cran-rlang (0.4.10-1) ... Setting up r-cran-gridbase (0.4-7-5) ... Setting up r-cran-assertthat (0.2.1-2) ... Setting up littler (0.3.12-1) ... Setting up r-cran-withr (2.4.1-1) ... Setting up r-cran-processx (3.4.5-1) ... Setting up r-cran-praise (1.0.0-4) ... Setting up r-cran-digest (0.6.27-1) ... Setting up r-cran-evaluate (0.14-2) ... Setting up r-cran-prettyunits (1.1.1-2) ... Setting up r-cran-fansi (0.4.2-1) ... Setting up r-cran-mass (7.3-53.1-1) ... Setting up r-cran-glue (1.4.2-1) ... Setting up r-cran-cli (2.3.0-1) ... Setting up r-cran-lifecycle (0.2.0-2) ... Setting up r-cran-rprojroot (2.0.2-1) ... Setting up r-cran-jsonlite (1.7.2+dfsg-1) ... Setting up r-cran-rstudioapi (0.13-1) ... Setting up r-cran-pkgconfig (2.0.3-2) ... Setting up r-cran-utf8 (1.1.4-2) ... Setting up r-cran-colorspace (2.0-0+dfsg-1) ... Setting up r-cran-plyr (1.8.6-2) ... Setting up r-cran-rcolorbrewer (1.1-2-3) ... Setting up r-cran-matrix (1.3-2-1) ... Setting up r-cran-mgcv (1.8-34-1) ... Setting up r-cran-ellipsis (0.3.1-1) ... Setting up r-cran-callr (3.5.1-1) ... Setting up r-cran-desc (1.2.0-3) ... Setting up r-cran-munsell (0.5.0-2) ... Setting up r-cran-scales (1.1.1-1) ... Setting up r-cran-pkgbuild (1.2.0-1) ... Setting up r-cran-vctrs (0.3.6-1) ... Setting up r-cran-pillar (1.4.7-1) ... Setting up r-cran-pkgload (1.1.0-1) ... Setting up r-cran-tibble (3.0.6+dfsg-1) ... Setting up r-cran-rematch2 (2.1.2-2) ... Setting up r-cran-waldo (0.2.3-2) ... Setting up r-cran-testthat (3.0.1-1) ... Setting up r-cran-isoband (0.2.3-2) ... Setting up r-cran-ggplot2 (3.3.3+dfsg-1) ... Setting up libvcflib-tools (1.0.2+dfsg-2) ... Processing triggers for libc-bin (2.31-12) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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... The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 157 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (2352 kB/s) Selecting previously unselected package libnumber-compare-perl. (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 ... 31799 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... Unpacking libfile-find-rule-perl (0.34-1) ... Selecting previously unselected package usrmerge. Preparing to unpack .../archives/usrmerge_25_all.deb ... Unpacking usrmerge (25) ... Setting up libtext-glob-perl (0.11-1) ... Setting up libnumber-compare-perl (0.03-1.1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up usrmerge (25) ... The system has been successfully converted. Processing triggers for man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. I: Building the package hostname: Temporary failure in name resolution I: Running cd /build/freebayes-1.3.5/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../freebayes_1.3.5-1_source.changes dpkg-buildpackage: info: source package freebayes dpkg-buildpackage: info: source version 1.3.5-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=meson --builddir=build dh_auto_clean -O--buildsystem=meson -O--builddir=build dh_autoreconf_clean -O--buildsystem=meson -O--builddir=build dh_clean -O--buildsystem=meson -O--builddir=build debian/rules binary dh binary --buildsystem=meson --builddir=build dh_update_autotools_config -O--buildsystem=meson -O--builddir=build dh_autoreconf -O--buildsystem=meson -O--builddir=build dh_auto_configure -O--buildsystem=meson -O--builddir=build cd build && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/aarch64-linux-gnu The Meson build system Version: 0.56.2 Source dir: /build/freebayes-1.3.5 Build dir: /build/freebayes-1.3.5/build Build type: native build Project name: freebayes Project version: 1.3.4 Using 'CFLAGS' from environment with value: '-g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security' Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now' Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2' C compiler for the host machine: cc (gcc 10.2.1 "cc (Debian 10.2.1-6) 10.2.1 20210110") C linker for the host machine: cc ld.bfd 2.35.2 Using 'CXXFLAGS' from environment with value: '-g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security' Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now' Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2' C++ compiler for the host machine: c++ (gcc 10.2.1 "c++ (Debian 10.2.1-6) 10.2.1 20210110") C++ linker for the host machine: c++ ld.bfd 2.35.2 Using 'CFLAGS' from environment with value: '-g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security' Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now' Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2' Using 'CXXFLAGS' from environment with value: '-g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security' Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now' Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2' Host machine cpu family: aarch64 Host machine cpu: aarch64 Found pkg-config: /usr/bin/pkg-config (0.29.2) Run-time dependency zlib found: YES 1.2.11 Run-time dependency liblzma found: YES 5.2.5 Run-time dependency threads found: YES Run-time dependency htslib found: YES 1.11-4 Library tabixpp found: YES Run-time dependency libvcflib found: YES 1.0 Run-time dependency libseqlib found: YES 1.0 Compiler for C++ supports arguments -fpermissive: YES Compiler for C++ supports arguments -Wno-reorder: YES Compiler for C++ supports arguments -Wno-sign-compare: YES Compiler for C++ supports arguments -Wno-unused-variable: YES Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES Program prove found: YES (/usr/bin/prove) Build targets in project: 3 Option optimization is: 0 [default: 3] Found ninja-1.10.1 at /usr/bin/ninja dh_auto_build -O--buildsystem=meson -O--builddir=build cd build && LC_ALL=C.UTF-8 ninja -j8 -v [1/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Bias.cpp.o -MF libfreebayes_common.a.p/src_Bias.cpp.o.d -o libfreebayes_common.a.p/src_Bias.cpp.o -c ../src/Bias.cpp [2/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Contamination.cpp.o -MF libfreebayes_common.a.p/src_Contamination.cpp.o.d -o libfreebayes_common.a.p/src_Contamination.cpp.o -c ../src/Contamination.cpp [3/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_CNV.cpp.o -MF libfreebayes_common.a.p/src_CNV.cpp.o.d -o libfreebayes_common.a.p/src_CNV.cpp.o -c ../src/CNV.cpp [4/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Dirichlet.cpp.o -MF libfreebayes_common.a.p/src_Dirichlet.cpp.o.d -o libfreebayes_common.a.p/src_Dirichlet.cpp.o -c ../src/Dirichlet.cpp [5/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_IndelAllele.cpp.o -MF libfreebayes_common.a.p/src_IndelAllele.cpp.o.d -o libfreebayes_common.a.p/src_IndelAllele.cpp.o -c ../src/IndelAllele.cpp [6/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Ewens.cpp.o -MF libfreebayes_common.a.p/src_Ewens.cpp.o.d -o libfreebayes_common.a.p/src_Ewens.cpp.o -c ../src/Ewens.cpp [7/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_BedReader.cpp.o -MF libfreebayes_common.a.p/src_BedReader.cpp.o.d -o libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp [8/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Multinomial.cpp.o -MF libfreebayes_common.a.p/src_Multinomial.cpp.o.d -o libfreebayes_common.a.p/src_Multinomial.cpp.o -c ../src/Multinomial.cpp [9/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_FBFasta.cpp.o -MF libfreebayes_common.a.p/src_FBFasta.cpp.o.d -o libfreebayes_common.a.p/src_FBFasta.cpp.o -c ../src/FBFasta.cpp [10/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_LeftAlign.cpp.o -MF libfreebayes_common.a.p/src_LeftAlign.cpp.o.d -o libfreebayes_common.a.p/src_LeftAlign.cpp.o -c ../src/LeftAlign.cpp [11/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_DataLikelihood.cpp.o -MF libfreebayes_common.a.p/src_DataLikelihood.cpp.o.d -o libfreebayes_common.a.p/src_DataLikelihood.cpp.o -c ../src/DataLikelihood.cpp [12/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Marginals.cpp.o -MF libfreebayes_common.a.p/src_Marginals.cpp.o.d -o libfreebayes_common.a.p/src_Marginals.cpp.o -c ../src/Marginals.cpp [13/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_NonCall.cpp.o -MF libfreebayes_common.a.p/src_NonCall.cpp.o.d -o libfreebayes_common.a.p/src_NonCall.cpp.o -c ../src/NonCall.cpp [14/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -MF libfreebayes_common.a.p/src_SegfaultHandler.cpp.o.d -o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -c ../src/SegfaultHandler.cpp [15/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Result.cpp.o -MF libfreebayes_common.a.p/src_Result.cpp.o.d -o libfreebayes_common.a.p/src_Result.cpp.o -c ../src/Result.cpp [16/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Allele.cpp.o -MF libfreebayes_common.a.p/src_Allele.cpp.o.d -o libfreebayes_common.a.p/src_Allele.cpp.o -c ../src/Allele.cpp ../src/Allele.cpp: In member function ‘const short int Allele::currentQuality() const’: ../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_GENOTYPE’ not handled in switch [-Wswitch] 160 | switch (this->type) { | ^ ../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_NULL’ not handled in switch [-Wswitch] [17/27] c++ -Ibamleftalign.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ bamleftalign.p/src_bamleftalign.cpp.o -MF bamleftalign.p/src_bamleftalign.cpp.o.d -o bamleftalign.p/src_bamleftalign.cpp.o -c ../src/bamleftalign.cpp [18/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Parameters.cpp.o -MF libfreebayes_common.a.p/src_Parameters.cpp.o.d -o libfreebayes_common.a.p/src_Parameters.cpp.o -c ../src/Parameters.cpp [19/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Sample.cpp.o -MF libfreebayes_common.a.p/src_Sample.cpp.o.d -o libfreebayes_common.a.p/src_Sample.cpp.o -c ../src/Sample.cpp [20/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Genotype.cpp.o -MF libfreebayes_common.a.p/src_Genotype.cpp.o.d -o libfreebayes_common.a.p/src_Genotype.cpp.o -c ../src/Genotype.cpp [21/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Utility.cpp.o -MF libfreebayes_common.a.p/src_Utility.cpp.o.d -o libfreebayes_common.a.p/src_Utility.cpp.o -c ../src/Utility.cpp In file included from ../ttmath/ttmathint.h:48, from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: ../ttmath/ttmathuint.h: In function ‘BigFloat big_exp(long double)’: ../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& x)+32).ttmath::UInt<2>::table[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& x)+32).ttmath::UInt<2>::table[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: ../ttmath/ttmathint.h:652:40: warning: ‘x.ttmath::UInt<8>::table[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 652 | UInt::table[i] = p.table[i]; | ~~~~~~~^ In file included from ../ttmath/ttmathint.h:48, from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: ../ttmath/ttmathuint.h: In function ‘long double logsumexp_probs(const std::vector&)’: ../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& maxNb)+32).ttmath::UInt<2>::table[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& maxNb)+32).ttmath::UInt<2>::table[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: ../ttmath/ttmathint.h:652:40: warning: ‘maxNb.ttmath::UInt<8>::table[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 652 | UInt::table[i] = p.table[i]; | ~~~~~~~^ In file included from ../ttmath/ttmathint.h:48, from ../ttmath/ttmathbig.h:46, from ../ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: ../ttmath/ttmathuint.h: In function ‘long double big2phred(const BigFloat&)’: ../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& result)+32).ttmath::UInt<2>::table[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& result)+32).ttmath::UInt<2>::table[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] ../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& result)+32).ttmath::UInt<2>::table[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] ../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& result)+32).ttmath::UInt<2>::table[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] [22/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_ResultData.cpp.o -MF libfreebayes_common.a.p/src_ResultData.cpp.o.d -o libfreebayes_common.a.p/src_ResultData.cpp.o -c ../src/ResultData.cpp [23/27] c++ -Ifreebayes.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ freebayes.p/src_freebayes.cpp.o -MF freebayes.p/src_freebayes.cpp.o.d -o freebayes.p/src_freebayes.cpp.o -c ../src/freebayes.cpp [24/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_AlleleParser.cpp.o -MF libfreebayes_common.a.p/src_AlleleParser.cpp.o.d -o libfreebayes_common.a.p/src_AlleleParser.cpp.o -c ../src/AlleleParser.cpp [25/27] rm -f libfreebayes_common.a && gcc-ar csrD libfreebayes_common.a libfreebayes_common.a.p/src_Allele.cpp.o libfreebayes_common.a.p/src_AlleleParser.cpp.o libfreebayes_common.a.p/src_BedReader.cpp.o libfreebayes_common.a.p/src_Bias.cpp.o libfreebayes_common.a.p/src_CNV.cpp.o libfreebayes_common.a.p/src_Contamination.cpp.o libfreebayes_common.a.p/src_DataLikelihood.cpp.o libfreebayes_common.a.p/src_Dirichlet.cpp.o libfreebayes_common.a.p/src_Ewens.cpp.o libfreebayes_common.a.p/src_FBFasta.cpp.o libfreebayes_common.a.p/src_Genotype.cpp.o libfreebayes_common.a.p/src_IndelAllele.cpp.o libfreebayes_common.a.p/src_LeftAlign.cpp.o libfreebayes_common.a.p/src_Marginals.cpp.o libfreebayes_common.a.p/src_Multinomial.cpp.o libfreebayes_common.a.p/src_NonCall.cpp.o libfreebayes_common.a.p/src_Parameters.cpp.o libfreebayes_common.a.p/src_Result.cpp.o libfreebayes_common.a.p/src_ResultData.cpp.o libfreebayes_common.a.p/src_Sample.cpp.o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o libfreebayes_common.a.p/src_Utility.cpp.o [26/27] c++ -o bamleftalign bamleftalign.p/src_bamleftalign.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group libfreebayes_common.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so -pthread /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/libvcflib.so /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/libsmithwaterman.so /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/libdisorder.so /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/libfastahack.so /usr/lib/aarch64-linux-gnu/libseqlib.so /usr/lib/libbwa.a -ltabixpp -Wl,--end-group [27/27] c++ -o freebayes freebayes.p/src_freebayes.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/freebayes-1.3.5=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group libfreebayes_common.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so -pthread /usr/lib/aarch64-linux-gnu/libhts.so -ltabixpp /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/libvcflib.so /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/libsmithwaterman.so /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/libdisorder.so /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/libfastahack.so /usr/lib/aarch64-linux-gnu/libseqlib.so /usr/lib/libbwa.a -ltabixpp -Wl,--end-group debian/rules override_dh_auto_test make[1]: Entering directory '/build/freebayes-1.3.5' mkdir -p test/bash-tap/ ln -s -t test/bash-tap /build/freebayes-1.3.5/debian/bash-tap/* mkdir -p test/test-simple-bash ln -s -t test/test-simple-bash /build/freebayes-1.3.5/debian/test-simple-bash/* dh_auto_test -- -v --timeout-multiplier 100 cd build && LC_ALL=C.UTF-8 MESON_TESTTHREADS=8 meson test -v --timeout-multiplier 100 ninja: Entering directory `/build/freebayes-1.3.5/build' ninja: no work to do. t/03_reference_bases.t .. 1..3 ok 1 - freebayes rejects invalid reference ok 2 - freebayes does not put uppercase IUPAC bases in VCFs ok 3 - freebayes does not put lowercase IUPAC bases in VCFs ok All tests successful. Files=1, Tests=3, 0 wallclock secs ( 0.06 usr 0.01 sys + 0.07 cusr 0.05 csys = 0.19 CPU) Result: PASS t/02_multi_bam.t .. 1..7 ok 1 - freebayes calls from two identical BAMs ok 2 - freebayes calls from two BAMs with different samples for different read groups ok 3 - freebayes calls from two BAMs with different technologies for different read groups ok 4 - freebayes rejects two BAMs with different samples for same read groups ok 5 - freebayes rejects two BAMs with different technologies for same read groups ok 6 - freebayes calls multiple alts from two different BAMs ok 7 - freebayes rejects two BAMs with the same name ok All tests successful. Files=1, Tests=7, 0 wallclock secs ( 0.07 usr 0.01 sys + 0.22 cusr 0.15 csys = 0.45 CPU) Result: PASS t/00_region_and_target_handling.t .. 1..12 ok 1 - ref:4-5 ref:6-7 are empty ok 2 - ref:4 ref:6 are empty ok 3 - ref:5-6 ref:7-8 ok 4 - ref:5 ref:7 ok 5 - ref:5- ok 6 - full output ok 7 - --targets t/../00_region_and_target_handling.t.bed ok 8 - --region ref ok 9 - ref:1,0- ok 10 - ref:1,0-1,1 ok 11 - ref:0-1 ok 12 - region outside of bounds error ok All tests successful. Files=1, Tests=12, 0 wallclock secs ( 0.07 usr 0.01 sys + 0.24 cusr 0.12 csys = 0.44 CPU) Result: PASS t/01b_call_variants.t .. 1..10 ok 1 - running in parallel makes no difference ok 2 - freebayes handles spaces in file names ok 3 - freebayes handles region and variant input even with : in contig names ok 4 - freebayes can handle spliced reads ok 5 - freebayes produces the expected number of lines of gVCF output ok 6 - freebayes produces the expected number of lines of gVCF output ok 7 - freebayes produces the expected number of lines of gVCF output ok 8 - the CNV map may be used to specify per-sample copy numbers ok 9 - freebayes makes the expected number of calls when capping coverage ok 10 - freebayes correctly uses CNV map with multiple entries ok All tests successful. Files=1, Tests=10, 14 wallclock secs ( 0.08 usr 0.01 sys + 14.02 cusr 0.79 csys = 14.90 CPU) Result: PASS [E::idx_find_and_load] Could not retrieve index file for '-' Random access with SetRegion not available for STDIN reading (no index file) ERROR(freebayes): Could not SetRegion to q:1..10000 t/01_call_variants.t: regel 107: 10331 Afgebroken freebayes -f tiny/q.fa.gz -@ tiny/q_spiked.vcf.gz -r q:1-10000 -l - < tiny/NA12878.chr22.tiny.bam > /dev/null 2> /dev/null t/01_call_variants.t .. 1..16 ok 1 - variant calling recovers most of the GiAB variants in a test region ok 2 - freebayes produces the same number of calls if targeted per site or called without targets ok 3 - a targets bed file can be used with the same effect as running by region ok 4 - reading from stdin or not makes no difference ok 5 - freebayes processes all alignments in BAM input ok 6 - freebayes processes all alignments in CRAM input ok 7 - freebayes correctly handles variant input ok 8 - freebayes puts required variants in output ok 9 - freebayes limits calls to input variants correctly ok 10 - freebayes reports all input variants even when there is no input data ok 11 - freebayes handles region and variant input ok 12 - freebayes limits to variant input correctly when region is given ok 13 - freebayes handles variant input and reading from stdin ok 14 - freebayes limits to variant input when reading from stdin ok 15 - freebayes handles region, stdin, and variant input ok 16 - ! ok All tests successful. Files=1, Tests=16, 28 wallclock secs ( 0.06 usr 0.01 sys + 21.15 cusr 4.54 csys = 25.76 CPU) Result: PASS 1/5 T00 OK 0.85s 2/5 T01 OK 28.15s 3/5 T01b OK 14.71s 4/5 T02 OK 0.81s 5/5 T03 OK 0.47s Ok: 5 Expected Fail: 0 Fail: 0 Unexpected Pass: 0 Skipped: 0 Timeout: 0 rm test/bash-tap/* rm test/test-simple-bash/* make[1]: Leaving directory '/build/freebayes-1.3.5' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=meson -O--builddir=build dh_prep -O--buildsystem=meson -O--builddir=build dh_auto_install -O--buildsystem=meson -O--builddir=build cd build && DESTDIR=/build/freebayes-1.3.5/debian/freebayes LC_ALL=C.UTF-8 ninja install [0/1] Installing files. Installing freebayes to /build/freebayes-1.3.5/debian/freebayes/usr/bin Installing bamleftalign to /build/freebayes-1.3.5/debian/freebayes/usr/bin dh_installdocs -O--buildsystem=meson -O--builddir=build dh_installchangelogs -O--buildsystem=meson -O--builddir=build dh_installexamples -O--buildsystem=meson -O--builddir=build dh_installsystemduser -O--buildsystem=meson -O--builddir=build dh_perl -O--buildsystem=meson -O--builddir=build dh_link -O--buildsystem=meson -O--builddir=build dh_strip_nondeterminism -O--buildsystem=meson -O--builddir=build dh_compress -O--buildsystem=meson -O--builddir=build dh_fixperms -O--buildsystem=meson -O--builddir=build dh_missing -O--buildsystem=meson -O--builddir=build dh_dwz -a -O--buildsystem=meson -O--builddir=build dh_strip -a -O--buildsystem=meson -O--builddir=build dh_makeshlibs -a -O--buildsystem=meson -O--builddir=build dh_shlibdeps -a -O--buildsystem=meson -O--builddir=build dh_installdeb -O--buildsystem=meson -O--builddir=build dh_gencontrol -O--buildsystem=meson -O--builddir=build dh_md5sums -O--buildsystem=meson -O--builddir=build dh_builddeb -O--buildsystem=meson -O--builddir=build dpkg-deb: building package 'freebayes-dbgsym' in '../freebayes-dbgsym_1.3.5-1_arm64.deb'. dpkg-deb: building package 'freebayes' in '../freebayes_1.3.5-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../freebayes_1.3.5-1_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: user script /srv/workspace/pbuilder/14298/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/14298/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/14298 and its subdirectories I: Current time: Thu Aug 11 22:50:24 +14 2022 I: pbuilder-time-stamp: 1660207824